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Group II and group III introns of twintrons: potential relationships with nuclear pre-mRNA introns
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pathway of an antibiotic tripeptide6. The mechanisms of hydrolysis of the ester bonds of triglycerides and the amide bond linking acetate to the tripeptide are similar, and it is not surprising that these enzymes show sequence similarity in the region of the catalytic site. Besides HSL, no long region of similarity between a mammalian lipase and its prokaryotic counterparts has been reported. This note also strengthens the hypothesis that HSL is a mosaic protein ] with a region sharing a common ancestry with some bacterial enzymes and other regions, such as the phosphorylation
sites, from a different origin. Clearly, the resolution of the three-dimensional structure of HSL will provide valuable information for a complete understanding of these unexpected similarities.
References
1 Langin,D. et al. (1993) Proc. Natl Acad. Sci. USA 90, 4897-4901 2 Derewenda,Z. S. and Derewenda,U. (1991) Biochem. Cell Biol. 69, 842-851 3 DoolitUe,R. F., Feng, D. F., Johnson, M. S. and McClure,M. A. (1986) Cold Spring Harbor Syrup. Quant. BioL 51, 447-455 4 Van Tilbeurgh,H. et aL (1993) Nature 362, 814-820
5 Feller,G., Thiry,M. and Gerday,C. (1991) DNA Cell Biol. 10, 381-388 6 Murakami,T. et al. (1986) Mol. Gen. Genet. 205, 42-50
DOMINIQUE LANGBN Institut Nationalde la Sant~et de la Recherche M6dicale U-317, B~timentL3, CHU Rangueil, F-31054Toulouse,France.
CECILIA HOLM Departmentof Medical and PhysiologicalChemistry 4, Lund University,P.O.Box 94, .~o2100 Lund, Sweden.
REVIEWS _
SINCE THE DISCOVERY of intervening sequences in 1977, introns have been classified into groups based on common mechanisms of excision and conserved intron features. The recognition of identical splicing pathways for group II and nuclear pre-mRNA introns, involving two successive transesterification reactions in which these introns are excised as 'lariats', has led to the hypothesis that these classes of introns are evolutionarily related ~,2. A corollary is the potential correspondence of structural/functional elements between the cis-encoded domains ol group II introns and the trans.acting splicing machinery of nuclear introns. Structural, functional and mechanistic aspects of this hypothesis have been
Group II and group III introns of twintrons' potential relationships with nuclear pre-mRNAintrons
Two new and important features of introns have emerged from analysis of the E u g / e n a g r a c i / i s chloroplast genome. On,e is a new class of introns, designated group III, that may be the close,.;t contemporaries to nuclear pre-mRNA introns. The second is introns that are interrupted by other introns termed twintrons.
reviewed ~ .
convincing group II core structures, due to either loss of domains l-IV or massGroup II introns of the chloroplastgenes of ive divergence from related group II Euglena gracilis The chloroplast genome of Euglena introns 7. By contrast, we find that most gracilis contains at least 155 introns, of the 74 Euglena group II introns do accounting for 39.2% of the genome 6. At have group II core structures, albeit least 74 of these are group II introns, with more relaxed pairing rules for both ranging in size from 277 to 671 nu- stems and tertiary interactions. Plastids cleotides (Fig. I). These introns have of Astasia longa, a related protist, cona conserved secondary structure of six tain similar group II introns. The core helical domains (I-VI) radiating from a structure of the smallest group II intron, central core. They are also found in a 270 nucleotide intron of the Astasia organellar genes of fungi and plants, rps2 gene, is shown in Fig. 2a. This and in prokaryotes. It has been pro- intron illustrates the secondary and terposed that many Euglena introns are tiary interactions characteristic of only 'group ll-like', because they lack group II introns, such as domains I-VI, exon-binding site-I (EBSl)-intron-binding site-10BS1), EBS2-IBS2, E-E', ~-~' D. W. Copertlno and R. B. Halllck are at the and the guided pair. All of the Euglena Department of Biochemistry and the group II introns possess the highly conDepartment of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA. served catalytic domain V as well as © 1993,ElsevierSciencePublishers,(UK) 0968-0004/93/$06.00
domain VI, although terminal loops of these domains can be variable7. Euglena group II introns also have the conserved 5'-boundary motif 5'-GUGYG, a domain I helical stem, and subdomains IC and ID. Domains II-IV can be very small (<15 nucleotides per domain). All of the Euglena group II introns contain EBSI in domain ID3 and the 7--~/interaction. Less conserved but usually present, although not readily apparent because the pairings are not solely Watson-Crick interactions, are EBS2-1BS2 pairing, the 'guided pair', and the e-e' interaction (Fig. 2a). Also, Euglena group II introns excise as lariats 8,9 (D. W. Copertino and R. B. Hallick, unpublished). Thus, Euglena and probably Astasia have bona fide group II introns, which are very important for studying the minimum structure 467
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III (Refs may well be a number of readers who are Overall, this designated volume w.i~lgroup be welcomed put off by the initial chemical input. It is, 11 andin this EMBL acby the majority10, of workers however, worth persevering with as there expanding field, and it provides cession number an X16004). is valuable information here both for exceilept companion the more genes Euglenato chloroplast researchers already working in the field cheadcally andcontain radiation-orientated 50 individual andcennewcomers (in particular new volumes, such group as that III by introns, yon SonntagL and in 18 postgraduate students, for whom this bringing together these contributions or more additional introns would from a number of leading experts, the -~ be a good sta;ting point)IIwho are within twintrons (see benot(5familiar with the subject but who wish editors have produced a timely volume ~ low). These introns to (or ..... ought to) become so. that will undoubtedly be used as a are in Q) the innarrow range The chapters are broken down into reference volume a large size number of of ...c 91-119 nucleotides (Fig. four labs. E major sections: chemistw and :::l measurement of damage to DNA by As with all new are a are 1). volumes, Group IIIthere introns Z reactive oxygen species; mechanism of number of niggles and minus points; generally V-rich. The inconDNA damage by oxidative stress; particular the occurrence of sensus 5'-boundary seconsequences of oxidative DNA damage; typographical errors reallyis 5'-NVNNG quencewhich of should and pro-oxidants and DNA damage. Each have been spotted in this of automatic related to era group II and part is preceded by a brief preface by the spell checkers, the non-uniformity of the pre-mRNA 5'nuclear editors. The first section begins with an chemical structures and equations, the splice sites. Group III inintriguing chapter by Ames and Shigenaga trons contain a 3'-domain, on the role of oxidants as major defined as abcdef(3-8 nucontributors to cancer and aginga Intron size (nucleotides) cleotide loop)f'e'd'A*c'b'a' justification, if ever one was needed, for the research that is being carried out in (4 nucleotides)-3'. This Figurecertainly 1 this area. This introduction splice siteforisOligonucleotides identical to S. Agtawal fed.) Protocols Size distribution of Euglena gracilis chloroplast provides food for thought as well as and Analogs -the Synthesis group andII Properties. domain introns. Individual group II and group III introns are Methods in Molecular Biology Vol. 20 Humana valuable information (and ammunition?) VI12,13. The 5'-side of the indicated. The group III intron mean isPress, 103 1993. $59.50 (xiv + 502 pages) ISBN fornucleotides. people whoThe would have us decrease distribution of group II introns 0 896is02347 7 stem (abcdef) is purineourbimodal daily intake of calories and minimize with peaks centered near 350 and 550 rich. Group III introns are ournucleotides. exposure toGroup certain chemicals, N. also H. Battey, spliced H. G. Dickinson and A. M. III and other twintrons are via a lariat interalthough adverts which encourage us to Heathedngton (eds) Post-translational indicated, (Scale on X-axis is discontinuous.) mediate utilizing the unModifications in Plants. Society for 'eat less and live longer' are unlikely to be pairedSeminar adenosine (A53 *) Experimental Biology Series VoL as scientifically correct or as elegantly Cambridge University Press, 1993. (xx required asfor domain VI during intron$89.95 excision presented this group chapter. IIThesplicing followingin within + 310 pages) ISBN 0 521 41181 5 chapters in the first section outline the to (0. W. Copertino and R. B. Hallick, vivo, and identifying alternatives
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5'-splice site, and Similarity at the overlap in places between different excision as lariats utilizing domain VI, authors' contributions, and, probably suggest that group III that introns are evolmost seriously, the fact the whole volume is printed thinII paper, utionarily relatedontorather group introns, whichstructures results in the contents some The of two groupof III introns pages being in visible wrong side, of Fig. on 2b.theThe 5'-region are shown and doesn't bode well forafter the lifetime one intron is modeled domainof ID the volume, given the undoubted use it of group II introns. This particular will have. intron contains potential EBS 1 and EBS2 elements. The 5'-region of the Reference other intron Thecan assume stable 1 von Sonntag, Chemical Basis of aRadiation Biology (1987) Taylorand in which theFrancis terminal loop is stem-loop V-rich. The V-rich loop may have more flexibility in base-pair interactions, MICHAEL DAVIES possibly interacting with the 5'-exon, as has been proposed for the interaction Department Chemistry, Universityloop of York,of US between ofthe conserved Heslington, York,UK Y015DD. snRNA and upstream exons 5. Group HI introns might be group II introns that require some domains in trans. For example, a trans-acting domain V could activate the first reaction 14 . Alternatively, in Rice trans (eds) may F. W. domains Hardson supplied and M. E. Microscopic Anatomy of Invertebrates Wileyreconstitute an entire group II intron Liss, 1993. $185.00 (xivas + 484 pages) is the caseISBN for secondary structure, 0 471 56119 3 the tseA locus in trans-splicing of the E. Haslam Shikimic Acid -Chlamydomonas Metabolism and psaA mRNA of the Metabolites Wiley-Liss, 1993. £75.00 (xii + 15 • A requirement chloroplast 387 pages) ISBN 0 471 93999 4 for transacting RNAs for group III splicing would P. and parallel A. D. Wheatley be N.anHobson obvious to theAnaerobic role of Digestion - Modem Theory and Practice snRNPs in nuclear pre-mRNA splicing. Elsevier, 1993. £65.00 (xi + 269 pages) ISBN
