Status of genome projects for nonpathogenic bacteria and archaea

Nelson, Karen E.; Paulsen, Ian T.; Heidelberg, John F.; Fraser, Claire M.

doi:10.1038/80235

Cited by 87 publications

(50 citation statements)

References 42 publications

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“…If one considers that a significant amount of predicted genes (Ϸ15-20%) is species-specific in every genome sequenced so far (19), we have characterized the large majority of the repertoire of each cell.…”

Section: Resultsmentioning

confidence: 99%

Trends between gene content and genome size in prokaryotic species with larger genomes

Konstantinidis

Tiedje

2004

Proc. Natl. Acad. Sci. U.S.A.

445

347

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Although the evolution process and ecological benefits of symbiotic species with small genomes are well understood, these issues remain poorly elucidated for free-living species with large genomes. We have compared 115 completed prokaryotic genomes by using the Clusters of Orthologous Groups database to determine whether there are changes with genome size in the proportion of the genome attributable to particular cellular processes, because this may reflect both cellular and ecological strategies associated with genome expansion. We found that large genomes are disproportionately enriched in regulation and secondary metabolism genes and depleted in protein translation, DNA replication, cell division, and nucleotide metabolism genes compared to mediumand small-sized genomes. Furthermore, large genomes do not accumulate noncoding DNA or hypothetical ORFs, because the portion of the genome devoted to these functions remained constant with genome size. Traits other than genome size or strain-specific processes are reflected by the dispersion around the mean for cell functions that showed no correlation with genome size. For example, Archaea had significantly more genes in energy production, coenzyme metabolism, and the poorly characterized category, and fewer in cell membrane biogenesis and carbohydrate metabolism than Bacteria. The trends we noted with genome size by using Clusters of Orthologous Groups were confirmed by our independent analysis with The Institute for Genomic Research's Comprehensive Microbial Resource and Kyoto Encyclopedia of Genes and Genomes' Orthology annotation databases. These trends suggest that larger genome-sized species may dominate in environments where resources are scarce but diverse and where there is little penalty for slow growth, such as soil.

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Section: Resultsmentioning

confidence: 99%

Trends between gene content and genome size in prokaryotic species with larger genomes

Konstantinidis

Tiedje

2004

Proc. Natl. Acad. Sci. U.S.A.

445

347

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“…The preparation of highmolecular-weight genomic DNA is necessary for technical reasons described elsewhere (13). More importantly, the possible expression of genes not detrimental to the B. subtilis host but otherwise hazardous had to be avoided (23). Therefore, the sequenced 3,573-kb genome of the unicellular photosynthetic bacterium Synechocystis, thought to be nonpathogenic, was the only available choice when this work started in 1997, 1 year after its sequence was reported (17).…”

Section: Resultsmentioning

confidence: 99%

Combining two genomes in one cell: Stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome

Itaya

Tsuge²,

Koizumi³

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

175

165

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Cloning the whole 3.5-megabase (Mb) genome of the photosynthetic bacterium Synechocystis PCC6803 into the 4.2-Mb genome of the mesophilic bacterium Bacillus subtilis 168 resulted in a 7.7-Mb composite genome. We succeeded in such unprecedented largesize cloning by progressively assembling and editing contiguous DNA regions that cover the entire Synechocystis genome. The strain containing the two sets of genome grew only in the B. subtilis culture medium where all of the cloning procedures were carried out. The high structural stability of the cloned Synechocystis genome was closely associated with the symmetry of the bacterial genome structure of the DNA replication origin (oriC) and its termination (terC) and the exclusivity of Synechocystis ribosomal RNA operon genes (rrnA and rrnB). Given the significant diversity in genome structure observed upon horizontal DNA transfer in nature, our stable laboratory-generated composite genome raised fundamental questions concerning two complete genomes in one cell. Our megasize DNA cloning method, designated megacloning, may be generally applicable to other genomes or genome loci of free-living organisms.bacterial genomes ͉ DNA assembly ͉ genome symmetry

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“…The recent availability of many completely sequenced microbial genomes (Nelson et al 2000) has facilitated studies aimed at discovery of lateral gene transfer (LGT). Although whole-genome comparisons have supported the overall structure of the 16s rRNA tree (Fitz-Gibbon and House 1999; Snel et al 1999), the importance of LGT as a major force in evolution has also come to light as a driving force in prokaryotic evolution (Doolittle 1999;Nelson et al 1999Nelson et al , 2000Campbell 2000).…”

Section: Discussionmentioning

confidence: 99%

Understanding the Adaptation of Halobacterium Species NRC-1 to Its Extreme Environment through Computational Analysis of Its Genome Sequence

Kennedy¹,

Ng²,

Salzberg³

et al. 2001

Genome Res.

308

267

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The genome of the halophilic archaeon Halobacterium sp. NRC-1 and predicted proteome have been analyzed by computational methods and reveal characteristics relevant to life in an extreme environment distinguished by hypersalinity and high solar radiation: (1) The proteome is highly acidic, with a median pI of 4.9 and mostly lacking basic proteins. This characteristic correlates with high surface negative charge, determined through homology modeling, as the major adaptive mechanism of halophilic proteins to function in nearly saturating salinity. (2) Codon usage displays the expected GC bias in the wobble position and is consistent with a highly acidic proteome. (3) Distinct genomic domains of NRC-1 with bacterial character are apparent by whole proteome BLAST analysis, including two gene clusters coding for a bacterial-type aerobic respiratory chain. This result indicates that the capacity of halophiles for aerobic respiration may have been acquired through lateral gene transfer. (4) Two regions of the large chromosome were found with relatively lower GC composition and overrepresentation of IS elements, similar to the minichromosomes. These IS-element-rich regions of the genome may serve to exchange DNA between the three replicons and promote genome evolution. (5) GC-skew analysis showed evidence for the existence of two replication origins in the large chromosome. This finding and the occurrence of multiple chromosomes indicate a dynamic genome organization with eukaryotic character.

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Status of genome projects for nonpathogenic bacteria and archaea

Cited by 87 publications

References 42 publications

Trends between gene content and genome size in prokaryotic species with larger genomes

Trends between gene content and genome size in prokaryotic species with larger genomes

Combining two genomes in one cell: Stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome

Understanding the Adaptation of Halobacterium Species NRC-1 to Its Extreme Environment through Computational Analysis of Its Genome Sequence

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