- Email: [email protected]
The genomic repair manual
MISCELLANEA
Paul Monaghan
Electron Microscopy, Haddow Laboratories, Institute of Cancer Research, 15 Cotswold Road,Sutton, Surrey, UK SM2 5NC.
membranes of ceils grown in vitro, where some of the approaches do not necessarily require a freezing step, and an elegant approach that provides an answer to the problem of preparing fracture replicas from defined regions or even individual cells. Freeze-fractured surfaces provide ideal material for immunocytochemical labelling, and a wealth of different approaches to colloidal gold labelling of fractured surfaces is described, thus allowing the structured features of the replicas to be correlated with specific
The genomic repair manual DNA Repair and Mutagenesis by Errol C. Friedberg, Graham C. Walker and Wolfram Siede, ASM Press, 1995. $79.00 (698 pages) ISBN 7 55587 088 8 Responses to DNA damage are of increasingly acknowledged importance; and this massive and authoritative survey, an extensively revised version of Friedberg’s previous 1985 milestone volume DIVA Repair, deals with them thoroughly. The intricate systems involved are perhaps best understood through the parable (from the Book of Usually Reliable Sources) of the mechanic, the policeman and the administrator. If you tell a mechanic that some complicated machinery is damaged, he will search through it, identify the damaged part, put it back into shape or, if it’s past mending, remove it and fit a new part. If you tell a policeman that something valuable has just been damaged, he will shout ‘Stop!’ and (left to follow his own inclinations) arrest everyone in sight. And if you tell an administrator that something important to you is damaged, he will not exactly do anything, but will arrange matters in a rather mysterious way, till you realize that, after all, you can put up with the damage. Similarly, there are complex systems for identifying, restoring, removing
368
0 1996 Elsevier Science Ltd
antigen constituents. A number of the following chapters in particular illustrate the power of this methodology, and topics include the investigation of viral infection and the identification of basement membrane components in deep-etched samples. Now that the field-emission scanning electron microscope (FESEM) is approaching the TEM in resolution, the SEM offers additional ways of imaging fractured and immunolabelled surfaces, and this is illustrated in a number of preparations.
Having read at least enough of the book to become enthused by the possibilities of the technique, is it sufficiently detailed for a novice to get cracking? Probably so, but there are sufficient pitfalls in the preparation and interpretation of freeze-fracture samples that a visit to a laboratory actively involved with the technique would considerably shorten the learning process. It seems, however, that the number of laboratories active in the field is shrinking -and that seems a pity.
and replacing damaged parts of DNA; and also, when DNA is damaged, cells produce powerful ‘stop’ signals that arrest passage through the cell cycle and give more time for repair systems to work; and, where damage is not repaired, cells have obscure mechanisms for tolerating it. If any of these systems fail to work, there is a chance that damaged cells may die or mutate. If the mutations are somatic and affect oncogenes, or tumour suppressor genes, cancer may result. Human genetic cancer-prone diseases have been identified that involve mutations affecting systems for repair, arrest and tolerance. Hence the interest in DNA damage and repair among the majority, who would like their stay in this world to be as long and