1 85166 958 2 basic free radicalbase chemistry of DNA, the Watson-Crick pairing for intron unpublished). The 5'-region some S. Introns within introns in chloroplast genes R. V. Benasson, E. J. Land and T. G.ofTmscott A. Kauffman The Origins of OrderSelf reactions and mechanisms that generate Excited III States and is Free Radicals in Biology introns almost identical to of secondary and tertiary interactions. group Euglena gracilis Organization and Selection in Evolution Oxford and Medicine Oxford University Press,Others 1993. University measurable lesions and the methods for Press, chloroplast 1993. £55.00genome (xviii + con709 domain 103 of group II introns. The Euglena £50.00 (xi + 431 pages) ISBN 0 19 855560 1 pages) ISBN 0 19 507951 5 carrying measurements. The last of of Group III out introns of the chloroplast genes possess similar stem-loop structures tains twelve known and three postuthese is relatively short and biased B. A. Bernard and B.EBS Shmot Euglena gracilis without an obvious (Fig.Pharmacology 2b). A few L. lated introns introns, or twinLarand and K,within G. Mann (eds) Proteolytic towards certain techniques used by the 6• The and the IIISkin Vol. 5 seem - Fromto Molecular Enzymes in Coagulation, Fibrinolysis, and Euglena and Astasia plastid genomes group introns containBiology only trons internal intron( s) are first author, but this may not be a major to Therapeutics Karger, 1993. $199.25 (viii + Complement Activation Part B - Complement of introns VI. also contain a unique class domain excised, thereby reconstituting the 196 pages) ISBN 3 8055 5776 0 drawback, as it improves the readability Activation, Fibrinolysis, and Nonmammalian Blood Coagulation Factors and Inhibitors. of the chapter, and this area is adequately C. M. A. Brett and A. M. O. Brett Methods in Enzymology VoL 223 Academic covered in a number of other, highly (b) Methods and Press, 1993. £50.00 (xxviii + 433 pages) Electrochemistry - Principles, EBS2 detailed, volumes on the market. Applications Oxford University Press, 1993. ISBN 0 12 182124 2 The chapters in the second section ~ AAA £25.00 (xxviv + 427 pages) ISBN 0 19 cu U U U U G,. W. YyC G EBS1 G. Prota and J. A. Kenney, Jr gradually move towards more complex 855388 9 A U ;. IA U A A Montagna, U U 1 U - Structure and Function Academic BlackUUA Skin U U biological systems, taking in the basic A Press, 1993. £54.00 (x + 158 pages) ISBN 0 P. M. A. Bmda, S. G. Oliver and P.UF. G. Simsinternal facets of hydrogen peroxide damage, intron U U A'U U 12 505260 X (eds) The Eukaryotic Genome - Organisation A;~U (112 ntl oxidative stress and calcium and Regulation. Society for General u;~u uU Cu J. Oleson. P. Tfelt-Hansen and K. M, A. Welch homeostasis, lipid peroxidation, and the Microbiology Symposium 50 Cambridge fhe Headaches Raven Press, 1993. chemistry of peroxyl radicals. The third University Press, 1993. £60.00/$120.00AU:'U~ (xiiUA~ (ed.~) ~ U UU VI u~=~u $208.00 (xxiv + 922 pages) ISBN 0 7817 + 395 pages) ISBN 0 521 44364 4 section considers the role of enzymes u-A ~:~8A* A-u external intron 0069 that repair damage (a thorough and u-A G·U ~:~ (96 ntl A A Y. P. Cruz Laboratory Exerc;.3es U- in 5'-UUGUGA CUU-A - u AUUU_3' A-U J. R. Foortmans fed.) Principles of Exercise complete article by Ramotar and Developmental Biology Academ:c Press, 1993. Biochemistry (2nd, revised edn) Medicine and Demple); an amusing, yet serious and £26.50 (xi + 241 o~ges) ISBN 0 12 198390 0 Sport Science VoL 38 Karger, 1993. provocative article on sex as a response Sfr.156.00/DM187.00/$125.00 VI (304 pages) S. Dobson and G. J. Van Esch Polychlorinated "U-A U U A-~ to oxidative damage; oxidative stress and ISBN 3 8055 5778 u. G Uc U 7 A- A * Biphenyls and Terphenyls (2nd edn) IPCS cell proliferation; and the role of oxidants UC ~:::~ ~:~ Environmental Health Criteria VoL 140 World UA. P6hler Engineering of Animals and use of ornithine decarboxylase exon , fed.) Genetic U-A A-U I exon Health Organization, 1993. SFr.70.00/$63.00 VCH, U A 1993. £15.50/DM38.00 (177 pages) measurements in studies on tumour 5'-C U GC U U UGU G GU U-A U A-U U C - AUU.CGUA G -3' (682 pages) ISBN 92 4 157140 3 ISBN 3 527 30041 4 A-U promotion. The final section then A-U CUu IF. Franks fed.) Protein Biotechnology- A. P(ihler fed.) UuU progresses to consider the development Genetic Engineering of U U 1993. Isolation, Characterization and Stabilization Microorganisms VCH, £15.50/ and role of radicals in the action of redoxUACUGU Humana Press, 1993. £87.00 (xi + 592 DM38.00 (viii + 178 pages) ISBN 3 527 cycling drugs; the mutagenicity of plant pages) ISBN 0 89603 230 2 30039 2 components; the effects of mineral fibres FigureD.2 J. Reen (eds) J. P. Robinson fed.) Handbook of Row and cigarette smoke in inducing DNA J. P. Gosling and Structural plastid (a) group II and (b) groupPress, III introns (see text for details). Tertiary interactions are indiCytometry Methods (2nd edn) Wiley, 1993. damage; andmodels finallyfor th,representative ;~ro-oxidant euglenoid Immunotechnology Portland 1993. in the 'guided pair'(ixinteraction (boxed bases). cated,ofincluding nucleotides £45.00 + 153 pages) ISBN 1 85578 035 6 £32.95 (xii + 246 pages) ISBN0 471 59634 5 actions food additives an(iinvolved nutrients.
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external Splicing of the external may well intron. be a number of readers who are put off results by the initial chemical input. It is, intron in exon ligation. Splicing however, worth intron persevering as there of the external beforewith removal of is valuable the internalinformation intron(s) here has both neverforbeen researchersDifferent already working in the of field twinobserved. categories and newcomers (in particular new trons vary in the composition and numpostgraduate students, for whom this ber of be introns Both who group would a good(Table sta;tingI).point) are II and group with III introns can but be who internal not familiar the subject wish and/or external intronsso.of twintrons. to (or ought to) become Ten of chapters the fifteen areinto simple The are twintrons broken down four major sections: chemistw and intron twintrons composed of one measurement of damageintron. to DNAGroup by II internal to another reactive oxygen species; twintrons in psbF, psbDmechanism and atpEofare DNA by oxidative stress;II intron each damage composed of a group consequences of oxidative DNAIIdamage; internal to another group intron9 and pro-oxidants and DNA damage. Each (Table I). Six twintrons are composed of part is preceded by a brief preface by the group IIIThe introns internal to other group editors. section begins with an 12 first 1II introns (Table I). The 'mixed' rps3 intriguing chapter by Ames and Shigenaga twintron a oxidants group II as intron on the roleis of majorin a group III intron 16 . to cancer and aging- a contributors The remaining are more justification, if ever twintrons one was needed, for the research that is being carried internal out in complex, containing multiple this area.(Table This introduction introns I). Intron 2certainly in rps18 is provides thought as well as composedfood of forfour distinct group III valuable information (and ammunition?) introns that are sequentially excised in for whoreactions17. would have us fourpeople splicing Thedecrease external our daily intake of calories and minimize is interrupted by a group III intron our exposure to certain chemicals, intron, which is encourage split into us three although advertsitself which to III introns. pieces two internal 'eat lessby and live longer' group are unlikely to be Thescientifically petB complex twintron excised in as correct or as iselegantly three sequential steps. The Thefollowing external presented as this chapter. group II intron is interrupted by group chapters in the first section outline the basic radical chemistry of DNA, II andfree group III introns. The yef8 the comreactions and mechanisms that generate plex twintron may be excised by altermeasurable lesions methods for nate pathways. In and the the major pathways carrying outismeasurements. The last of II the intron excised as three group these is relatively short and biased introns. Excision of internal introns is towards certain techniques used by the not ordered. A secondary pathway for author, but this may not be a major this complex twintron involving drawback, as it improves the readability excision of a novel group III intron of the chapter, and this area is adequately from internal group II structures is covered in a number of other, highly under study (L. Hong R. B. Hallick, detailed, volumes on theand market. unpublished). The chapters in the second section gradually move towards more complex biological systems, taking in the basic Formation and stability of twintrons facets of hydrogen Group II intronsperoxide can actdamage, as mobile l8 . calcium oxidative stress and genetic elements The formation of homeostasis, peroxidation, twintrons is lipid most probably and a the conchemistry third sequence of ofperoxyl intronsradicals. movingThe into presection considers9 the role of enzymes existing introns . The mechanism of that repair damage (a thorough and group II article intron bymobility complete Ramotarmay and involve reverse splicing, reverse transcription Demple); an amusing, yet serious and and recombination of as thea response resulting provocative article on sex with damage; genomic DNN,18. ConsetoeDNA oxidative oxidative stress and quently, target-site intron cell proliferation; andselection the role offor oxidants mediated by the insertion should bedecarboxylase and use of ornithine measurements in studies on tumour normal exon-intron recognition elements promotion. The group final section then involved in II splicing, i.e. progresses consider the development EB51-IBS1, toEB52-IBS2, and the gUided and of radicals in theoccurred action of within redoxpair,role If reverse splicing cycling drugs; mutagenicitya oftwintron plant an intron of the a pre-mRNA, components; the effects of mineral fibres would be formed. This mechanism may and cigarette smoke in inducing DNA account for site-specific deletions in the damage; and finally th, ;~ro-oxidant yeast mitochondrial cox} gene. Mueller actions of food additives an(i nutrients.
Table I. w.i~l Summary of Euglena gracilis chloroplast Overall, this volume be welcomed overlap in placestwintrons between different by the majority of workers in this authors' contributions, and, probably Size seriously, the fact thatSize(s) expanding field, andSize it provides an most the whole (nucleotides) Internalon rather(nucleotides) (nucleotides) Gene/intron No exceilept companion to the moreExternal volume is printed thin paper, cheadcally and radiation-orientated which 355 resultsII in the contents 402of some 757 II 1 atpf.l volumes, such as that by yon SonntagL in pages being visible on the wrong 424 II 618 side, psbFl 1042 I 2 bringing together these and well for the 463 doesn't bode II 635lifetime of 1098 contributions 3 psbIJ.i from aycf8·i number of leading the use it II, II the undoubted 601,393 358 volume, given 1352 experts, the 4 404, 106 editors have produced 399 have. 11.111 909 a timely volume petB·1 will 5 NO (with 0115) NO NO" psbIJ.8 3658 6 will that undoubtedly be used as a NO (with ol1s) NO NO 7 psbC·2 reference volume in4143 a large number of Reference III 111 204 93 psbK·2 8 labs. 1 von Sonntag, The ChemicalBasis of Radiation 96 Biology (1987) III 112 rp116-3 208 9 Taylorand Francis all new volumes, there are a 114 III 96 210 10As with rpoCi·i number of niggles and minus points; in 111 III 102 213 11 rpoCl-3 particular the occurrence of 198 III 96 102 12 rpoCi·i1 MICHAEL DAVIES III (with orf) 101 1504 typographical which shouldI really 13 psbC·4 errors1605 409this era of automatic 99 II 310 II 14 been rps3·ispotted in have 110,106,112 107 111(111,111) III of the 15 checkers, rps18·2 spell the 434 non-uniformity Departmentof Chemistry,Universityof York, chemical structures and equations, the Heslington, York,UK Y015DD. aND, not determined.
