Chromosomes in the Rocky Mountains

COMMENT 20 Davis, A.P. and Justice, M.J. (1998) Mamm. Genome 9, 345–348 21 Steingrimsson, E. et al. (1994) Nat.

Genet. 8, 256–263 22 Bultman, S.J., Michaud, E.J. and Woychik, R.P. (1992) Cell 71,

1195–1204 23 Michaud, E.J. et al. (1997) J. Endocrinol. 155, 207–209

M E E T I N G R E P O RT

Chromosomes in the Rocky Mountains YEAST CHROMOSOME STRUCTURE, REPLICATION AND SEGREGATION, SNOWMASS, CO, USA, 8–13 AUGUST 1998. A group of about 200 peoThe segregation sesG1 S ple met in the beautiful sions provided models of mountains of Colorado outthe chromatin structure of Clb5p Dbf4p side Aspen to discuss the curthe centromere. The S. P Cdc45p rent state of affairs of yeast cerevisiae centromere is Mcm2p Helicase chromosomes. The awesmall (0.1 kb) compared some power of molecular with other eukaryotes, ORC genetic analysis of budding including S. pombe (50 kb) Cdc45p (Saccharomyces cerevisiae) and humans (1000 kb)2 and fission (Schizosaccharo(Louise Clarke, Univ. of Cdc28p Cdc7p myces pombe) yeasts was California, USA). Only one demonstrated in every presmicrotubule binds this DNA replication entation and poster. This simple kinetochore, while included the ability to many microtubules bind a delete and mutate many FIGURE 1. Phosphorylation by both Cdc7p/Dbf4p and Cdc28p/Clb5p human one. Chromatin genes at will, tagging pro- kinases initiates DNA replication. In G1 phase, Cdc28p–Clb5p structure of the centromere teins for biochemical and protein kinase loads Cdc45p protein onto the ORC–MCM complex is important for recognimicroscopic studies, using at the origin. Subsequently, Cdc7p protein kinase is activated by tion by the microtubule. binding to Dbf4p, and phosphorylates the Mcm2p protein to two-hybrid and synthetic activate an origin helicase and initiate DNA replication. This special nucleosomal lethality screens to establish structure is composed of a genetic interactions, and multiprotein complex of using nucleotide arrays to query the sessions provided a detailed picture histones and several centromereentire genome. Because of the large of trans-acting (multiprotein com- specific proteins (Doug Koshland, number of human homologues, of plexes) and cis-acting elements (ori- Carnergie Inst., USA). As seen for which many are mutated in human gins), which regulate the initiation of replication, protein phosphorylation disease (40% of known human disease DNA replication1 (Fig. 1). The ORC regulates the process, but in reverse. genes have a yeast homologue – multiprotein complex binds origin Ipl1 kinase decreases, while Glc7p Philip Heiter, Univ. of British chromatin and shifts resident nucleo- phosphatase increases the binding of Columbia, Canada), the ability to somes (Steve Bell, MIT, USA). A microtubules to the kinetochore use yeast as a model system to series of changes in chromatin struc- (Clarence Chan, Univ. of Texas, USA; study human disease cannot be ture occur at origins by the addition Tony Hyman, EMBL, Germany). of other proteins (Cdc6p, Mcm2p, Motors are important for chromooveremphasized. This was the fifth biennial meet- -7p, Mcm10p) during the G1 to S some movement on the spindle with ing of this type sponsored by FASEB. phase transition ( Judith Campbell, one dynein (2) end motor and six As in the past, the talks and posters Cal Tech., USA; Ming Lei, Cornell, kinesin (1) end motors, of which a focused on the replication, segre- USA). Replication is initiated by combination of Cin8p and Kar3p or gation and structure of yeast chromo- phosphorylation of some of these Kip3p will suffice (Andy Hoyt, Johns somes. The keynote address by Walt proteins by both Cdk1p–CLB and Hopkins, USA). In the chromosome Fangman (Univ. of Washington, USA) Cdc7p/Dbf4p protein kinases (John structure sessions, the talks focused pointed out the important landmarks Diffley, ICRF, UK; Robert Sclafani, on transcriptional silencing3 at the for yeast chromosome studies, which Univ. of Colorado, USA). Pre-meiotic mating loci, at the rDNA (Ref. 4) and included the discovery of DNA DNA replication also requires at telomeres. The Ku70/Ku80 (Hdf1p sequences that define origins (ARS), Cdk1p–CLB action (Curt Wittenberg, = Ku70p, Hdf2p = Ku80) proteins, centromeres (CEN) and telomeres. Scripps, USA). The ‘licensing factor’, which are used for VDJ non-homOther landmarks included the ability which makes replication origins olgous recombination and the repair to identify important regulatory competent for firing, is composed of of double-stranded DNA breaks in proteins by the analysis of cdc (cell the Mcm protein complex that is mammals, are important players in divison cycle) mutants. Many talks loaded by Cdc6p protein after mito- this regulation5. The four Sir proteins focused on some cdc mutant or its sis and then leaves the yeast nucleus are limiting for silencing. Telomeres serve as regulators by soaking up or protein product. The replication in G2/M ( Joachim Li, UCSF, USA). TIG NOVEMBER 1998 VOL. 14 NO. 11 0168-9525/98/$ – see front matter © 1998 Elsevier Science All rights reserved. PII: S0168-9525(98)01610-2