comfortable as possible. If the mutations are in the germ line, evolution may result; this is not so obviously a bad thing as cancer, and not so widely studied, but still of great interest to several biologists. Therefore, Friedberg, Walker and Siede have performed a great service by compiling an analysis of almost all that was known (to autumn 1994) about these complexities. They are very clear about the nature of agents that damage DNA - the world is a dangerous place to be alive in, particularly for a DNA molecule, and the various forms of spontaneous and induced damage are described concisely, with emphasis on the ubiquitous damaging agents, air and water. When it comes to responses to damage: well, in terms of the parable, the mechanic’s work of repair is well understood. The general approach is to start by explaining the very thoroughly explored systems of prokaryotes (in practice, Escherichia co/i);
next, to show how these also occur in more complex forms in lower eukaryotes (essentially Saccharomyces cerevisiae; Schizosaccharomyces pombe hardly gets a look-in, and Drosophila should not really be classed as ‘lower’); and, finally, to extrapolate to the genetically and biochemically less tractable mammalian systems. For damage reversal systems (photoreactivation and alkyltransferases), base excision repair, nucleotide excision repair and mismatch repair, this scheme works well. Where there are unsolved mysteries the most paradoxical, perhaps, being trichothiodystrophy and Cockayne’s syndrome, where a clear defect in nucleotide excision repair is not associated with an increased risk of cancer the evidence is clearly presented and the reader left to think. But neither policework nor administration (cell-cycle arrest and tolerance), nor mutagenesis after failures in the damage response, are so well served by this approach. This is no fault of the authors. Researchers have very reasonably acquired masses of data where such things can be studied easily, in bacteria and yeast, but much less for mammalian systems. But while the biological imperatives of repair are similar in macro- and, microorganisms, for arrest and tolerance they are not. In multicellular organisms, survival of the individual may require the sacrifice of particular cells with DNA damage, since dead cells cannot mutate and form tumours; in yeast and bacteria, the individual cell is the organism, and its survival is paramount. Therefore, it is no surprise that E. co/i has a much-studied SOS response, in which extensive damage induces systems that allow replication to proceed, no matter how inaccurately
trends in CELL BIOLOGY (Vol. 6) September 1996
or mutagenically; nor that mammalian cells respond to excessive damage by programmed cell death; nor that macro-systems have, here, not been wonderFully illuminated by micro-organisms. What does come as a surprise is that budding yeast, although micro enough, also have a programmed celldeath system, as shown by thesecond most puzzling work that Friedberg et a/. cite’. Perhaps, yeast should really
be regarded as degenerate macroorganisms; they can, after all, form filamentous hyphae2. The most puzzling work cited, howis the announcement of ever, Cairnsian mutagenesis3 - bacterial mutations that occur more readily if they are beneficial to the organism a phenomenon of enormous interest to evolutionary theorists, and still quite unresolved. Perhaps the next edition . . .
References 1 BENNETT,C. B., LEWIS,A. L., BALDWIN, K. K. and RESNIK,M. A. (1993) Proc. Nat/. Acad. Sci. U. S. A. 87, 5613-5617 2 CIMENO, C. J., LJUNCDAHL, P. O., STYLES,C. A. and FISH, G. R. (1992) Cell 68, 1077-l 090 3 CAIRNS, I., OVERBAUGH,1. and MILLER,S. (1988) Nature 335, 142-l 45