and colleagues (Ref. 19; M. W. Mueller petB and yef8 complex twintrons are et aI., unpublished) have proposed that both interrupted in domain ID where the coxI all mobilized into EBSI S. Agtawal fed.)intron Protocolsis for Oligonucleotides F. W.is located. Hardson Domain and M. VjVI E. insertions Rice (eds) and Analogs - Synthesis and Properties. Microscopic of Invertebrates WileyexpectedAnatomy to disrupt 5'-exon release splicing-compatible locations in the are Methods in Molecular Biology Vol. 20 Humana Liss, 1993. $185.00 (xiv + 484 pages) ISBN and nucleophilic activity of the cox1 aI5a and aI5b introns, in effect genPress, 1993. $59.50 (xiv + 502 pages) ISBN 0 471 56119 3 erating twintrons. Instability caused by unpaired adenosine during lariat for0 896 02347 7 E. Haslam Shikimic Acid - Metabolism and Insertions in domain I would transient tandem duplication of all mation. Metabolites Wiley-Liss, 1993. £75.00 (xii + N. H. Battey, H. G. Dickinson A. M. disrupt of the catalytic core, formation results in high-frequency cox1 and deletions 387 pages) ISBN 0 471 93999 4 Heathedngton (eds) Post-translational with end pointsinat the 3'-endSociety of all and Modifications Plants. for binding of domain V, and/or exon P. N. Hobson Positions and A. D. Wheatley Anaerobic within nonessenExperimental BiologytoSeminar SeriesEBS-Iike VoL 53 recognition. sites adjacent cryptic Digestion - Modem Theory and Practice Cambridge University Press, 1993.intermedi$89.95 (xx tial regions of group II introns suchISBN as sequences. The postulated Elsevier, 1993. £65.00 (xi + 269 pages) + 310 pages) ISBN 0 521 41181 5 1 85166 IV 958 2 be interrupted by introncan ates with a duplicated all group II domain proteinThe genes andof are unlikely intron (Le. introns introns) have encoded R. V. Benasson, E. J. within Land and T. G. Tmscott S. A. Kauffman Origins OrderSelf Excited and Free Radicals in Biology sites for and stable internal introns. not beenStates isolated. Organization Selection in Evolution Oxford and Medicine twintrons Oxford University 1993. University Press, 1993. formation £55.00 (xviiican + 709 twintron be Although could Press, be lost by Therefore, £50.00 (xi + 431 pages) ISBN 0 19 855560 1 pages) ISBN 0 19 507951 5 as an in vivo insertional mutarecombination or accumulation of viewed B. A. Bernard and B. Shmot Pharmacology system. imprecise deletions, the twintrons of genesis L. Larand and K, G. Mann (eds) Proteolytic and the Skin Vol. 5 - From Biology in Coagulation, Fibrinolysis, and intron inserA 'hot-spot' for group III Euglena chloroplast genesMolecular are stable. If Enzymes to Therapeutics Karger, 1993. $199.25 (viii + Complement Activation Part B - Complement tion is within domain VI, where six of the internal introns disrupted essential 196 pages) ISBN 3 8055 5776 0 Activation, Fibrinolysis, and Nonmammalian known insertions occur (Fig. functional domains of external introns, the BloodtenCoagulation Factors and Inhibitors. C. M. A.stability Brett and A. be M. expected. O. Brett 3b). Methods in Enzymology 223 Academic Three are within VoL potential stemtwintron would Electrochemistry - Principles, Methods and Press, 1993. £50.00 (xxviii + 433 pages) of the Correct splicing Applications Oxford University Press, 1993. ISBN 0 12 182124 2 internal a ISBN 0 19 £25.00 intron (xxviv +would 427 be pages) (a) W. Montagna, G. Prota and J. A. Kenney, Jr prerequisite for external 855388 9 Black Skin - Structure and Function Academic intron splicing, and exP. M. A. Bmda, S. G. Oliver and P. F. G. Sims Press, 1993. £54.00 (x + 158 pages) ISBN 0 pression the interrupted (eds) TheofEukaryotic Genome - Organisation 12 505260 X Internal introns of for General gene and 7.9•Regulation. Society Oleson. P. Tfelt-Hansen and K. M, A. Welch Microbiology Symposium several twintrons inter-50 Cambridge J. University Press, 1993. £60.00/$120.00 (xii (ed.~) fhe Headaches Raven Press, 1993. rupt known functional $208.00 (xxiv + 922 pages) ISBN 0 7817 + 395 pages) ISBN 0 521 44364 4 domains defined in vitro, 0069 8 Y. P. the Cruz catalytically Laboratory Exerc;.3es in within J. R. Foortmans fed.) Principles of Exercise Developmental Biology Academ:c I, V, Press, 1993. Biochemistry (2nd, corevised edn) Medicine and important domains £26.50 (xi + 241 o~ges) ISBN 0 12 198390 0 Sport Science VoL 38 Karger, 1993. and VI (Fig. 3). The inter'" Sfr.156.00/DM187.00/$125.00 (304 pages) ( b) nal intronsand of G. theJ.psbF and Polychlorinated S. Dobson Van Esch ISBN 3 8055 5778 7 Biphenyls and Terphenyls psbD twintrons are both(2nd edn) IPCS Environmental Health Criteria VoL 140 World A. P6hler fed.) Genetic Engineering of Animals located between the secrps18-2c Health Organization, 1993. SFr.70.00/$63.00 VCH, 1993. £15.50/DM38.00 (177 pages) ond third pairs 3 psbC ISBN 3 527 30041rpslS-2b (682 and pages) ISBNbase 92 4 157140 4 : 'poC1-11 within the upper stem of IF. Franks fed.) Protein BiotechnologyA. P(ihler fed.) Genetic Engineering of domain V of the external Isolation, Characterization and Stabilization Microorganisms VCH, 1993. £15.50/ intron, while that of the Humana Press, 1993. £87.00 (xi + 592 DM38.00 (viii + 178 pages) ISBN 3 527 atpE is 230 within pages)twintron ISBN 0 89603 2 30039 2 Figure 3 the loop of domain VI Twintron insertion sites of internal introns in func· J. P. Gosling and D. J. Reen (eds) J. P. Robinson fed.) Handbook of Row (Fig. 3a). The external tional dornains of external (a) group II and (b) group Immunotechnology Portland Press, 1993. Cytometry Methods (2nd edn) Wiley, 1993. introns. group II +introns of ISBN the 1 85578III035 £45.00 (ix 153 pages) 6 £32.95 (xii + 246 pages) ISBN0 471 59634 5 (JJ
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TI8S 18 - DECEMBER 1993
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orwelcomed less and may well be a number of readers who are Overall, thisnucleotides volume w.i~l be put off by the initial chemical input. It is, Euglenoid between by the majorityothers of workers in this2S0 and however, worth persevering with as there plastid expanding field, andnucleotides it provides in an length. 1000 groupexceilept III is valuable information here both for companion to the more Intramolecular base pairresearchers already working in the field cheadcally anding radiation-orientated within the larger and newcomers (in particular new volumes, suchintrons as that by yon reduce SonntagLthe in may postgraduate students, for whom this bringing together these contributions proximity of splice sites wouldFungal be a good sta;tingPlant point) who are Euglenoid from a number of leading experts, the and branch sites to paralnotmitochondria familiar with the subject but who wish editors have produced a timely volume organelle plastid 2 22 lel the small introns to (or ought to) become so. that will undoubtedly be used as a 1. . (self-splicing) group II group II group The chapters are broken down into reference volumeSome in a large number[ ofand group II introns encode four major sections: chemistw and labs. measurement of damage to DNA by As with all new volumes, there are a'mapolypeptides termed reactive oxygen species; mechanism of number of niggles and minus points; turases', which are in reNuclear Prokaryotic DNA damage by oxidative stress; ? particular the occurrence of q uired for efficient splicgroup II damage; pre-mRNA consequences of oxidative DNA typographical ing errors which should really and/or intron mobility and pro-oxidants and(self-splicing) DNA damage. Each+ snRNAs have been spotted in this era of automatic in ViV01S. These maturases part is preceded by a brief preface by the spell checkers, the non-uniformity of the are thought to bind and editors. The first section begins with an chemical structures and equations, the stabilize catalytically acintriguing chapter by Ames and Shigenaga tive RNA. All five intronon the role of oxidants as major encoded open reading contributors to cancerProgenitor and aging- a II frames (orfs) in the justification, if ever one group was needed, for the research that is being carried out in genome of the Euglena this area. This introduction certainly are within S. Agtawal fed.)chloroplast Protocols for Oligonucleotides provides food for thought as well Figure 4 as and Analogs -twintrons Synthesis6. In andaddition Properties. to Methods in Molecular Biology Vol. 20 Humana valuable (and ammunition?) Model information for the evolutionary relationship of bacterial, ycf13, there are two oris Press, 1993. $59.50 (xiv + 502 pages) ISBN plastid have and nuclear introns from a comformitochondrial, people who would us decrease 0 896 02347 7 within each of the twinancestor. ourmon daily intake of calories and minimize trons in psbC intron 2 our exposure to certain chemicals, N. H. Battey, (177 H. G.and Dickinson and A.and M. 241 codons) although adverts which encourage us to Heathedngton (eds) Post-translational loopless structures in the are S'-region intron 8 in(281Plants. and S06Society codons). Modifications for 'eat and live longer' unlikelyoftothe be psbD intron, possiblycorrect defining a second func- Although Experimentalmotifs Biology characteristic Seminar Series of VoL re53 as scientifically or as elegantly Cambridge University Press, $89.95are (xx transcriptases (and 1993. maturases) tional domain. domain act as verse presented as thisThis chapter. The may following + 310 pages) ISBNof 0 521 41181 5 23 , in some these polypeptides present a S'-exon/intron chapters in the first recognition section outlineelement the
t
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basic free chemistry DNA,guided the II EBSIof and similar toradical the group reactions and mechanisms that within generate the pair. Alternatively, insertions measurable lesions and the methods for a S'-base-paired domain may disrupt carrying measurements. 5'-last andof 3'minimal out distance betweenThe these is relatively short and biased splice sites. towards certain techniques used by the The internal and external introns of author, but this may not be a major the group III twintrons are all within the drawback, as it improves the readability size for and group introns with one of therange chapter, thisIIIarea is adequately I):ofthe internal exception covered in a(Table number other, highlyintron of the psbC twintron detailed, volumes on the(intron market.4) is 1504 nucleotides long, with an open reading The chapters in the second section 2o (D. gradually towards more 458 codons W.complex Copertino frame of move biological in the basicycfi3 Hallick,taking unpublished). and R. B.systems, facets of hydrogen (Ref. 6; previouslyperoxide known damage, as orf458) of oxidative andiscalcium the psbCstress twintron located in the loop homeostasis, lipid Therefore, peroxidation, the of a 5'-domain. theand narrow chemistry of peroxyl radicals. The third size range of group III introns is not section considers the role of enzymes absolute. Large size variations are possthat repair damage (a thorough and ible, but perhaps extra sequence must complete article by Ramotar and be confined to only yet select regions Demple); an amusing, serious and of a group III core structure. The most relprovocative article on sex as a response of group III introns may evant feature to oxidative damage; oxidative stress and be proliferation; the three-dimensional conformation cell and the role of oxidants and use RNA, of ornithine decarboxylase of the with the distance between measurements studies tumourVI (3'the S'-splice in site and on domain promotion. final section then splice site)The being most critical. Most progresses to consider development may the achieve this congroup III introns and role of radicals the action of redoxformation by size inalone. A similar recycling drugs; the mutagenicity of plant lationship between size and core struccomponents; the effects of mineral fibres ture has been proposed for yeast and cigarette smoke in inducing DNA nuclear and introns, exhibit bimodal damage; finallywhich th, ;~ro-oxidant size distribution, with some at 100 actions of food additives an(i nutrients.