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M E E T I N G R E P O RT releasing Sir proteins from the Ku70p–Ku80p telomerase complex (David Shore, Univ. of Geneva, Switzerland). Cdc13p protein binds single-stranded DNA at the Ku70p–Ku80p telomerase complex (Vicki Lundblad, Baylor, USA). Nuclear organization of telomeres is important with telomeres located at the nuclear periphery (Sussan Gasser, ISREC, Switzerland). Targetting DNA to the periphery using a ER–Golgi anchoring signal can produce silencing (Rolf Sternglanz, SUNY, USA). Hence, any gene brought to the nuclear periphery will

be silenced by the Sir protein complex. In summary, the importance of chromatin structure was evident in all sessions. Yeast origins, centromeres and telomeres bind elegant multiprotein complexes that act as regulatory machines to change chromatin structure and to allow important cellular processes to occur.

Further reading 1 Dutta, A. and Bell, S.P. (1997) Annu. Rev. Cell Dev. Biol. 13, 293–332 2 Pluta, A.F. et al. (1995) Science 270, 1591–1594

3 Loo, S. and Rine, J. (1995) Annu. Rev. Cell Dev. Biol. 11, 519–548 4 Smith, J.S. and Boeke, J.D. (1997) Genes Dev. 11, 241–254 5 Weaver, D.T. (1995) Trends Genet. 11, 388–392

Robert A. Sclafani [email protected] Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, 4200 E. Ninth Avenue, Denver, CO 80262, USA.

LETTER

Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles Sequencing of multiple complete genomes of bacteria and archaea makes it possible to perform systematic, genome-scale comparisons that aim to delineate the genomic complement of a particular phenotype. Recently, the first genome of a hyperthermophilic bacterium, Aquifex aeolicus, has been sequenced1. Previous studies based on rRNA and aminoacyl-tRNA analysis had suggested a very early divergence of Aquifex from the rest of the bacteria2,3. Aquifex is

exceptional among bacteria in that it occupies the hyperthermophilic niche otherwise dominated by archaea2. In the published analysis of the Aquifex genome, it has been concluded that the genome sequence yielded ‘only a few specific indications of thermophily’1. With three genomes of extreme thermophilic archaea (Methanococcus jannaschii, Methanobacterium thermoautotrophicum and Archaeoglobus fulgidus) currently available4–6, we

TABLE 1. ‘Archaeal’ genes in bacterial genomes Bacterial speciesa

Reliable best hits to archaeal proteinsb

Aquifex aeolicus Bacillus subtilis Synechocystis sp. Borrelia burgdorferi Escherichia coli

246 (16.2%) 207 (5.0%) 126 (4.0%) 45 (3.6%) 99 (2.3%)

aThe

data on Haemophilus influenzae, Helicobacter pylori (Proteobacteria), Mycoplasma genitalium and Mycoplasma pneumoniae (Gram-positive bacteria) are not shown because, in these species, the majority of the best hits are to homologs from larger genomes within the same phylogenetic lineages, namely E. coli and B. subtilis, respectively. bAll database hits with associated expectation (e) values <1023 were analyzed; a ‘reliable best hit’ was registered when the e-value with an archaeal protein was lower than that with any bacterial or eukaryotic protein by at least a factor of 100. TIG NOVEMBER 1998 VOL. 14 NO. 11 0168-9525/98/$ – see front matter. Published by Elsevier Science. PII: S0168-9525(98)01553-4

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reasoned that a detailed comparison of the Aquifex and archaeal genomes could reveal genome-scale adaptations for thermophily. The protein sequences encoded in all complete bacterial genomes were compared with the nonredundant protein sequence database using the gapped BLAST program7, and a phylogenetic breakdown was automatically produced using the TAX_COLLECTOR program (Ref. 8, and D.R. Walker, unpublished). The results show that the fraction of Aquifex gene products that have archaeal proteins as clear best hits is by far greater than for each of the other bacteria (Table 1). Taking the fraction of ‘archaeal’ genes in Bacillus subtilis (Table 1) as a conservative estimate for the random expectation in a bacterial genome and using the normal approximation of the binomial distribution, it could be estimated that the excess of ‘archaeal’ genes in Aquifex could not be explained by a random fluctuation, with p<<10210. A reciprocal comparison showed that, for proteins encoded in each of the three archaeal genomes, Aquifex proteins are the best hits significantly more frequently than proteins from other bacteria, even those with genomes 2–3 times larger than the Aquifex genome, such as Synechocystis sp. or B. subtilis (Table 2). In a complementary analysis, bacterial proteins were compared with