MEETING ANNOUNCEMENT
,,,
European Congress for Molecular Cell Biology, Brighton, UK, 22-25 March 199P
Programme
of Symposia
Regutation in the Nucleus U. Laemmli (Geneva), 5. Casser (Lausanne), J. Hoeijmakers (Rotterdam), R. Laskey (Cambridge), 8. Tjian (Berkeley)
’
Cell Cycle and D-,-‘ ------* tZ”Cl”plPZ,L K, Nasmyth (Vienna}, J. Diffley (1.ondonI D. Koshland (USA). C. Lehner (Tiibingen), J. M. Pet&s (Vienna) ~ ”
I
Targeting to Endosom-* ..-rl ’*‘--**--* W. Hinzik& (Lausanne), K. von Figura (Germany), H. Rieiman (B&j Cytoplasmic Coats Involved in Membrane Pro tein Traffic M. Rolbinson (Cambridge), C. Kaiser (USA), M. Letourneur (Basle), k. Schekman (USA)
Microtubules and Organelle Movement T. Kreis (Geneva), N. Hirokawa (Japan), 1 E. Mandelkow (Germany), T. Schroer (Baltimore), R. Vale (USA) Ce44Adhesion and Signal Transduction W. Birchmeier (Berlin), D. Cheresh (San Diego), B. Gumbiner (New York)
I
Exocytosis and Recycfing D. Cutler (London), J. Bonifacino (USA), P. de Camilli, (Yale), R. Kelly (UCSF), C. Schiavo (London), W. Stoorvogel (Utrecht) Unconventional Myosins M. Bahler (rijbingen), D. Louvard (Paris), C. Mont&l (Baltimore), M. Mooseker (Yale) Traffic Between Nucleus and Cytoplasm R. Laskey (Cambridge), 11.Aebi (Basle), C. Blobel (New York), D. Gijrlich (Heidelberg), R. Luhrmann (Marburg), I. Mattaj (Heidelberg)
~
Epithelial Cell Adhesion and Polarity R. Kemler (Freiburgf, P. Ekblom (Uppsala), E. Knust (Cologne), J. Netson (Stanford), F. Watt (London)
”
1
,1,1(_ 111, I*
I
Biogenesis of Mitochondria and Chforoplasts,. ,,,,li,jj,, ‘1‘,““‘:! C. Schatz ( Basle), K. Cline (Gainsville), N. Pfanner (Fieiburg), J. ,011 c ” I$ ‘W I:],,,,, I&:‘ I’.. +*t:*n ,,‘, Pathways in MHC Class 41Presen,.,,,. H. Geuze (Utrecht), 5. Amiqorena (Paris), M. Kleijmeer‘(Amste~dam), P.-Cresswell (US/9, J, Neefjes (Utrecht), C. Watts (UK)
Biological Function of Chaperones C. Georgopoulos (Cceneva), A. Helen/us (New Haven), F.1.anger (Germany), C. Suzuki (Switzerland), D. 0. Tof& (USA)
Programmed Cell Death ) M. Raff (London). B. Earnshaw (Edinburahl. G. Evan (London). ” ’ H. Stel&r (Boston), C.ihomps&‘iChicaqoj
Dept of Biomedical Science, University of Ulster, Coleraine, Co. Londonderry, Ireland UK BT52 1 SA.
”
ECBO 97 Provisional
C. Stephen Downes
PC
tsitive and Negative Regulators of Nerve Cell G.rowth F. Walsh ILondon). M. Filbin INew York), C. Goodman (Berke&!y), R. Klein‘(Heidelbe& A. Pinijlondon)
I
Eoithefiat/Mesenchvmal Transition J. PI Thiery iParis), C. irchmeier (Berlin); P. Comoglio (Turin), E. Gerhardi (Cambrid,@ , Ceil Membrane Permeable Peotides *# ,,, I P. Doherty (London), D. P. Lane (bundee),’ .,,{il’I,,, S. Olsnes (Oslo), A. Prochiantz (Paris) ‘+?” ,a,,:,:ai I, Protein Translocation Across Membranes ”‘: “‘“““““i.,, ‘,,A:I:, B. Dobberstein (Heidelberg), Economu (Greece), 1,,“, T. Rapaport (USA), P.Sanson@% (Paris) Endoplasmic Reticulum/Golgi Dynamics H. Pelham (Cambridge), J. lippincott-Schwartz (USA). :,:,:,: Annexins S. Moss (London), V. Gerke (Muenster),:q ‘I”*’ R. Huber (Martinsreid), K. Simons (EMBL) +,& Database Information and its Application B. Dujon (Paris), A. Goffeau (Louvain), G. Poste (SmithKline Beecham)
j
,&~~ 1IIi ,@# 111,1” 1’’
j##i’ Regulation of the Actin Cytoskeleton by GTPases 111I’ T. Mitchison (UC%), J. Gallan (USA), A. Hal4 (London) ,,l:l,il, ‘, ! Further symposia in preparation: Cyclins and Cyclin Dependent Kinase Inhibitors Molecular Cell Biology of Endothelia
/
The Plenary Lecture Programme will be appearing shortly. In addition to the symposia and plenary lectures, there will be special-interest group meetings, poster sessions and a trade exhibition.