470
the and intron-encoded itR.isV.not yet known Benasson, E. J. ifLand T. G. Tmscott Excited States and Free are Radicals in Biology in Euglena involved in proteins and Medicine Oxford University Press, 1993. either splicing and/or intron mobility. £50.00 (xi + 431 pages) ISBN 0 19 855560 1 Based on preliminary western-blot analyB. A.at Bernard and ofB. the Shmot Pharmacology intron-encoded sis, least one and the Skin is Vol.expressed 5 - From Molecular Biology ods, ycfI3, (K. P. Jenkins to Therapeutics Karger, 1993. $199.25 (viii + R. B. Hallick, unpublished). and 196 pages) ISBN 3 8055 5776 0 C. M. A. Brettof and M. O. Brett Common features groupA.II, group III and Electrochemistry Principles, Methods and nuclear pre-mRNA- introns Applications Oxford University Press, 1993. Group(xxviv III introns shouldISBN be 0con£25.00 + 427 pages) 19 sidered 855388 9in parallel with group II and
nuclear introns. Group II, group III and P. M. A. Bmda, S. G. Oliver and P. F. G. Sims pre-mRNAGenome introns are all nuclear (eds) The Eukaryotic - Organisation excised via lariat Society intermediates using and Regulation. for General Microbiology Symposiumas cis-acting 50 Cambridge internal adenosines nuUniversity Press, 1993. £60.00/$120.00 (xii cleophiles. Group II/III introns contain + 395 pages) ISBN 0 521 44364 4 an unpaired adenosine stabilized by base-pairing cis within Exerc;.3es domain VI, Y. P. Cruz in Laboratory in Developmental Biology Academ:c Press, inter1993. whereas the U2-snRNA-UACUMC £26.50 (xi + 241 o~ges) ISBN 0 12 198390 0 action in nuclear introns stabilizes this 3,1224. nucleophile S. Dobson andinG.trans J. Van Esch Polychlorinated Biphenyls and other Terphenyls (2ndsimilarities edn) IPCS There are potential Environmental Criteria VoLof140 World nuclear between the Health catalyic cores Health Organization, 1993. SFr.70.00/$63.00 II introns. The 5'and 3'and group (682 pages) ISBN 92 4 157140 3 exons in both systems are positioned at IF. Biotechnologythe Protein conserved loop of US the Franks core byfed.) Isolation, Characterization and Stabilization 5 versus for nuclear introns Humana Press, 1993. £87.00 EBSI (xi + and 592 7 the guided for 230 group pages) ISBN 0pair 89603 2 II introns ,25.26. Interaction at the S'-splice site by U6 for J. P. Gosling 2i D. J. Reen (eds) nuclear introns andis similar to the1993. E-E' Immunotechnology Portland Press, 25 Also, interaction for pages) group ISBN II introns £45.00 (ix + 153 1 85578• 035 6
4 may correspond the U2-U6 interaction overlap in places between different the group II catalyticand, domain V14. to authors' contributions, probably Group II intron recogmost seriously, theboundaries fact that theare whole volumeiniscis printed on rather thinbypaper, during splicing the 5'· nized which results in the contents of some splice site; domain VI; and tertiary pages being visible side, interactions suchon the aswrong EBSl-IBSl, and doesn'tthe bode well for the and lifetime of EBS2-IBS2, guided pair, the c-£' the volume, given the undoubted use it and y-y' interactions 7.25.26. Elements will have. likely to be required for recognition of group III splice boundaries other than Reference the S'-boundary and domain 1 von Sonntag, The sequence ChemicalBasis of Radiation (1987) Tayloridentified. and Francis Group II, VI Biology have not been group III and nuclear pre-mRNA introns all have similar S'-splice sites_ The U at MICHAEL DAVIES +2 and the G at +S are conserved in all three systems, and probably influence Departmentofselection. Chemistry,University of York, splice-site If cryptic 5'-splice Heslington, York,UK Y015DD. sites are nearby, alternative splicing can occur. In Euglena, there are several examples of alternative S'- and/or Jsplice site utilization involving excision of internal introns of group III 12,17. Imprecise twintrons of F. W. Hardson and M. E.splicing Rice (eds) Microscopic Anatomy of Invertebrates Wileyinternal introns should still be permissLiss,for1993. (xiv + The 484 use pages) ISBN of mulive gene$185.00 expression. 0 471 56119 3 tiple splice sites has also been E. Haslam for Shikimic Acid group - Metabolism and observed a single III intron, Metabolites Wiley-Liss, 1993. £75.00 (xii + in out-of-frame ligation of resulting 387 pages) ISBN 0 471 93999 4 exons for the rp112 gene (R. G. Drager P. N. Hobson A. D. Wheatley Anaerobic R. B. andHallick, unpublished). and Digestion - Modem Theory and Practice II core structure preWhereas group Elsevier, 1993. £65.00 (xi + 269 pages) ISBN 1 85166the 958use 2 of alternate splice sites, cludes the of extensive cis-tertiary interacS. A.lack Kauffman The Origins of Order- Self tions in group III and in nuclear introns Organization and Selection Evolution Oxford University Press, (xviii + and 709 may account for1993. both£55.00 mis-splicing pages) ISBNsplicing. 0 19 507951 5 alternative the Proteolytic S'-splice analyses L. Mutational Larand and K, G. Mannof(eds) Enzymes in these Coagulation, Fibrinolysis, and site support conclusions for yeast Complement Activation Part B - Complement nuclear introns. For example, mutation Activation, Fibrinolysis, and Nonmammalian in and activation of of the Coagulation G at +5 results Blood Factors Inhibitors. 28 , 223 Methods 5'-cleavage in Enzymology VoL cryptic sites The Academic G at +5, Press, 1993. (xxviii 433bepages) possibly with£50.00 the U at +2, +may part ISBN 0 12 182124 2 of a catalytic core shared by nuclear. W. Montagna, Prota III andintrons. J. A. Kenney, Jr II, and G.group The G group Black Skinto- Structure andfor Function Academic of appears be crucial activation Press, 1993. £54.00 (x + 158 pages) ISBN 0 the correct phosphodiester bond, 12 505260 X recognition by the nucleophilic 2'-OH J. Oleson. P. Tfelt-Hansen and K. M, A. Welch during lariat formation, and perhaps (ed.~) fhe Headaches Raven Press, 1993. other within the $208.00important (xxiv + 922contacts pages) ISBN 0 7817 active8 site. 0069 formation may of not be J. Twintron R. Foortmans fed.) Principles Exercise Euglena chloroplast genes. restricted Biochemistryto(2nd, revised edn) Medicine and Sport large Sciencenuclear VoL introns 38 Karger, Some may 1993. have Sfr.156.00/DM187.00/$125.00 (304 pages) formed from multiple, smaller introns. ISBN 3 8055 5778 7 Intron excision of large nuclear preA. P6hler fed.) Genetic of Animals mRNA introns could Engineering occur in sequential VCH, 1993. £15.50/DM38.00 (177 pages) steps from internal splice boundaries. ISBN 3 527 30041 4 Such an organization of multiple 5'- and A. P(ihlersites fed.) could Geneticalso Engineering of 3'-splice result in Microorganisms VCH, 1993. £15.50/ alternative splice-site selection. Thus, DM38.00 (viii + 178 pages) ISBN 3 527 twintron 30039 2 formation by intron insertion into pre-existing introns is one potential J. P. Robinson fed.) Handbook of Row mechanism for the(2nd origin alternative Cytometry Methods edn)ofWiley, 1993. splicing12.16.1,. £32.95 (xii + 246 pages) ISBN0 471 59634 5
487
TIBS 1 8 - DECEMBER 1993 The recent discovery of self-splicing group II introns in prokaryotes 29 is suggestive of an evolutionary relationship between bacterial, mitochondrial, chloroplast and nuclear introns as shown in Fig. 4. These classes of introns could have a common evolutionary ancestor. Nuclear and group IIi introns appear to represent an example of convergent evolution from an ancestral, self-splicing RNA that was also a mobile genetic element. If splicing of group III introns involved transacting RNAs analogous to nuclear snRNPs, the character|zation o! these RNAs would provide an important new insight into the evolution of the spliceosome. Some of the contemporary parallels between group ili and nuclear introns are quite striking, including the conserved 5'-boundary, lariat formation, lack of internal structure and the ability to use alternate splice boundaries.
Acknowledgements We wish to thank Rob Drager, Ling Hong and Mitch Favreau for contri-
butions to the work described; and Christine Guthrie and Roy Parker for discussion and critical reading of the manuscript.
References 1 Cech, T. R. (1986) Cell 44, 207-210 2 Sharp, P. A. (1985) Cell 42, 397-400 3 Jacquier, A. (1990) Trends Biochem. Sci. 15, 351-354 4 Madhani, H. D. and Guthrie, C. (1992) Cell 71, 803-817 5 Newman, A. J. and Norman, C= (1992) Cell 68, 743-754 6 Hallick, R. B. et aL (1993) Nucleic Acids Res. 2:t. 3537-3544 7 Michel, F., Umesono, K. and Ozeki, H. (1989) Gene 82, 5-30 8 Koller, B., Clarke, J. and Delius, H. (1985) EMBO J. 4, 2445-2450 9 Copertino, D. W. and Hallick, R. B. (1991) EMBO J. 10, 433-442 10 Christopher, D. A. and Hallick, R. B. (1989) Nucleic Acids Res. 17, 7591-7608 11 Siemeister, G., Buchholz, C. and Hachtel, W. (1990) Mol. Gen. Genet. 220, 425-432 12 Copertino, D. W., Shigeoka, S. and Hallick, R. B. (1992) EMBOJ. 11, 5041-5050 13 Drager, R. G. and Hallick, R. B. (1993) Curr. Genet. 23, 271-280 I 4 Jarrell, K. A., Dietrich, R. C. and Perlman, P. S. (1988) MoL Cell. Biol. 8,
2361-2366 15 Goldschmidt-Clermont, M. et aL (1991) Cell 65, 135-143 16 Copertino, D. W., Christopher, D. A. and Hallick, R. B. (1991) Nucleic Acids Res. 19, 6491-6497 17 Drager, R. G. and Hallick, R. B. (1993) Nucleic Acids Res. 21, 2389-2394 18 Lambowitz, A. M. and Belfort, M. (1993) Annu. Rev. Biochem. 62, 587-622 19 Mueller, M. W., Eskes, R., AIImaier, M. and Schweyen, R..1. Nature (in press) 20 Montandon, P. E., Vasserot, A. and Stutz, E. (1986) Curr. Genet. 11, 35-39 21 Parker, R. and Patterson, B. (1987) in Molecular Biology of RNA: New Perspectives (Dudock, B. and Inouye, M., eds), pp. 133-149, Academic Press 22 Goguel, V. and Rosbash, M. (1993) Cell 72, 893-901 23 Mohr, G., Perlman, P. S. and Lambowitz, A. M. Nucleic Acids Res. (in press) 24 Parker, R., Siliciano, P. G. and Guthrie, C. (1987) Cell 49, 229-239 25 Jacquier, A. and Jacquesson-Breuleux, N. (1991) J. MoL Biol. 219, 415-428 26 Jacquier, A. and Michel, F. (1990) J. Mol. Biol. 213, 437-447 27 Wassarman, D. A. and Steitz, J. A. (1992) Science 257, 1918-1925 28 Guthrie, C. (1991) Science 253, 157-163 29 Ferat, J-L. and Michel, F. (1993) Nature 364, 358-361
ONE OF THE most successful ways of
studying gene function is the analysis of phenotypes that arise when the activity of an individual gene is varied In a defined way by outside stimuli. A number of regulatory systems permit this approach in the bacterium Escherichia coil; and in the budding yeast Saccharomyces cerevisiae numerous valuable insights into gene function have been obtained by utilizing the GAL system, in these systems, the activity of Regulated gene expression systems for the study of gene function in a gene can be studied by controlling its prokaryotes and yeast have been available for several years. However, expression at the transcriptional level comparable systems in higher organisms are more complex and problemthrough the use of natural metabolites atic. Recently, regulatory proteins from distant species have been used to or their derivatives as specific effecestablish highly specific control systems in eukaryotic cells. This is posstors. When properly applied, such conible because their action can be modulated by effectors that are inert to trol systems not only allow us to create the physiology of the organism or cell and therefore do not elicit pleioreversible on/off switches for a gene's tropic effects. Such monospecific regulatory circuits c,~en up new possiactivity, but also to adjust the expresbilities for the study of gene function in vivo. sion to defined levels. The latter possibility will, in particular, further our understanding of gene function, since In E. coil, transcription control sys- Ref. 1) usually suffer from one or both quantitative parameters frequently define metabolic or developmental tems based on regulatory elements of the following problems: (1) the such as the lactose operon allow the inducer (such as heavy-metal ions, states. tight control of a gene of interest. steroid hormones or heat shock) However, no comparable general evokes pleiotropic effects that compliM. Gossen,A. L. Bonlnand H. BuJardare at methodology is presently available for cate the analysis of the resulting phenothe ZMBH-Zentrumfor MolekulareBiologie, vertebrate cells. The commonly used type; and (2) many promoter systems UniversitStHeidelberg,Im NeuenheimerFeld endogenous systems (for review see have high basal levels of activity in the 282, D-69120Heidelberg,Germany.
