A Theoretical Limit to Coding Space in Chromosomes of Bacteria

Jackson, Julius H.; Harrison, Scott H.; Herring, Patricia A.

doi:10.1089/15362310252780861

Cited by 7 publications

(6 citation statements)

References 12 publications

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“…Riesia (1.79−2.7 genes/my to 14.29−20 gene/my). However, this must be interpreted with caution because short hypothetical genes may contribute little or nothing to a bacterial phenotype ( Jackson et al 2002 , Lerat and Ochman 2005 , Konstantinidis et al 2006 ). Therefore, we might expect only the rate of genes loss for genes with a known role to represent gene loss impacting the bacterial phenotype.…”

Section: Discussionmentioning

confidence: 99%

Genome Sequence of Candidatus Riesia pediculischaeffi, Endosymbiont of Chimpanzee Lice, and Genomic Comparison of Recently Acquired Endosymbionts from Human and Chimpanzee Lice

Boyd

Allen

Crécy‐Lagard

et al. 2014

G3 Genes|Genomes|Genetics

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The obligate-heritable endosymbionts of insects possess some of the smallest known bacterial genomes. This is likely due to loss of genomic material during symbiosis. The mode and rate of this erosion may change over evolutionary time: faster in newly formed associations and slower in long-established ones. The endosymbionts of human and anthropoid primate lice present a unique opportunity to study genome erosion in newly established (or young) symbionts. This is because we have a detailed phylogenetic history of these endosymbionts with divergence dates for closely related species. This allows for genome evolution to be studied in detail and rates of change to be estimated in a phylogenetic framework. Here, we sequenced the genome of the chimpanzee louse endosymbiont (Candidatus Riesia pediculischaeffi) and compared it with the closely related genome of the human body louse endosymbiont. From this comparison, we found evidence for recent genome erosion leading to gene loss in these endosymbionts. Although gene loss was detected, it was not significantly greater than in older endosymbionts from aphids and ants. Additionally, we searched for genes associated with B-vitamin synthesis in the two louse endosymbiont genomes because these endosymbionts are believed to synthesize essential B vitamins absent in the louse’s diet. All of the expected genes were present, except those involved in thiamin synthesis. We failed to find genes encoding for proteins involved in the biosynthesis of thiamin or any complete exogenous means of salvaging thiamin, suggesting there is an undescribed mechanism for the salvage of thiamin. Finally, genes encoding for the pantothenate de novo biosynthesis pathway were located on a plasmid in both taxa along with a heat shock protein. Movement of these genes onto a plasmid may be functionally and evolutionarily significant, potentially increasing production and guarding against the deleterious effects of mutation. These data add to a growing resource of obligate endosymbiont genomes and to our understanding of the rate and mode of genome erosion in obligate animal-associated bacteria. Ultimately sequencing additional louse p-endosymbiont genomes will provide a model system for studying genome evolution in obligate host associated bacteria.

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Section: Discussionmentioning

confidence: 99%

Genome Sequence of Candidatus Riesia pediculischaeffi, Endosymbiont of Chimpanzee Lice, and Genomic Comparison of Recently Acquired Endosymbionts from Human and Chimpanzee Lice

Boyd

Allen

Crécy‐Lagard

et al. 2014

G3 Genes|Genomes|Genetics

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“…However, since few organisms have been studied as extensively as E. coli , we expect that many of the unknown genes in other organisms will ultimately turn out to be functional. In fact, in 2002 nearly one-third of E. coli ORFs lacked functional annotation or orthology in other genomes (Jackson et al 2002). As of 2010, only 5% of ORFs remain unidentified at any level.…”

Section: Discussionmentioning

confidence: 99%

Reduced mRNA Secondary-Structure Stability Near the Start Codon Indicates Functional Genes in Prokaryotes

Keller

Mis

Jia

et al. 2011

Genome Biology and Evolution

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Several recent studies have found that selection acts on synonymous mutations at the beginning of genes to reduce mRNA secondary-structure stability, presumably to aid in translation initiation. This observation suggests that a metric of relative mRNA secondary-structure stability, ZΔG, could be used to test whether putative genes are likely to be functionally important. Using the Escherichia coli genome, we compared the mean ZΔG of genes with known functions, genes with known orthologs, genes where function and orthology are unknown, and pseudogenes. Genes in the first two categories demonstrated similar levels of selection for reduced stability (increased ZΔG), whereas for pseudogenes stability did not differ from our null expectation. Surprisingly, genes where function and orthology were unknown were also not different from the null expectation, suggesting that many of these open reading frames are not functionally important. We extended our analysis by constructing a Bayesian phylogenetic mixed model based on data from 145 prokaryotic genomes. As in E. coli, genes with no known function had consistently lower ZΔG, even though we expect that many of the currently unannotated genes will ultimately have their functional utility discovered. Our findings suggest that functional genes tend to evolve increased ZΔG, whereas nonfunctional ones do not. Therefore, ZΔG may be a useful metric for identifying genes of potentially important function and could be used to target genes for further functional study.

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“…Their relatively small genomes and theoretical calculations suggested that only a maximum of ? of their DNA codes for functional genes (52). The supposed constraint may impose metabolic limitations that require, lead or force the development of genomic economies.…”

Section: Reactionmentioning

confidence: 99%

The necessity of combining genomic and enzymatic data to infer metabolic function and pathways in the smallest bacteria amino acid purine and pyrimidine metabolism in mollicutes

Pollack

2002

Front Biosci

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Bacteria of the class Mollicutes have no cell wall. One species, Mycoplasma genitalium is the personification of the simplest form of independent cell-free life. Its small genome (580 kbp) is the smallest of any cell. Mollicutes have unique metabolic properties, perhaps because of their limited coding space and high mutability. Based on 16S rRNA analyses the Mollicutes Mycoplasma gallisepticum is thought to be the most mutable bacteria. Enzyme activities found in most Bacteria are absent from Mollicutes. The functions of apparently absent genes and enzymes can apparently be fulfilled by other genes and their expression products that have multiple capabilities. Because of these and other properties predictions of their metabolism based only on, e.g., either annotation, enzymatic assay, proteomic studies or structural analyses is problematic. To obtain a more confident appraisal of the functional capabilities of these simplest cells genomic and enzymatic data were combined to obtain a "metabolic consensus". The consensus is represented by a biochemical circuit for central metabolism involving purine and pyrimidine interconversions and their linkages to amino acid metabolism, glycolysis and the pentose phosphate pathway in three human Mollicutes pathogens: Mycoplasma pneumoniae, Mycoplasma genitalium and Ureaplasma urealyticum.

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A Theoretical Limit to Coding Space in Chromosomes of Bacteria

Cited by 7 publications

References 12 publications

Genome Sequence of Candidatus Riesia pediculischaeffi, Endosymbiont of Chimpanzee Lice, and Genomic Comparison of Recently Acquired Endosymbionts from Human and Chimpanzee Lice

Genome Sequence of Candidatus Riesia pediculischaeffi, Endosymbiont of Chimpanzee Lice, and Genomic Comparison of Recently Acquired Endosymbionts from Human and Chimpanzee Lice

Reduced mRNA Secondary-Structure Stability Near the Start Codon Indicates Functional Genes in Prokaryotes

The necessity of combining genomic and enzymatic data to infer metabolic function and pathways in the smallest bacteria amino acid purine and pyrimidine metabolism in mollicutes

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