/
Details on how to obtain
more information
L trends in CELL BIOLOGY (Vol. 6) September 1996
about the meeting
can be found on p. 358 /
369
Paul Monaghan
Electron Microscopy, Haddow Laboratories, Institute of Cancer Research, 15 Cotswold Road,Sutton, Surrey, UK SM2 5NC.
membranes of ceils grown in vitro, where some of the approaches do not necessarily require a freezing step, and an elegant approach that provides an answer to the problem of preparing fracture replicas from defined regions or even individual cells. Freeze-fractured surfaces provide ideal material for immunocytochemical labelling, and a wealth of different approaches to colloidal gold labelling of fractured surfaces is described, thus allowing the structured features of the replicas to be correlated with specific
The genomic repair manual DNA Repair and Mutagenesis by Errol C. Friedberg, Graham C. Walker and Wolfram Siede, ASM Press, 1995. $79.00 (698 pages) ISBN 7 55587 088 8 Responses to DNA damage are of increasingly acknowledged importance; and this massive and authoritative survey, an extensively revised version of Friedberg’s previous 1985 milestone volume DIVA Repair, deals with them thoroughly. The intricate systems involved are perhaps best understood through the parable (from the Book of Usually Reliable Sources) of the mechanic, the policeman and the administrator. If you tell a mechanic that some complicated machinery is damaged, he will search through it, identify the damaged part, put it back into shape or, if it’s past mending, remove it and fit a new part. If you tell a policeman that something valuable has just been damaged, he will shout ‘Stop!’ and (left to follow his own inclinations) arrest everyone in sight. And if you tell an administrator that something important to you is damaged, he will not exactly do anything, but will arrange matters in a rather mysterious way, till you realize that, after all, you can put up with the damage. Similarly, there are complex systems for identifying, restoring, removing
368
0 1996 Elsevier Science Ltd
antigen constituents. A number of the following chapters in particular illustrate the power of this methodology, and topics include the investigation of viral infection and the identification of basement membrane components in deep-etched samples. Now that the field-emission scanning electron microscope (FESEM) is approaching the TEM in resolution, the SEM offers additional ways of imaging fractured and immunolabelled surfaces, and this is illustrated in a number of preparations.
Having read at least enough of the book to become enthused by the possibilities of the technique, is it sufficiently detailed for a novice to get cracking? Probably so, but there are sufficient pitfalls in the preparation and interpretation of freeze-fracture samples that a visit to a laboratory actively involved with the technique would considerably shorten the learning process. It seems, however, that the number of laboratories active in the field is shrinking -and that seems a pity.
and replacing damaged parts of DNA; and also, when DNA is damaged, cells produce powerful ‘stop’ signals that arrest passage through the cell cycle and give more time for repair systems to work; and, where damage is not repaired, cells have obscure mechanisms for tolerating it. If any of these systems fail to work, there is a chance that damaged cells may die or mutate. If the mutations are somatic and affect oncogenes, or tumour suppressor genes, cancer may result. Human genetic cancer-prone diseases have been identified that involve mutations affecting systems for repair, arrest and tolerance. Hence the interest in DNA damage and repair among the majority, who would like their stay in this world to be as long