© 1993,ElsevierSciencePublishers,(UK) 0968-0004/93/$06.00
471
DECEMBER 1993
pathway of an antibiotic tripeptide6. The mechanisms of hydrolysis of the ester bonds of triglycerides and the amide bond linking acetate to the tripeptide are similar, and it is not surprising that these enzymes show sequence similarity in the region of the catalytic site. Besides HSL, no long region of similarity between a mammalian lipase and its prokaryotic counterparts has been reported. This note also strengthens the hypothesis that HSL is a mosaic protein ] with a region sharing a common ancestry with some bacterial enzymes and other regions, such as the phosphorylation
sites, from a different origin. Clearly, the resolution of the three-dimensional structure of HSL will provide valuable information for a complete understanding of these unexpected similarities.
References
1 Langin,D. et al. (1993) Proc. Natl Acad. Sci. USA 90, 4897-4901 2 Derewenda,Z. S. and Derewenda,U. (1991) Biochem. Cell Biol. 69, 842-851 3 DoolitUe,R. F., Feng, D. F., Johnson, M. S. and McClure,M. A. (1986) Cold Spring Harbor Syrup. Quant. BioL 51, 447-455 4 Van Tilbeurgh,H. et aL (1993) Nature 362, 814-820
5 Feller,G., Thiry,M. and Gerday,C. (1991) DNA Cell Biol. 10, 381-388 6 Murakami,T. et al. (1986) Mol. Gen. Genet. 205, 42-50
DOMINIQUE LANGBN Institut Nationalde la Sant~et de la Recherche M6dicale U-317, B~timentL3, CHU Rangueil, F-31054Toulouse,France.
CECILIA HOLM Departmentof Medical and PhysiologicalChemistry 4, Lund University,P.O.Box 94, .~o2100 Lund, Sweden.
REVIEWS _
SINCE THE DISCOVERY of intervening sequences in 1977, introns have been classified into groups based on common mechanisms of excision and conserved intron features. The recognition of identical splicing pathways for group II and nuclear pre-mRNA introns, involving two successive transesterification reactions in which these introns are excised as 'lariats', has led to the hypothesis that these classes of introns are evolutionarily related ~,2. A corollary is the potential correspondence of structural/functional elements between the cis-encoded domains ol group II introns and the trans.acting splicing machinery of nuclear introns. Structural, functional and mechanistic aspects of this hypothesis have been
Group II and group III introns of twintrons' potential relationships with nuclear pre-mRNAintrons
Two new and important features of introns have emerged from analysis of the E u g / e n a g r a c i / i s chloroplast genome. On,e is a new class of introns, designated group III, that may be the close,.;t contemporaries to nuclear pre-mRNA introns. The second is introns that are interrupted by other introns termed twintrons.
reviewed ~ .
convincing group II core structures, due to either loss of domains l-IV or massGroup II introns of the chloroplastgenes of ive divergence from related group II Euglena gracilis The chloroplast genome of Euglena introns 7. By contrast, we find that most gracilis contains at least 155 introns, of the 74 Euglena group II introns do accounting for 39.2% of the genome 6. At have group II core structures, albeit least 74 of these are group II introns, with more relaxed pairing rules for both ranging in size from 277 to 671 nu- stems and tertiary interactions. Plastids cleotides (Fig. I). These introns have of Astasia longa, a related protist, cona conserved secondary structure of six tain similar group II introns. The core helical domains (I-VI) radiating from a structure of the smallest group II intron, central core. They are also found in a 270 nucleotide intron of the Astasia organellar genes of fungi and plants, rps2 gene, is shown in Fig. 2a. This and in prokaryotes. It has been pro- intron illustrates the secondary and terposed that many Euglena introns are tiary interactions characteristic of only 'group ll-like', because they lack group II introns, such as domains I-VI, exon-binding site-I (EBSl)-intron-binding site-10BS1), EBS2-IBS2, E-E', ~-~' D. W. Copertlno and R. B. Halllck are at the and the guided pair. All of the Euglena Department of Biochemistry and the group II introns possess the highly conDepartment of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA. served catalytic domain V as well as © 1993,ElsevierSciencePublishers,(UK) 0968-0004/93/$06.00
domain VI, although terminal loops of these domains can be variable7. Euglena group II introns also have the conserved 5'-boundary motif 5'-GUGYG, a domain I helical stem, and subdomains IC and ID. Domains II-IV can be very small (<15 nucleotides per domain). All of the Euglena group II introns contain EBSI in domain ID3 and the 7--~/interaction. Less conserved but usually present, although not readily apparent because the pairings are not solely Watson-Crick interactions, are EBS2-1BS2 pairing, the 'guided pair', and the e-e' interaction (Fig. 2a). Also, Euglena group II introns excise as lariats 8,9 (D. W. Copertino and R. B. Hallick, unpublished). Thus, Euglena and probably Astasia have bona fide group II introns, which are very important for studying the minimum structure 467
TIBS 1 8 - D E C E M B E R 1 9 9 3
III (Refs may well be a number of readers who are Overall, this designated volume w.i~lgroup be welcomed put off by the initial chemical input. It is, 11 andin this EMBL acby the majority10, of workers however, worth persevering with as there expanding field, and it provides cession number an X16004). is valuable information here both for exceilept companion the more genes Euglenato chloroplast researchers already working in the field cheadcally andcontain radiation-orientated 50 individual andcennewcomers (in particular new volumes, such group as that III by introns, yon SonntagL and in 18 postgraduate students, for whom this bringing together these contributions or more additional introns would from a number of leading experts, the -~ be a good sta;ting point)IIwho are within twintrons (see benot(5familiar with the subject but who wish editors have produced a timely volume ~ low). These introns to (or ..... ought to) become so. that will undoubtedly be used as a are in Q) the innarrow range The chapters are broken down into reference volume a large size number of of ...c 91-119 nucleotides (Fig. four labs. E major sections: chemistw and :::l measurement of damage to DNA by As with all new are a are 1). volumes, Group IIIthere introns Z reactive oxygen species; mechanism of number of niggles and minus points; generally V-rich. The inconDNA damage by oxidative stress; particular the occurrence of sensus 5'-boundary seconsequences of oxidative DNA damage; typographical errors reallyis 5'-NVNNG quencewhich of should and pro-oxidants and DNA damage. Each have been spotted in this of automatic related to era group II and part is preceded by a brief preface by the spell checkers, the non-uniformity of the pre-mRNA 5'nuclear editors. The first section begins with an chemical structures and equations, the splice sites. Group III inintriguing chapter by Ames and Shigenaga trons contain a 3'-domain, on the role of oxidants as major defined as abcdef(3-8 nucontributors to cancer and aginga Intron size (nucleotides) cleotide loop)f'e'd'A*c'b'a' justification, if ever one was needed, for the research that is being carried out in (4 nucleotides)-3'. This Figurecertainly 1 this area. This introduction splice siteforisOligonucleotides identical to S. Agtawal fed.) Protocols Size distribution of Euglena gracilis chloroplast provides food for thought as well as and Analogs -the Synthesis group andII Properties. domain introns. Individual group II and group III introns are Methods in Molecular Biology Vol. 20 Humana valuable information (and ammunition?) VI12,13. The 5'-side of the indicated. The group III intron mean isPress, 103 1993. $59.50 (xiv + 502 pages) ISBN fornucleotides. people whoThe would have us decrease distribution of group II introns 0 896is02347 7 stem (abcdef) is purineourbimodal daily intake of calories and minimize with peaks centered near 350 and 550 rich. Group III introns are ournucleotides. exposure toGroup certain chemicals, N. also H. Battey, spliced H. G. Dickinson and A. M. III and other twintrons are via a lariat interalthough adverts which encourage us to Heathedngton (eds) Post-translational indicated, (Scale on X-axis is discontinuous.) mediate utilizing the unModifications in Plants. Society for 'eat less and live longer' are unlikely to be pairedSeminar adenosine (A53 *) Experimental Biology Series VoL as scientifically correct or as elegantly Cambridge University Press, 1993. (xx required asfor domain VI during intron$89.95 excision presented this group chapter. IIThesplicing followingin within + 310 pages) ISBN 0 521 41181 5 chapters in the first section outline the to (0. W. Copertino and R. B. Hallick, vivo, and identifying alternatives
e
TI BS 18 - DECEMBER 1993
5'-splice site, and Similarity at the overlap in places between different excision as lariats utilizing domain VI, authors' contributions, and, probably suggest that group III that introns are evolmost seriously, the fact the whole volume is printed thinII paper, utionarily relatedontorather group introns, whichstructures results in the contents some The of two groupof III introns pages being in visible wrong side, of Fig. on 2b.theThe 5'-region are shown and doesn't bode well forafter the lifetime one intron is modeled domainof ID the volume, given the undoubted use it of group II introns. This particular will have. intron contains potential EBS 1 and EBS2 elements. The 5'-region of the Reference other intron Thecan assume stable 1 von Sonntag, Chemical Basis of aRadiation Biology (1987) Taylorand in which theFrancis terminal loop is stem-loop V-rich. The V-rich loop may have more flexibility in base-pair interactions, MICHAEL DAVIES possibly interacting with the 5'-exon, as has been proposed for the interaction Department Chemistry, Universityloop of York,of US between ofthe conserved Heslington, York,UK Y015DD. snRNA and upstream exons 5. Group HI introns might be group II introns that require some domains in trans. For example, a trans-acting domain V could activate the first reaction 14 . Alternatively, in Rice trans (eds) may F. W. domains Hardson supplied and M. E. Microscopic Anatomy of Invertebrates Wileyreconstitute an entire group II intron Liss, 1993. $185.00 (xivas + 484 pages) is the caseISBN for secondary structure, 0 471 56119 3 the tseA locus in trans-splicing of the E. Haslam Shikimic Acid -Chlamydomonas Metabolism and psaA mRNA of the Metabolites Wiley-Liss, 1993. £75.00 (xii + 15 • A requirement chloroplast 387 pages) ISBN 0 471 93999 4 for transacting RNAs for group III splicing would P. and parallel A. D. Wheatley be N.anHobson obvious to theAnaerobic role of Digestion - Modem Theory and Practice snRNPs in nuclear pre-mRNA splicing. Elsevier, 1993. £65.00 (xi + 269 pages) ISBN
