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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

YidC sequences from Parcubacteria have a unique region of charged residues. Positively charged residues at neutral pH are colored red; negatively charged residues are colored blue; histidine residues, which are positively charged below pH 6.0, are colored purple. The display was generated using UGENE (Okonechnikov et al., 2012).
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Figure 6: YidC sequences from Parcubacteria have a unique region of charged residues. Positively charged residues at neutral pH are colored red; negatively charged residues are colored blue; histidine residues, which are positively charged below pH 6.0, are colored purple. The display was generated using UGENE (Okonechnikov et al., 2012).

Mentions: Signal recognition particle (SRP) binds the signal peptide sequence of nascent proteins and delivers them to Sec export systems at the membrane for proper trafficking (Akopian et al., 2013). It is a ribonucleoprotein, consisting of a single polypeptide (encoded by ffh) and the 4.5S RNA (encoded by ffs). Neither gene has been detected in any of the Parcubacteria genomes. Recently, it has been demonstrated that alleles of YidC from Rhodopirellula baltica and Oceanicaulis alexandrii, which contain an extended C-terminal region enriched in positively-charged amino acids, can partially complement a deletion of SRP in E. coli (Seitl et al., 2014). There are two forms of YidC; one is composed solely of a domain that interacts with SecD and the transmembrane segments of nascent integral membrane proteins, and the other has an additional N-terminal periplasmic domain of undetermined function. The YidC present in Parcubacteria is of the former type. Multiple sequence alignment comparing parcubacterial YidC sequences to those from model organisms including R. baltica and O. alexandrii shows that it has a novel internal region which is enriched for charged residues (both positive and negative) (Figure 6). It does not, however, have an extended positively charged region at its C-terminus. Possibly this YidC variant, in combination with the small volume of OD1 cells, is sufficient for proper protein trafficking. It is also of note that the OD1 genomes have a smaller percentage of genes with recognizable signal peptides (on average 3%) (Table 3), perhaps relaxing the requirement for efficient trafficking.


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

Nelson WC, Stegen JC - Front Microbiol (2015)

YidC sequences from Parcubacteria have a unique region of charged residues. Positively charged residues at neutral pH are colored red; negatively charged residues are colored blue; histidine residues, which are positively charged below pH 6.0, are colored purple. The display was generated using UGENE (Okonechnikov et al., 2012).
© Copyright Policy
Related In: Results  -  Collection

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

Figure 6: YidC sequences from Parcubacteria have a unique region of charged residues. Positively charged residues at neutral pH are colored red; negatively charged residues are colored blue; histidine residues, which are positively charged below pH 6.0, are colored purple. The display was generated using UGENE (Okonechnikov et al., 2012).
Mentions: Signal recognition particle (SRP) binds the signal peptide sequence of nascent proteins and delivers them to Sec export systems at the membrane for proper trafficking (Akopian et al., 2013). It is a ribonucleoprotein, consisting of a single polypeptide (encoded by ffh) and the 4.5S RNA (encoded by ffs). Neither gene has been detected in any of the Parcubacteria genomes. Recently, it has been demonstrated that alleles of YidC from Rhodopirellula baltica and Oceanicaulis alexandrii, which contain an extended C-terminal region enriched in positively-charged amino acids, can partially complement a deletion of SRP in E. coli (Seitl et al., 2014). There are two forms of YidC; one is composed solely of a domain that interacts with SecD and the transmembrane segments of nascent integral membrane proteins, and the other has an additional N-terminal periplasmic domain of undetermined function. The YidC present in Parcubacteria is of the former type. Multiple sequence alignment comparing parcubacterial YidC sequences to those from model organisms including R. baltica and O. alexandrii shows that it has a novel internal region which is enriched for charged residues (both positive and negative) (Figure 6). It does not, however, have an extended positively charged region at its C-terminus. Possibly this YidC variant, in combination with the small volume of OD1 cells, is sufficient for proper protein trafficking. It is also of note that the OD1 genomes have a smaller percentage of genes with recognizable signal peptides (on average 3%) (Table 3), perhaps relaxing the requirement for efficient trafficking.

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