and comfortable as possible. If the mutations are in the germ line, evolution may result; this is not so obviously a bad thing as cancer, and not so widely studied, but still of great interest to several biologists. Therefore, Friedberg, Walker and Siede have performed a great service by compiling an analysis of almost all that was known (to autumn 1994) about these complexities. They are very clear about the nature of agents that damage DNA - the world is a dangerous place to be alive in, particularly for a DNA molecule, and the various forms of spontaneous and induced damage are described concisely, with emphasis on the ubiquitous damaging agents, air and water. When it comes to responses to damage: well, in terms of the parable, the mechanic’s work of repair is well understood. The general approach is to start by explaining the very thoroughly explored systems of prokaryotes (in practice, Escherichia co/i);
next, to show how these also occur in more complex forms in lower eukaryotes (essentially Saccharomyces cerevisiae; Schizosaccharomyces pombe hardly gets a look-in, and Drosophila should not really be classed as ‘lower’); and, finally, to extrapolate to the genetically and biochemically less tractable mammalian systems. For damage reversal systems (photoreactivation and alkyltransferases), base excision repair, nucleotide excision repair and mismatch repair, this scheme works well. Where there are unsolved mysteries the most paradoxical, perhaps, being trichothiodystrophy and Cockayne’s syndrome, where a clear defect in nucleotide excision repair is not associated with an increased risk of cancer the evidence is clearly presented and the reader left to think. But neither policework nor administration (cell-cycle arrest and tolerance), nor mutagenesis after failures in the damage response, are so well served by this approach. This is no fault of the authors. Researchers have very reasonably acquired masses of data where such things can be studied easily, in bacteria and yeast, but much less for mammalian systems. But while the biological imperatives of repair are similar in macro- and, microorganisms, for arrest and tolerance they are not. In multicellular organisms, survival of the individual may require the sacrifice of particular cells with DNA damage, since dead cells cannot mutate and form tumours; in yeast and bacteria, the individual cell is the organism, and its survival is paramount. Therefore, it is no surprise that E. co/i has a much-studied SOS response, in which extensive damage induces systems that allow replication to proceed, no matter how inaccurately
trends in CELL BIOLOGY (Vol. 6) September 1996
or mutagenically; nor that mammalian cells respond to excessive damage by programmed cell death; nor that macro-systems have, here, not been wonderFully illuminated by micro-organisms. What does come as a surprise is that budding yeast, although micro enough, also have a programmed celldeath system, as shown by thesecond most puzzling work that Friedberg et a/. cite’. Perhaps, yeast should really
be regarded as degenerate macroorganisms; they can, after all, form filamentous hyphae2. The most puzzling work cited, howis the announcement of ever, Cairnsian mutagenesis3 - bacterial mutations that occur more readily if they are beneficial to the organism a phenomenon of enormous interest to evolutionary theorists, and still quite unresolved. Perhaps the next edition . . .
References 1 BENNETT,C. B., LEWIS,A. L., BALDWIN, K. K. and RESNIK,M. A. (1993) Proc. Nat/. Acad. Sci. U. S. A. 87, 5613-5617 2 CIMENO, C. J., LJUNCDAHL, P. O., STYLES,C. A. and FISH, G. R. (1992) Cell 68, 1077-l 090 3 CAIRNS, I., OVERBAUGH,1. and MILLER,S. (1988) Nature 335, 142-l 45
MEETING ANNOUNCEMENT
,,,
