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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

Coverage and %G+C of C7867-008 scaffold region containing CytO genes. %G+C was calculated across 120 nt windows with a step size of 30 nt. IGV (Thorvaldsdottir et al., 2013) was used to display the data.
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Figure 4: Coverage and %G+C of C7867-008 scaffold region containing CytO genes. %G+C was calculated across 120 nt windows with a step size of 30 nt. IGV (Thorvaldsdottir et al., 2013) was used to display the data.

Mentions: Examining the genomes of putatively free-living organisms endemic to an oxic environment, we expected to find evidence of aerobic metabolism, which had not previously been identified in an OD1 genome. Intriguingly, only 3 of the 8 C7867 genomes contained genes suggesting the capability of using O2 as a terminal electron acceptor. Genomes C7867-007 and C7867-008 each contain all four subunits of cytochrome bo(3) ubiquinol oxidase (CytO). We believe the attribution of CytO to these bins to be correct because the genes: (1) had coverage and composition values consistent with other regions of the scaffolds (Figure 4) and other scaffolds in the bins; (2) are located at equivalent locations in the middle of long contigs in each of the independently-assembled bins; and (3) phylogenetic trees of the concatenated protein sequences of the CytO subunits (Figure S1) and a valyl-tRNA ligase (Figure S2) found on the same scaffold show similar branching patterns. In Escherichia coli, CytO is the primary respiratory oxidase under high oxygen tension. A membrane-bound, quinone-dependent NAD(P)H dehydrogenase passes electrons to ubiquinone, which then shuttles them to CytO (Dinamarca et al., 2002). CytO then reduces O2 to H2O and pumps protons across the cytoplasmic membrane to generate proton motive force (PMF), which can then be used to generate ATP through the F1F0 ATP synthase. Although F1F0 ATP synthase is not part of the OD1 core genome, being present in only 10 of the 17 genomes examined, the C7867-007 and C7867-008 genomes both contain complete gene clusters for the F1F0 ATP synthase. No membrane-bound, quinone-dependent NAD(P)H dehydrogenases were identified in either genome, nor are there any apparent quinone biosynthesis genes.


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

Nelson WC, Stegen JC - Front Microbiol (2015)

Coverage and %G+C of C7867-008 scaffold region containing CytO genes. %G+C was calculated across 120 nt windows with a step size of 30 nt. IGV (Thorvaldsdottir et al., 2013) was used to display the data.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 4: Coverage and %G+C of C7867-008 scaffold region containing CytO genes. %G+C was calculated across 120 nt windows with a step size of 30 nt. IGV (Thorvaldsdottir et al., 2013) was used to display the data.
Mentions: Examining the genomes of putatively free-living organisms endemic to an oxic environment, we expected to find evidence of aerobic metabolism, which had not previously been identified in an OD1 genome. Intriguingly, only 3 of the 8 C7867 genomes contained genes suggesting the capability of using O2 as a terminal electron acceptor. Genomes C7867-007 and C7867-008 each contain all four subunits of cytochrome bo(3) ubiquinol oxidase (CytO). We believe the attribution of CytO to these bins to be correct because the genes: (1) had coverage and composition values consistent with other regions of the scaffolds (Figure 4) and other scaffolds in the bins; (2) are located at equivalent locations in the middle of long contigs in each of the independently-assembled bins; and (3) phylogenetic trees of the concatenated protein sequences of the CytO subunits (Figure S1) and a valyl-tRNA ligase (Figure S2) found on the same scaffold show similar branching patterns. In Escherichia coli, CytO is the primary respiratory oxidase under high oxygen tension. A membrane-bound, quinone-dependent NAD(P)H dehydrogenase passes electrons to ubiquinone, which then shuttles them to CytO (Dinamarca et al., 2002). CytO then reduces O2 to H2O and pumps protons across the cytoplasmic membrane to generate proton motive force (PMF), which can then be used to generate ATP through the F1F0 ATP synthase. Although F1F0 ATP synthase is not part of the OD1 core genome, being present in only 10 of the 17 genomes examined, the C7867-007 and C7867-008 genomes both contain complete gene clusters for the F1F0 ATP synthase. No membrane-bound, quinone-dependent NAD(P)H dehydrogenases were identified in either genome, nor are there any apparent quinone biosynthesis genes.

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