1 85166 958 2 basic free radicalbase chemistry of DNA, the Watson-Crick pairing for intron unpublished). The 5'-region some S. Introns within introns in chloroplast genes R. V. Benasson, E. J. Land and T. G.ofTmscott A. Kauffman The Origins of OrderSelf reactions and mechanisms that generate Excited III States and is Free Radicals in Biology introns almost identical to of secondary and tertiary interactions. group Euglena gracilis Organization and Selection in Evolution Oxford and Medicine Oxford University Press,Others 1993. University measurable lesions and the methods for Press, chloroplast 1993. £55.00genome (xviii + con709 domain 103 of group II introns. The Euglena £50.00 (xi + 431 pages) ISBN 0 19 855560 1 pages) ISBN 0 19 507951 5 carrying measurements. The last of of Group III out introns of the chloroplast genes possess similar stem-loop structures tains twelve known and three postuthese is relatively short and biased B. A. Bernard and B.EBS Shmot Euglena gracilis without an obvious (Fig.Pharmacology 2b). A few L. lated introns introns, or twinLarand and K,within G. Mann (eds) Proteolytic towards certain techniques used by the 6• The and the IIISkin Vol. 5 seem - Fromto Molecular Enzymes in Coagulation, Fibrinolysis, and Euglena and Astasia plastid genomes group introns containBiology only trons internal intron( s) are first author, but this may not be a major to Therapeutics Karger, 1993. $199.25 (viii + Complement Activation Part B - Complement of introns VI. also contain a unique class domain excised, thereby reconstituting the 196 pages) ISBN 3 8055 5776 0 drawback, as it improves the readability Activation, Fibrinolysis, and Nonmammalian Blood Coagulation Factors and Inhibitors. of the chapter, and this area is adequately C. M. A. Brett and A. M. O. Brett Methods in Enzymology VoL 223 Academic covered in a number of other, highly (b) Methods and Press, 1993. £50.00 (xxviii + 433 pages) Electrochemistry - Principles, EBS2 detailed, volumes on the market. Applications Oxford University Press, 1993. ISBN 0 12 182124 2 The chapters in the second section ~ AAA £25.00 (xxviv + 427 pages) ISBN 0 19 cu U U U U G,. W. YyC G EBS1 G. Prota and J. A. Kenney, Jr gradually move towards more complex 855388 9 A U ;. IA U A A Montagna, U U 1 U - Structure and Function Academic BlackUUA Skin U U biological systems, taking in the basic A Press, 1993. £54.00 (x + 158 pages) ISBN 0 P. M. A. Bmda, S. G. Oliver and P.UF. G. Simsinternal facets of hydrogen peroxide damage, intron U U A'U U 12 505260 X (eds) The Eukaryotic Genome - Organisation A;~U (112 ntl oxidative stress and calcium and Regulation. Society for General u;~u uU Cu J. Oleson. P. Tfelt-Hansen and K. M, A. Welch homeostasis, lipid peroxidation, and the Microbiology Symposium 50 Cambridge fhe Headaches Raven Press, 1993. chemistry of peroxyl radicals. The third University Press, 1993. £60.00/$120.00AU:'U~ (xiiUA~ (ed.~) ~ U UU VI u~=~u $208.00 (xxiv + 922 pages) ISBN 0 7817 + 395 pages) ISBN 0 521 44364 4 section considers the role of enzymes u-A ~:~8A* A-u external intron 0069 that repair damage (a thorough and u-A G·U ~:~ (96 ntl A A Y. P. Cruz Laboratory Exerc;.3es U- in 5'-UUGUGA CUU-A - u AUUU_3' A-U J. R. Foortmans fed.) Principles of Exercise complete article by Ramotar and Developmental Biology Academ:c Press, 1993. Biochemistry (2nd, revised edn) Medicine and Demple); an amusing, yet serious and £26.50 (xi + 241 o~ges) ISBN 0 12 198390 0 Sport Science VoL 38 Karger, 1993. provocative article on sex as a response Sfr.156.00/DM187.00/$125.00 VI (304 pages) S. Dobson and G. J. Van Esch Polychlorinated "U-A U U A-~ to oxidative damage; oxidative stress and ISBN 3 8055 5778 u. G Uc U 7 A- A * Biphenyls and Terphenyls (2nd edn) IPCS cell proliferation; and the role of oxidants UC ~:::~ ~:~ Environmental Health Criteria VoL 140 World UA. P6hler Engineering of Animals and use of ornithine decarboxylase exon , fed.) Genetic U-A A-U I exon Health Organization, 1993. SFr.70.00/$63.00 VCH, U A 1993. £15.50/DM38.00 (177 pages) measurements in studies on tumour 5'-C U GC U U UGU G GU U-A U A-U U C - AUU.CGUA G -3' (682 pages) ISBN 92 4 157140 3 ISBN 3 527 30041 4 A-U promotion. The final section then A-U CUu IF. Franks fed.) Protein Biotechnology- A. P(ihler fed.) UuU progresses to consider the development Genetic Engineering of U U 1993. Isolation, Characterization and Stabilization Microorganisms VCH, £15.50/ and role of radicals in the action of redoxUACUGU Humana Press, 1993. £87.00 (xi + 592 DM38.00 (viii + 178 pages) ISBN 3 527 cycling drugs; the mutagenicity of plant pages) ISBN 0 89603 230 2 30039 2 components; the effects of mineral fibres FigureD.2 J. Reen (eds) J. P. Robinson fed.) Handbook of Row and cigarette smoke in inducing DNA J. P. Gosling and Structural plastid (a) group II and (b) groupPress, III introns (see text for details). Tertiary interactions are indiCytometry Methods (2nd edn) Wiley, 1993. damage; andmodels finallyfor th,representative ;~ro-oxidant euglenoid Immunotechnology Portland 1993. in the 'guided pair'(ixinteraction (boxed bases). cated,ofincluding nucleotides £45.00 + 153 pages) ISBN 1 85578 035 6 £32.95 (xii + 246 pages) ISBN0 471 59634 5 actions food additives an(iinvolved nutrients.
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external Splicing of the external may well intron. be a number of readers who are put off results by the initial chemical input. It is, intron in exon ligation. Splicing however, worth intron persevering as there of the external beforewith removal of is valuable the internalinformation intron(s) here has both neverforbeen researchersDifferent already working in the of field twinobserved. categories and newcomers (in particular new trons vary in the composition and numpostgraduate students, for whom this ber of be introns Both who group would a good(Table sta;tingI).point) are II and group with III introns can but be who internal not familiar the subject wish and/or external intronsso.of twintrons. to (or ought to) become Ten of chapters the fifteen areinto simple The are twintrons broken down four major sections: chemistw and intron twintrons composed of one measurement of damageintron. to DNAGroup by II internal to another reactive oxygen species; twintrons in psbF, psbDmechanism and atpEofare DNA by oxidative stress;II intron each damage composed of a group consequences of oxidative DNAIIdamage; internal to another group intron9 and pro-oxidants and DNA damage. Each (Table I). Six twintrons are composed of part is preceded by a brief preface by the group IIIThe introns internal to other group editors. section begins with an 12 first 1II introns (Table I). The 'mixed' rps3 intriguing chapter by Ames and Shigenaga twintron a oxidants group II as intron on the roleis of majorin a group III intron 16 . to cancer and aging- a contributors The remaining are more justification, if ever twintrons one was needed, for the research that is being carried internal out in complex, containing multiple this area.(Table This introduction introns I). Intron 2certainly in rps18 is provides thought as well as composedfood of forfour distinct group III valuable information (and ammunition?) introns that are sequentially excised in for whoreactions17. would have us fourpeople splicing Thedecrease external our daily intake of calories and minimize is interrupted by a group III intron our exposure to certain chemicals, intron, which is encourage split into us three although advertsitself which to III introns. pieces two internal 'eat lessby and live longer' group are unlikely to be Thescientifically petB complex twintron excised in as correct or as iselegantly three sequential steps. The Thefollowing external presented as this chapter. group II intron is interrupted by group chapters in the first section outline the basic radical chemistry of DNA, II andfree group III introns. The yef8 the comreactions and mechanisms that generate plex twintron may be excised by altermeasurable lesions methods for nate pathways. In and the the major pathways carrying outismeasurements. The last of II the intron excised as three group these is relatively short and biased introns. Excision of internal introns is towards certain techniques used by the not ordered. A secondary pathway for author, but this may not be a major this complex twintron involving drawback, as it improves the readability excision of a novel group III intron of the chapter, and this area is adequately from internal group II structures is covered in a number of other, highly under study (L. Hong R. B. Hallick, detailed, volumes on theand market. unpublished). The chapters in the second section gradually move towards more complex biological systems, taking in the basic Formation and stability of twintrons facets of hydrogen Group II intronsperoxide can actdamage, as mobile l8 . calcium oxidative stress and genetic elements The formation of homeostasis, peroxidation, twintrons is lipid most probably and a the conchemistry third sequence of ofperoxyl intronsradicals. movingThe into presection considers9 the role of enzymes existing introns . The mechanism of that repair damage (a thorough and group II article intron bymobility complete Ramotarmay and involve reverse splicing, reverse transcription Demple); an amusing, yet serious and and recombination of as thea response resulting provocative article on sex with damage; genomic DNN,18. ConsetoeDNA oxidative oxidative stress and quently, target-site intron cell proliferation; andselection the role offor oxidants mediated by the insertion should bedecarboxylase and use of ornithine measurements in studies on tumour normal exon-intron recognition elements promotion. The group final section then involved in II splicing, i.e. progresses consider the development EB51-IBS1, toEB52-IBS2, and the gUided and of radicals in theoccurred action of within redoxpair,role If reverse splicing cycling drugs; mutagenicitya oftwintron plant an intron of the a pre-mRNA, components; the effects of mineral fibres would be formed. This mechanism may and cigarette smoke in inducing DNA account for site-specific deletions in the damage; and finally th, ;~ro-oxidant yeast mitochondrial cox} gene. Mueller actions of food additives an(i nutrients.
Table I. w.i~l Summary of Euglena gracilis chloroplast Overall, this volume be welcomed overlap in placestwintrons between different by the majority of workers in this authors' contributions, and, probably Size seriously, the fact thatSize(s) expanding field, andSize it provides an most the whole (nucleotides) Internalon rather(nucleotides) (nucleotides) Gene/intron No exceilept companion to the moreExternal volume is printed thin paper, cheadcally and radiation-orientated which 355 resultsII in the contents 402of some 757 II 1 atpf.l volumes, such as that by yon SonntagL in pages being visible on the wrong 424 II 618 side, psbFl 1042 I 2 bringing together these and well for the 463 doesn't bode II 635lifetime of 1098 contributions 3 psbIJ.i from aycf8·i number of leading the use it II, II the undoubted 601,393 358 volume, given 1352 experts, the 4 404, 106 editors have produced 399 have. 11.111 909 a timely volume petB·1 will 5 NO (with 0115) NO NO" psbIJ.8 3658 6 will that undoubtedly be used as a NO (with ol1s) NO NO 7 psbC·2 reference volume in4143 a large number of Reference III 111 204 93 psbK·2 8 labs. 1 von Sonntag, The ChemicalBasis of Radiation 96 Biology (1987) III 112 rp116-3 208 9 Taylorand Francis all new volumes, there are a 114 III 96 210 10As with rpoCi·i number of niggles and minus points; in 111 III 102 213 11 rpoCl-3 particular the occurrence of 198 III 96 102 12 rpoCi·i1 MICHAEL DAVIES III (with orf) 101 1504 typographical which shouldI really 13 psbC·4 errors1605 409this era of automatic 99 II 310 II 14 been rps3·ispotted in have 110,106,112 107 111(111,111) III of the 15 checkers, rps18·2 spell the 434 non-uniformity Departmentof Chemistry,Universityof York, chemical structures and equations, the Heslington, York,UK Y015DD. aND, not determined.