European Congress for Molecular Cell Biology, Brighton, UK, 22-25 March 199P
Programme
of Symposia
Regutation in the Nucleus U. Laemmli (Geneva), 5. Casser (Lausanne), J. Hoeijmakers (Rotterdam), R. Laskey (Cambridge), 8. Tjian (Berkeley)
’
Cell Cycle and D-,-‘ ------* tZ”Cl”plPZ,L K, Nasmyth (Vienna}, J. Diffley (1.ondonI D. Koshland (USA). C. Lehner (Tiibingen), J. M. Pet&s (Vienna) ~ ”
I
Targeting to Endosom-* ..-rl ’*‘--**--* W. Hinzik& (Lausanne), K. von Figura (Germany), H. Rieiman (B&j Cytoplasmic Coats Involved in Membrane Pro tein Traffic M. Rolbinson (Cambridge), C. Kaiser (USA), M. Letourneur (Basle), k. Schekman (USA)
Microtubules and Organelle Movement T. Kreis (Geneva), N. Hirokawa (Japan), 1 E. Mandelkow (Germany), T. Schroer (Baltimore), R. Vale (USA) Ce44Adhesion and Signal Transduction W. Birchmeier (Berlin), D. Cheresh (San Diego), B. Gumbiner (New York)
I
Exocytosis and Recycfing D. Cutler (London), J. Bonifacino (USA), P. de Camilli, (Yale), R. Kelly (UCSF), C. Schiavo (London), W. Stoorvogel (Utrecht) Unconventional Myosins M. Bahler (rijbingen), D. Louvard (Paris), C. Mont&l (Baltimore), M. Mooseker (Yale) Traffic Between Nucleus and Cytoplasm R. Laskey (Cambridge), 11.Aebi (Basle), C. Blobel (New York), D. Gijrlich (Heidelberg), R. Luhrmann (Marburg), I. Mattaj (Heidelberg)
~
Epithelial Cell Adhesion and Polarity R. Kemler (Freiburgf, P. Ekblom (Uppsala), E. Knust (Cologne), J. Netson (Stanford), F. Watt (London)
”
1
,1,1(_ 111, I*
I
Biogenesis of Mitochondria and Chforoplasts,. ,,,,li,jj,, ‘1‘,““‘:! C. Schatz ( Basle), K. Cline (Gainsville), N. Pfanner (Fieiburg), J. ,011 c ” I$ ‘W I:],,,,, I&:‘ I’.. +*t:*n ,,‘, Pathways in MHC Class 41Presen,.,,,. H. Geuze (Utrecht), 5. Amiqorena (Paris), M. Kleijmeer‘(Amste~dam), P.-Cresswell (US/9, J, Neefjes (Utrecht), C. Watts (UK)
Biological Function of Chaperones C. Georgopoulos (Cceneva), A. Helen/us (New Haven), F.1.anger (Germany), C. Suzuki (Switzerland), D. 0. Tof& (USA)
Programmed Cell Death ) M. Raff (London). B. Earnshaw (Edinburahl. G. Evan (London). ” ’ H. Stel&r (Boston), C.ihomps&‘iChicaqoj
Dept of Biomedical Science, University of Ulster, Coleraine, Co. Londonderry, Ireland UK BT52 1 SA.
”
ECBO 97 Provisional
C. Stephen Downes
PC
tsitive and Negative Regulators of Nerve Cell G.rowth F. Walsh ILondon). M. Filbin INew York), C. Goodman (Berke&!y), R. Klein‘(Heidelbe& A. Pinijlondon)
I
Eoithefiat/Mesenchvmal Transition J. PI Thiery iParis), C. irchmeier (Berlin); P. Comoglio (Turin), E. Gerhardi (Cambrid,@ , Ceil Membrane Permeable Peotides *# ,,, I P. Doherty (London), D. P. Lane (bundee),’ .,,{il’I,,, S. Olsnes (Oslo), A. Prochiantz (Paris) ‘+?” ,a,,:,:ai I, Protein Translocation Across Membranes ”‘: “‘“““““i.,, ‘,,A:I:, B. Dobberstein (Heidelberg), Economu (Greece), 1,,“, T. Rapaport (USA), P.Sanson@% (Paris) Endoplasmic Reticulum/Golgi Dynamics H. Pelham (Cambridge), J. lippincott-Schwartz (USA). :,:,:,: Annexins S. Moss (London), V. Gerke (Muenster),:q ‘I”*’ R. Huber (Martinsreid), K. Simons (EMBL) +,& Database Information and its Application B. Dujon (Paris), A. Goffeau (Louvain), G. Poste (SmithKline Beecham)
j
,&~~ 1IIi ,@# 111,1” 1’’
j##i’ Regulation of the Actin Cytoskeleton by GTPases 111I’ T. Mitchison (UC%), J. Gallan (USA), A. Hal4 (London) ,,l:l,il, ‘, ! Further symposia in preparation: Cyclins and Cyclin Dependent Kinase Inhibitors Molecular Cell Biology of Endothelia
/
The Plenary Lecture Programme will be appearing shortly. In addition to the symposia and plenary lectures, there will be special-interest group meetings, poster sessions and a trade exhibition.
/
Details on how to obtain
more information
L trends in CELL BIOLOGY (Vol. 6) September 1996
about the meeting
can be found on p. 358 /
369