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The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle.

Nelson WC, Stegen JC - Front Microbiol (2015)

Bottom Line: The organisms have small (generally <1 Mb) genomes with severely reduced metabolic capabilities.We have reconstructed 8 partial to near-complete OD1 genomes from oxic groundwater samples, and compared them against existing genomic data.Gene sets for biosynthesis of cofactors, amino acids, nucleotides, and fatty acids are absent entirely or greatly reduced.

View Article: PubMed Central - PubMed

Affiliation: Microbiology, Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA.

ABSTRACT
Candidate phylum OD1 bacteria (also referred to as Parcubacteria) have been identified in a broad range of anoxic environments through community survey analysis. Although none of these species have been isolated in the laboratory, several genome sequences have been reconstructed from metagenomic sequence data and single-cell sequencing. The organisms have small (generally <1 Mb) genomes with severely reduced metabolic capabilities. We have reconstructed 8 partial to near-complete OD1 genomes from oxic groundwater samples, and compared them against existing genomic data. The conserved core gene set comprises 202 genes, or ~28% of the genomic complement. "Housekeeping" genes and genes for biosynthesis of peptidoglycan and Type IV pilus production are conserved. Gene sets for biosynthesis of cofactors, amino acids, nucleotides, and fatty acids are absent entirely or greatly reduced. The only aspects of energy metabolism conserved are the non-oxidative branch of the pentose-phosphate shunt and central glycolysis. These organisms also lack some activities conserved in almost all other known bacterial genomes, including signal recognition particle, pseudouridine synthase A, and FAD synthase. Pan-genome analysis indicates a broad genotypic diversity and perhaps a highly fluid gene complement, indicating historical adaptation to a wide range of growth environments and a high degree of specialization. The genomes were examined for signatures suggesting either a free-living, streamlined lifestyle, or a symbiotic lifestyle. The lack of biosynthetic capabilities and DNA repair, along with the presence of potential attachment and adhesion proteins suggest that the Parcubacteria are ectosymbionts or parasites of other organisms. The wide diversity of genes that potentially mediate cell-cell contact suggests a broad range of partner/prey organisms across the phylum.

No MeSH data available.


Related in: MedlinePlus

Distribution of gene conservation across the Parcubacteria genomes. Shaded subsections represent degree of conservation across all genomes, with the lowest black section representing genes conserved in 13–17 genomes, the gray section conserved in 2–12 genomes, etc. to the top white section representing genes unique to a single organism.
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Figure 3: Distribution of gene conservation across the Parcubacteria genomes. Shaded subsections represent degree of conservation across all genomes, with the lowest black section representing genes conserved in 13–17 genomes, the gray section conserved in 2–12 genomes, etc. to the top white section representing genes unique to a single organism.

Mentions: Determination of conserved genes across various taxonomic ranks can provide information about the evolutionary history of a lineage (Zhang and Sievert, 2014), thus we examined the ortholog families to define a core genome for the OD1 phylum. Since most of the genome sequences are incomplete, genes present in 13 or more of the 17 genomes were considered part of the core (Figure 3). A set of 202 ortholog families was identified, comprising 18–31% of the estimated total gene complement of OD1 genomes. Over half of the core genes also had a conserved position adjacent to at least one other core gene. Many of the rest appear to have a conserved position within their respective sub-groups [i.e., the OD1-i group or the C7867 clade (see Figure 2)]. Core genes included DNA replication functions, cell division proteins, transcription machinery, translation machinery, protein folding and trafficking genes, and genes for peptidoglycan biosynthesis (Table S1). Few genes for biosynthesis of amino acids or nucleotides were part of the core, and only nine genes in the core have no known function, limiting the number of functions that may be present as novel genes. Although most genes central to glycolysis are conserved, enolase and pyruvate kinase were only identified in 10 and 11 of the genomes, respectively. A conserved gene cluster contains activities central to the non-oxidative branch of the pentose phosphate pathway. The genes for a type IV pilus and competence proteins ComEC, ComF, and DprA (also known as Smf) are also in the conserved core.


