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

Abstract

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.

Scaling laws in bacterial genomes: A side-effect of selection of mutational robustness?

“…10 and 11 show, our experiments with RAevol reproduce qualitatively the scaling laws observed in the prokaryotic kingdom (Cases et al, 2003;van Nimwegen, 2003;Konstantinidis and Tiedje, 2004;Molina and van Nimwegen, 2008). Small genomes with few genes only have a very basic regulation activity while large ones develop complex regulation networks with many genes.…”

“…Through the analysis of the annotated sequences, it was shown that the number of genes in each functional category scales as a power-law of the total number of genes in the genome and that the exponent of this law depends on the functional role of the family: the number of transcription factors (TFs), in particular, scales quadratically with the total number of genes while metabolic genes scale at most linearly with it (van Nimwegen, 2003;Molina and van Nimwegen, 2008). Moreover, this increase is also correlated with the size of the genome (Konstantinidis and Tiedje, 2004). These results suggest that the intricacy of regulation networks grows faster than the size of the network itself.…”

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

“…On average, the genomes of soil prokaryotes are larger than those inhabiting aquatic ecosystems 27 or the human gut 28 . These relatively large genomes are thought to provide soil-dwelling bacteria with a more diverse genetic inventory to enhance survival in conditions where resources are diverse, but sparse 29,30 . However, the Ca.…”

Genomic versatility and functional variation between two dominant heterotrophic symbionts of deep-sea Osedax worms

“…In general, large genomes are thought to be more ecologically versatile (Konstantinidis and Tiedje, 2004), which would thus be important for an environmentally acquired symbiont that has both free-living and host-associated stages. The estimated genome sizes of the Osedax symbionts, larger than free-living relatives, and similar to the facultative intracellular endosymbiont Teredinibacter turnerae of the marine shipworm bivalve (Table 1; Yang et al, 2009), indirectly suggests a possible retention of genes for both free-living and intracellular existence.…”