and colleagues (Ref. 19; M. W. Mueller petB and yef8 complex twintrons are et aI., unpublished) have proposed that both interrupted in domain ID where the coxI all mobilized into EBSI S. Agtawal fed.)intron Protocolsis for Oligonucleotides F. W.is located. Hardson Domain and M. VjVI E. insertions Rice (eds) and Analogs - Synthesis and Properties. Microscopic of Invertebrates WileyexpectedAnatomy to disrupt 5'-exon release splicing-compatible locations in the are Methods in Molecular Biology Vol. 20 Humana Liss, 1993. $185.00 (xiv + 484 pages) ISBN and nucleophilic activity of the cox1 aI5a and aI5b introns, in effect genPress, 1993. $59.50 (xiv + 502 pages) ISBN 0 471 56119 3 erating twintrons. Instability caused by unpaired adenosine during lariat for0 896 02347 7 E. Haslam Shikimic Acid - Metabolism and Insertions in domain I would transient tandem duplication of all mation. Metabolites Wiley-Liss, 1993. £75.00 (xii + N. H. Battey, H. G. Dickinson A. M. disrupt of the catalytic core, formation results in high-frequency cox1 and deletions 387 pages) ISBN 0 471 93999 4 Heathedngton (eds) Post-translational with end pointsinat the 3'-endSociety of all and Modifications Plants. for binding of domain V, and/or exon P. N. Hobson Positions and A. D. Wheatley Anaerobic within nonessenExperimental BiologytoSeminar SeriesEBS-Iike VoL 53 recognition. sites adjacent cryptic Digestion - Modem Theory and Practice Cambridge University Press, 1993.intermedi$89.95 (xx tial regions of group II introns suchISBN as sequences. The postulated Elsevier, 1993. £65.00 (xi + 269 pages) + 310 pages) ISBN 0 521 41181 5 1 85166 IV 958 2 be interrupted by introncan ates with a duplicated all group II domain proteinThe genes andof are unlikely intron (Le. introns introns) have encoded R. V. Benasson, E. J. within Land and T. G. Tmscott S. A. Kauffman Origins OrderSelf Excited and Free Radicals in Biology sites for and stable internal introns. not beenStates isolated. Organization Selection in Evolution Oxford and Medicine twintrons Oxford University 1993. University Press, 1993. formation £55.00 (xviiican + 709 twintron be Although could Press, be lost by Therefore, £50.00 (xi + 431 pages) ISBN 0 19 855560 1 pages) ISBN 0 19 507951 5 as an in vivo insertional mutarecombination or accumulation of viewed B. A. Bernard and B. Shmot Pharmacology system. imprecise deletions, the twintrons of genesis L. Larand and K, G. Mann (eds) Proteolytic and the Skin Vol. 5 - From Biology in Coagulation, Fibrinolysis, and intron inserA 'hot-spot' for group III Euglena chloroplast genesMolecular are stable. If Enzymes to Therapeutics Karger, 1993. $199.25 (viii + Complement Activation Part B - Complement tion is within domain VI, where six of the internal introns disrupted essential 196 pages) ISBN 3 8055 5776 0 Activation, Fibrinolysis, and Nonmammalian known insertions occur (Fig. functional domains of external introns, the BloodtenCoagulation Factors and Inhibitors. C. M. A.stability Brett and A. be M. expected. O. Brett 3b). Methods in Enzymology 223 Academic Three are within VoL potential stemtwintron would Electrochemistry - Principles, Methods and Press, 1993. £50.00 (xxviii + 433 pages) of the Correct splicing Applications Oxford University Press, 1993. ISBN 0 12 182124 2 internal a ISBN 0 19 £25.00 intron (xxviv +would 427 be pages) (a) W. Montagna, G. Prota and J. A. Kenney, Jr prerequisite for external 855388 9 Black Skin - Structure and Function Academic intron splicing, and exP. M. A. Bmda, S. G. Oliver and P. F. G. Sims Press, 1993. £54.00 (x + 158 pages) ISBN 0 pression the interrupted (eds) TheofEukaryotic Genome - Organisation 12 505260 X Internal introns of for General gene and 7.9•Regulation. Society Oleson. P. Tfelt-Hansen and K. M, A. Welch Microbiology Symposium several twintrons inter-50 Cambridge J. University Press, 1993. £60.00/$120.00 (xii (ed.~) fhe Headaches Raven Press, 1993. rupt known functional $208.00 (xxiv + 922 pages) ISBN 0 7817 + 395 pages) ISBN 0 521 44364 4 domains defined in vitro, 0069 8 Y. P. the Cruz catalytically Laboratory Exerc;.3es in within J. R. Foortmans fed.) Principles of Exercise Developmental Biology Academ:c I, V, Press, 1993. Biochemistry (2nd, corevised edn) Medicine and important domains £26.50 (xi + 241 o~ges) ISBN 0 12 198390 0 Sport Science VoL 38 Karger, 1993. and VI (Fig. 3). The inter'" Sfr.156.00/DM187.00/$125.00 (304 pages) ( b) nal intronsand of G. theJ.psbF and Polychlorinated S. Dobson Van Esch ISBN 3 8055 5778 7 Biphenyls and Terphenyls psbD twintrons are both(2nd edn) IPCS Environmental Health Criteria VoL 140 World A. P6hler fed.) Genetic Engineering of Animals located between the secrps18-2c Health Organization, 1993. SFr.70.00/$63.00 VCH, 1993. £15.50/DM38.00 (177 pages) ond third pairs 3 psbC ISBN 3 527 30041rpslS-2b (682 and pages) ISBNbase 92 4 157140 4 : 'poC1-11 within the upper stem of IF. Franks fed.) Protein BiotechnologyA. P(ihler fed.) Genetic Engineering of domain V of the external Isolation, Characterization and Stabilization Microorganisms VCH, 1993. £15.50/ intron, while that of the Humana Press, 1993. £87.00 (xi + 592 DM38.00 (viii + 178 pages) ISBN 3 527 atpE is 230 within pages)twintron ISBN 0 89603 2 30039 2 Figure 3 the loop of domain VI Twintron insertion sites of internal introns in func· J. P. Gosling and D. J. Reen (eds) J. P. Robinson fed.) Handbook of Row (Fig. 3a). The external tional dornains of external (a) group II and (b) group Immunotechnology Portland Press, 1993. Cytometry Methods (2nd edn) Wiley, 1993. introns. group II +introns of ISBN the 1 85578III035 £45.00 (ix 153 pages) 6 £32.95 (xii + 246 pages) ISBN0 471 59634 5 (JJ
469 487
TI8S 18 - DECEMBER 1993
TIBS 1 8 - D E C E M B E R 1 9 9 3
orwelcomed less and may well be a number of readers who are Overall, thisnucleotides volume w.i~l be put off by the initial chemical input. It is, Euglenoid between by the majorityothers of workers in this2S0 and however, worth persevering with as there plastid expanding field, andnucleotides it provides in an length. 1000 groupexceilept III is valuable information here both for companion to the more Intramolecular base pairresearchers already working in the field cheadcally anding radiation-orientated within the larger and newcomers (in particular new volumes, suchintrons as that by yon reduce SonntagLthe in may postgraduate students, for whom this bringing together these contributions proximity of splice sites wouldFungal be a good sta;tingPlant point) who are Euglenoid from a number of leading experts, the and branch sites to paralnotmitochondria familiar with the subject but who wish editors have produced a timely volume organelle plastid 2 22 lel the small introns to (or ought to) become so. that will undoubtedly be used as a 1. . (self-splicing) group II group II group The chapters are broken down into reference volumeSome in a large number[ ofand group II introns encode four major sections: chemistw and labs. measurement of damage to DNA by As with all new volumes, there are a'mapolypeptides termed reactive oxygen species; mechanism of number of niggles and minus points; turases', which are in reNuclear Prokaryotic DNA damage by oxidative stress; ? particular the occurrence of q uired for efficient splicgroup II damage; pre-mRNA consequences of oxidative DNA typographical ing errors which should really and/or intron mobility and pro-oxidants and(self-splicing) DNA damage. Each+ snRNAs have been spotted in this era of automatic in ViV01S. These maturases part is preceded by a brief preface by the spell checkers, the non-uniformity of the are thought to bind and editors. The first section begins with an chemical structures and equations, the stabilize catalytically acintriguing chapter by Ames and Shigenaga tive RNA. All five intronon the role of oxidants as major encoded open reading contributors to cancerProgenitor and aging- a II frames (orfs) in the justification, if ever one group was needed, for the research that is being carried out in genome of the Euglena this area. This introduction certainly are within S. Agtawal fed.)chloroplast Protocols for Oligonucleotides provides food for thought as well Figure 4 as and Analogs -twintrons Synthesis6. In andaddition Properties. to Methods in Molecular Biology Vol. 20 Humana valuable (and ammunition?) Model information for the evolutionary relationship of bacterial, ycf13, there are two oris Press, 1993. $59.50 (xiv + 502 pages) ISBN plastid have and nuclear introns from a comformitochondrial, people who would us decrease 0 896 02347 7 within each of the twinancestor. ourmon daily intake of calories and minimize trons in psbC intron 2 our exposure to certain chemicals, N. H. Battey, (177 H. G.and Dickinson and A.and M. 241 codons) although adverts which encourage us to Heathedngton (eds) Post-translational loopless structures in the are S'-region intron 8 in(281Plants. and S06Society codons). Modifications for 'eat and live longer' unlikelyoftothe be psbD intron, possiblycorrect defining a second func- Although Experimentalmotifs Biology characteristic Seminar Series of VoL re53 as scientifically or as elegantly Cambridge University Press, $89.95are (xx transcriptases (and 1993. maturases) tional domain. domain act as verse presented as thisThis chapter. The may following + 310 pages) ISBNof 0 521 41181 5 23 , in some these polypeptides present a S'-exon/intron chapters in the first recognition section outlineelement the
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basic free chemistry DNA,guided the II EBSIof and similar toradical the group reactions and mechanisms that within generate the pair. Alternatively, insertions measurable lesions and the methods for a S'-base-paired domain may disrupt carrying measurements. 5'-last andof 3'minimal out distance betweenThe these is relatively short and biased splice sites. towards certain techniques used by the The internal and external introns of author, but this may not be a major the group III twintrons are all within the drawback, as it improves the readability size for and group introns with one of therange chapter, thisIIIarea is adequately I):ofthe internal exception covered in a(Table number other, highlyintron of the psbC twintron detailed, volumes on the(intron market.4) is 1504 nucleotides long, with an open reading The chapters in the second section 2o (D. gradually towards more 458 codons W.complex Copertino frame of move biological in the basicycfi3 Hallick,taking unpublished). and R. B.systems, facets of hydrogen (Ref. 6; previouslyperoxide known damage, as orf458) of oxidative andiscalcium the psbCstress twintron located in the loop homeostasis, lipid Therefore, peroxidation, the of a 5'-domain. theand narrow chemistry of peroxyl radicals. The third size range of group III introns is not section considers the role of enzymes absolute. Large size variations are possthat repair damage (a thorough and ible, but perhaps extra sequence must complete article by Ramotar and be confined to only yet select regions Demple); an amusing, serious and of a group III core structure. The most relprovocative article on sex as a response of group III introns may evant feature to oxidative damage; oxidative stress and be proliferation; the three-dimensional conformation cell and the role of oxidants and use RNA, of ornithine decarboxylase of the with the distance between measurements studies tumourVI (3'the S'-splice in site and on domain promotion. final section then splice site)The being most critical. Most progresses to consider development may the achieve this congroup III introns and role of radicals the action of redoxformation by size inalone. A similar recycling drugs; the mutagenicity of plant lationship between size and core struccomponents; the effects of mineral fibres ture has been proposed for yeast and cigarette smoke in inducing DNA nuclear and introns, exhibit bimodal damage; finallywhich th, ;~ro-oxidant size distribution, with some at 100 actions of food additives an(i nutrients.