The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle.

Nelson WC, Stegen JC - Front Microbiol (2015)

Distribution of gene conservation across the Parcubacteria genomes. Shaded subsections represent degree of conservation across all genomes, with the lowest black section representing genes conserved in 13–17 genomes, the gray section conserved in 2–12 genomes, etc. to the top white section representing genes unique to a single organism.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4508563&req=5

Figure 3: Distribution of gene conservation across the Parcubacteria genomes. Shaded subsections represent degree of conservation across all genomes, with the lowest black section representing genes conserved in 13–17 genomes, the gray section conserved in 2–12 genomes, etc. to the top white section representing genes unique to a single organism.
Mentions: Determination of conserved genes across various taxonomic ranks can provide information about the evolutionary history of a lineage (Zhang and Sievert, 2014), thus we examined the ortholog families to define a core genome for the OD1 phylum. Since most of the genome sequences are incomplete, genes present in 13 or more of the 17 genomes were considered part of the core (Figure 3). A set of 202 ortholog families was identified, comprising 18–31% of the estimated total gene complement of OD1 genomes. Over half of the core genes also had a conserved position adjacent to at least one other core gene. Many of the rest appear to have a conserved position within their respective sub-groups [i.e., the OD1-i group or the C7867 clade (see Figure 2)]. Core genes included DNA replication functions, cell division proteins, transcription machinery, translation machinery, protein folding and trafficking genes, and genes for peptidoglycan biosynthesis (Table S1). Few genes for biosynthesis of amino acids or nucleotides were part of the core, and only nine genes in the core have no known function, limiting the number of functions that may be present as novel genes. Although most genes central to glycolysis are conserved, enolase and pyruvate kinase were only identified in 10 and 11 of the genomes, respectively. A conserved gene cluster contains activities central to the non-oxidative branch of the pentose phosphate pathway. The genes for a type IV pilus and competence proteins ComEC, ComF, and DprA (also known as Smf) are also in the conserved core.

Bottom Line: The organisms have small (generally <1 Mb) genomes with severely reduced metabolic capabilities.We have reconstructed 8 partial to near-complete OD1 genomes from oxic groundwater samples, and compared them against existing genomic data.Gene sets for biosynthesis of cofactors, amino acids, nucleotides, and fatty acids are absent entirely or greatly reduced.

View Article: PubMed Central - PubMed

Affiliation: Microbiology, Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA.

ABSTRACT
Candidate phylum OD1 bacteria (also referred to as Parcubacteria) have been identified in a broad range of anoxic environments through community survey analysis. Although none of these species have been isolated in the laboratory, several genome sequences have been reconstructed from metagenomic sequence data and single-cell sequencing. The organisms have small (generally <1 Mb) genomes with severely reduced metabolic capabilities. We have reconstructed 8 partial to near-complete OD1 genomes from oxic groundwater samples, and compared them against existing genomic data. The conserved core gene set comprises 202 genes, or ~28% of the genomic complement. "Housekeeping" genes and genes for biosynthesis of peptidoglycan and Type IV pilus production are conserved. Gene sets for biosynthesis of cofactors, amino acids, nucleotides, and fatty acids are absent entirely or greatly reduced. The only aspects of energy metabolism conserved are the non-oxidative branch of the pentose-phosphate shunt and central glycolysis. These organisms also lack some activities conserved in almost all other known bacterial genomes, including signal recognition particle, pseudouridine synthase A, and FAD synthase. Pan-genome analysis indicates a broad genotypic diversity and perhaps a highly fluid gene complement, indicating historical adaptation to a wide range of growth environments and a high degree of specialization. The genomes were examined for signatures suggesting either a free-living, streamlined lifestyle, or a symbiotic lifestyle. The lack of biosynthetic capabilities and DNA repair, along with the presence of potential attachment and adhesion proteins suggest that the Parcubacteria are ectosymbionts or parasites of other organisms. The wide diversity of genes that potentially mediate cell-cell contact suggests a broad range of partner/prey organisms across the phylum.

No MeSH data available.


Related in: MedlinePlus