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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

Nucleotide usage and modification at positions 38, 39, and 40 of tRNAs. For each isotype, the three columns represent positions 38, 39, and 40 (in relation to E. coli standard). Color sections represent nucleotide and modification data. (A) Modomics nucleotide and modification data; (B) GtRNAdb nucleotide data; (C) OD1 nucleotide data.
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Figure 5: Nucleotide usage and modification at positions 38, 39, and 40 of tRNAs. For each isotype, the three columns represent positions 38, 39, and 40 (in relation to E. coli standard). Color sections represent nucleotide and modification data. (A) Modomics nucleotide and modification data; (B) GtRNAdb nucleotide data; (C) OD1 nucleotide data.

Mentions: Pseudouridine synthase A (PSA), encoded by the truA gene, modifies uridine bases at positions 38, 39, and 40 within the anti-codon stem-loop in tRNAs to enhance stability. The Modomics database (Machnicka et al., 2013) contains sequences of RNAs, including experimentally determined positions and species of modified bases. Analysis of bacterial sequences deposited in the Modomics database reveals variance in the activity of PSA modification at the three positions and between tRNA isotypes. Where modification is observed, it is usually predominant at only one of the three positions, and a majority of the U residues is modified (Figure 5A). Because of the limited dataset available in Modomics (24 species represented, many only partially), we also examined nucleotide usage at tRNA positions 38, 39, and 40 in 630 sequenced genomes in the GtRNAdb (Chan and Lowe, 2009). These results generally agreed with the Modomics analysis, with T found predominantly at positions in isoforms where pseudouridine modification was observed in the Modomics data (Figure 5B), usually position 38 or 39. Examination of predicted tRNAs from OD1 genomes shows that the OD1 populations have reduced T usage in positions 38 and 39 of isoforms that are targets of PSA activity (e.g., tRNA-Lys39, tRNA-Met39, tRNA-Phe39), the exception being tRNA-Tyr39 (Figure 5C). T is preferentially replaced by a C or G residue in most isoforms, which could help stabilize the stem loop structure due to the additional hydrogen bond present in G-C base pairs relative to A-T base pairs. Curiously, T usage is elevated at positions in isoforms that are not targets of PSA, for example tRNA-Ala39, tRNA-Val38, and tRNA-Val39. These results are consistent with the hypothesis that the Parcubacteria have evolved to preclude the necessity for PSA function through altered sequence content in the anti-codon stem loop.


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

Nelson WC, Stegen JC - Front Microbiol (2015)

Nucleotide usage and modification at positions 38, 39, and 40 of tRNAs. For each isotype, the three columns represent positions 38, 39, and 40 (in relation to E. coli standard). Color sections represent nucleotide and modification data. (A) Modomics nucleotide and modification data; (B) GtRNAdb nucleotide data; (C) OD1 nucleotide data.
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Related In: Results  -  Collection

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Figure 5: Nucleotide usage and modification at positions 38, 39, and 40 of tRNAs. For each isotype, the three columns represent positions 38, 39, and 40 (in relation to E. coli standard). Color sections represent nucleotide and modification data. (A) Modomics nucleotide and modification data; (B) GtRNAdb nucleotide data; (C) OD1 nucleotide data.
Mentions: Pseudouridine synthase A (PSA), encoded by the truA gene, modifies uridine bases at positions 38, 39, and 40 within the anti-codon stem-loop in tRNAs to enhance stability. The Modomics database (Machnicka et al., 2013) contains sequences of RNAs, including experimentally determined positions and species of modified bases. Analysis of bacterial sequences deposited in the Modomics database reveals variance in the activity of PSA modification at the three positions and between tRNA isotypes. Where modification is observed, it is usually predominant at only one of the three positions, and a majority of the U residues is modified (Figure 5A). Because of the limited dataset available in Modomics (24 species represented, many only partially), we also examined nucleotide usage at tRNA positions 38, 39, and 40 in 630 sequenced genomes in the GtRNAdb (Chan and Lowe, 2009). These results generally agreed with the Modomics analysis, with T found predominantly at positions in isoforms where pseudouridine modification was observed in the Modomics data (Figure 5B), usually position 38 or 39. Examination of predicted tRNAs from OD1 genomes shows that the OD1 populations have reduced T usage in positions 38 and 39 of isoforms that are targets of PSA activity (e.g., tRNA-Lys39, tRNA-Met39, tRNA-Phe39), the exception being tRNA-Tyr39 (Figure 5C). T is preferentially replaced by a C or G residue in most isoforms, which could help stabilize the stem loop structure due to the additional hydrogen bond present in G-C base pairs relative to A-T base pairs. Curiously, T usage is elevated at positions in isoforms that are not targets of PSA, for example tRNA-Ala39, tRNA-Val38, and tRNA-Val39. These results are consistent with the hypothesis that the Parcubacteria have evolved to preclude the necessity for PSA function through altered sequence content in the anti-codon stem loop.

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