470
the and intron-encoded itR.isV.not yet known Benasson, E. J. ifLand T. G. Tmscott Excited States and Free are Radicals in Biology in Euglena involved in proteins and Medicine Oxford University Press, 1993. either splicing and/or intron mobility. £50.00 (xi + 431 pages) ISBN 0 19 855560 1 Based on preliminary western-blot analyB. A.at Bernard and ofB. the Shmot Pharmacology intron-encoded sis, least one and the Skin is Vol.expressed 5 - From Molecular Biology ods, ycfI3, (K. P. Jenkins to Therapeutics Karger, 1993. $199.25 (viii + R. B. Hallick, unpublished). and 196 pages) ISBN 3 8055 5776 0 C. M. A. Brettof and M. O. Brett Common features groupA.II, group III and Electrochemistry Principles, Methods and nuclear pre-mRNA- introns Applications Oxford University Press, 1993. Group(xxviv III introns shouldISBN be 0con£25.00 + 427 pages) 19 sidered 855388 9in parallel with group II and
nuclear introns. Group II, group III and P. M. A. Bmda, S. G. Oliver and P. F. G. Sims pre-mRNAGenome introns are all nuclear (eds) The Eukaryotic - Organisation excised via lariat Society intermediates using and Regulation. for General Microbiology Symposiumas cis-acting 50 Cambridge internal adenosines nuUniversity Press, 1993. £60.00/$120.00 (xii cleophiles. Group II/III introns contain + 395 pages) ISBN 0 521 44364 4 an unpaired adenosine stabilized by base-pairing cis within Exerc;.3es domain VI, Y. P. Cruz in Laboratory in Developmental Biology Academ:c Press, inter1993. whereas the U2-snRNA-UACUMC £26.50 (xi + 241 o~ges) ISBN 0 12 198390 0 action in nuclear introns stabilizes this 3,1224. nucleophile S. Dobson andinG.trans J. Van Esch Polychlorinated Biphenyls and other Terphenyls (2ndsimilarities edn) IPCS There are potential Environmental Criteria VoLof140 World nuclear between the Health catalyic cores Health Organization, 1993. SFr.70.00/$63.00 II introns. The 5'and 3'and group (682 pages) ISBN 92 4 157140 3 exons in both systems are positioned at IF. Biotechnologythe Protein conserved loop of US the Franks core byfed.) Isolation, Characterization and Stabilization 5 versus for nuclear introns Humana Press, 1993. £87.00 EBSI (xi + and 592 7 the guided for 230 group pages) ISBN 0pair 89603 2 II introns ,25.26. Interaction at the S'-splice site by U6 for J. P. Gosling 2i D. J. Reen (eds) nuclear introns andis similar to the1993. E-E' Immunotechnology Portland Press, 25 Also, interaction for pages) group ISBN II introns £45.00 (ix + 153 1 85578• 035 6
4 may correspond the U2-U6 interaction overlap in places between different the group II catalyticand, domain V14. to authors' contributions, probably Group II intron recogmost seriously, theboundaries fact that theare whole volumeiniscis printed on rather thinbypaper, during splicing the 5'· nized which results in the contents of some splice site; domain VI; and tertiary pages being visible side, interactions suchon the aswrong EBSl-IBSl, and doesn'tthe bode well for the and lifetime of EBS2-IBS2, guided pair, the c-£' the volume, given the undoubted use it and y-y' interactions 7.25.26. Elements will have. likely to be required for recognition of group III splice boundaries other than Reference the S'-boundary and domain 1 von Sonntag, The sequence ChemicalBasis of Radiation (1987) Tayloridentified. and Francis Group II, VI Biology have not been group III and nuclear pre-mRNA introns all have similar S'-splice sites_ The U at MICHAEL DAVIES +2 and the G at +S are conserved in all three systems, and probably influence Departmentofselection. Chemistry,University of York, splice-site If cryptic 5'-splice Heslington, York,UK Y015DD. sites are nearby, alternative splicing can occur. In Euglena, there are several examples of alternative S'- and/or Jsplice site utilization involving excision of internal introns of group III 12,17. Imprecise twintrons of F. W. Hardson and M. E.splicing Rice (eds) Microscopic Anatomy of Invertebrates Wileyinternal introns should still be permissLiss,for1993. (xiv + The 484 use pages) ISBN of mulive gene$185.00 expression. 0 471 56119 3 tiple splice sites has also been E. Haslam for Shikimic Acid group - Metabolism and observed a single III intron, Metabolites Wiley-Liss, 1993. £75.00 (xii + in out-of-frame ligation of resulting 387 pages) ISBN 0 471 93999 4 exons for the rp112 gene (R. G. Drager P. N. Hobson A. D. Wheatley Anaerobic R. B. andHallick, unpublished). and Digestion - Modem Theory and Practice II core structure preWhereas group Elsevier, 1993. £65.00 (xi + 269 pages) ISBN 1 85166the 958use 2 of alternate splice sites, cludes the of extensive cis-tertiary interacS. A.lack Kauffman The Origins of Order- Self tions in group III and in nuclear introns Organization and Selection Evolution Oxford University Press, (xviii + and 709 may account for1993. both£55.00 mis-splicing pages) ISBNsplicing. 0 19 507951 5 alternative the Proteolytic S'-splice analyses L. Mutational Larand and K, G. Mannof(eds) Enzymes in these Coagulation, Fibrinolysis, and site support conclusions for yeast Complement Activation Part B - Complement nuclear introns. For example, mutation Activation, Fibrinolysis, and Nonmammalian in and activation of of the Coagulation G at +5 results Blood Factors Inhibitors. 28 , 223 Methods 5'-cleavage in Enzymology VoL cryptic sites The Academic G at +5, Press, 1993. (xxviii 433bepages) possibly with£50.00 the U at +2, +may part ISBN 0 12 182124 2 of a catalytic core shared by nuclear. W. Montagna, Prota III andintrons. J. A. Kenney, Jr II, and G.group The G group Black Skinto- Structure andfor Function Academic of appears be crucial activation Press, 1993. £54.00 (x + 158 pages) ISBN 0 the correct phosphodiester bond, 12 505260 X recognition by the nucleophilic 2'-OH J. Oleson. P. Tfelt-Hansen and K. M, A. Welch during lariat formation, and perhaps (ed.~) fhe Headaches Raven Press, 1993. other within the $208.00important (xxiv + 922contacts pages) ISBN 0 7817 active8 site. 0069 formation may of not be J. Twintron R. Foortmans fed.) Principles Exercise Euglena chloroplast genes. restricted Biochemistryto(2nd, revised edn) Medicine and Sport large Sciencenuclear VoL introns 38 Karger, Some may 1993. have Sfr.156.00/DM187.00/$125.00 (304 pages) formed from multiple, smaller introns. ISBN 3 8055 5778 7 Intron excision of large nuclear preA. P6hler fed.) Genetic of Animals mRNA introns could Engineering occur in sequential VCH, 1993. £15.50/DM38.00 (177 pages) steps from internal splice boundaries. ISBN 3 527 30041 4 Such an organization of multiple 5'- and A. P(ihlersites fed.) could Geneticalso Engineering of 3'-splice result in Microorganisms VCH, 1993. £15.50/ alternative splice-site selection. Thus, DM38.00 (viii + 178 pages) ISBN 3 527 twintron 30039 2 formation by intron insertion into pre-existing introns is one potential J. P. Robinson fed.) Handbook of Row mechanism for the(2nd origin alternative Cytometry Methods edn)ofWiley, 1993. splicing12.16.1,. £32.95 (xii + 246 pages) ISBN0 471 59634 5
487
TIBS 1 8 - DECEMBER 1993 The recent discovery of self-splicing group II introns in prokaryotes 29 is suggestive of an evolutionary relationship between bacterial, mitochondrial, chloroplast and nuclear introns as shown in Fig. 4. These classes of introns could have a common evolutionary ancestor. Nuclear and group IIi introns appear to represent an example of convergent evolution from an ancestral, self-splicing RNA that was also a mobile genetic element. If splicing of group III introns involved transacting RNAs analogous to nuclear snRNPs, the character|zation o! these RNAs would provide an important new insight into the evolution of the spliceosome. Some of the contemporary parallels between group ili and nuclear introns are quite striking, including the conserved 5'-boundary, lariat formation, lack of internal structure and the ability to use alternate splice boundaries.
Acknowledgements We wish to thank Rob Drager, Ling Hong and Mitch Favreau for contri-
butions to the work described; and Christine Guthrie and Roy Parker for discussion and critical reading of the manuscript.
References 1 Cech, T. R. (1986) Cell 44, 207-210 2 Sharp, P. A. (1985) Cell 42, 397-400 3 Jacquier, A. (1990) Trends Biochem. Sci. 15, 351-354 4 Madhani, H. D. and Guthrie, C. (1992) Cell 71, 803-817 5 Newman, A. J. and Norman, C= (1992) Cell 68, 743-754 6 Hallick, R. B. et aL (1993) Nucleic Acids Res. 2:t. 3537-3544 7 Michel, F., Umesono, K. and Ozeki, H. (1989) Gene 82, 5-30 8 Koller, B., Clarke, J. and Delius, H. (1985) EMBO J. 4, 2445-2450 9 Copertino, D. W. and Hallick, R. B. (1991) EMBO J. 10, 433-442 10 Christopher, D. A. and Hallick, R. B. (1989) Nucleic Acids Res. 17, 7591-7608 11 Siemeister, G., Buchholz, C. and Hachtel, W. (1990) Mol. Gen. Genet. 220, 425-432 12 Copertino, D. W., Shigeoka, S. and Hallick, R. B. (1992) EMBOJ. 11, 5041-5050 13 Drager, R. G. and Hallick, R. B. (1993) Curr. Genet. 23, 271-280 I 4 Jarrell, K. A., Dietrich, R. C. and Perlman, P. S. (1988) MoL Cell. Biol. 8,
2361-2366 15 Goldschmidt-Clermont, M. et aL (1991) Cell 65, 135-143 16 Copertino, D. W., Christopher, D. A. and Hallick, R. B. (1991) Nucleic Acids Res. 19, 6491-6497 17 Drager, R. G. and Hallick, R. B. (1993) Nucleic Acids Res. 21, 2389-2394 18 Lambowitz, A. M. and Belfort, M. (1993) Annu. Rev. Biochem. 62, 587-622 19 Mueller, M. W., Eskes, R., AIImaier, M. and Schweyen, R..1. Nature (in press) 20 Montandon, P. E., Vasserot, A. and Stutz, E. (1986) Curr. Genet. 11, 35-39 21 Parker, R. and Patterson, B. (1987) in Molecular Biology of RNA: New Perspectives (Dudock, B. and Inouye, M., eds), pp. 133-149, Academic Press 22 Goguel, V. and Rosbash, M. (1993) Cell 72, 893-901 23 Mohr, G., Perlman, P. S. and Lambowitz, A. M. Nucleic Acids Res. (in press) 24 Parker, R., Siliciano, P. G. and Guthrie, C. (1987) Cell 49, 229-239 25 Jacquier, A. and Jacquesson-Breuleux, N. (1991) J. MoL Biol. 219, 415-428 26 Jacquier, A. and Michel, F. (1990) J. Mol. Biol. 213, 437-447 27 Wassarman, D. A. and Steitz, J. A. (1992) Science 257, 1918-1925 28 Guthrie, C. (1991) Science 253, 157-163 29 Ferat, J-L. and Michel, F. (1993) Nature 364, 358-361
ONE OF THE most successful ways of
studying gene function is the analysis of phenotypes that arise when the activity of an individual gene is varied In a defined way by outside stimuli. A number of regulatory systems permit this approach in the bacterium Escherichia coil; and in the budding yeast Saccharomyces cerevisiae numerous valuable insights into gene function have been obtained by utilizing the GAL system, in these systems, the activity of Regulated gene expression systems for the study of gene function in a gene can be studied by controlling its prokaryotes and yeast have been available for several years. However, expression at the transcriptional level comparable systems in higher organisms are more complex and problemthrough the use of natural metabolites atic. Recently, regulatory proteins from distant species have been used to or their derivatives as specific effecestablish highly specific control systems in eukaryotic cells. This is posstors. When properly applied, such conible because their action can be modulated by effectors that are inert to trol systems not only allow us to create the physiology of the organism or cell and therefore do not elicit pleioreversible on/off switches for a gene's tropic effects. Such monospecific regulatory circuits c,~en up new possiactivity, but also to adjust the expresbilities for the study of gene function in vivo. sion to defined levels. The latter possibility will, in particular, further our understanding of gene function, since In E. coil, transcription control sys- Ref. 1) usually suffer from one or both quantitative parameters frequently define metabolic or developmental tems based on regulatory elements of the following problems: (1) the such as the lactose operon allow the inducer (such as heavy-metal ions, states. tight control of a gene of interest. steroid hormones or heat shock) However, no comparable general evokes pleiotropic effects that compliM. Gossen,A. L. Bonlnand H. BuJardare at methodology is presently available for cate the analysis of the resulting phenothe ZMBH-Zentrumfor MolekulareBiologie, vertebrate cells. The commonly used type; and (2) many promoter systems UniversitStHeidelberg,Im NeuenheimerFeld endogenous systems (for review see have high basal levels of activity in the 282, D-69120Heidelberg,Germany.
© 1993,ElsevierSciencePublishers,(UK) 0968-0004/93/$06.00
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