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Complete Genome of Ignavibacterium album, a Metabolically Versatile, Flagellated, Facultative Anaerobe from the Phylum Chlorobi.

Liu Z, Frigaard NU, Vogl K, Iino T, Ohkuma M, Overmann J, Bryant DA - Front Microbiol (2012)

Bottom Line: The occurrence of genes encoding enzymes for CO(2) fixation as well as other enzymes of the reductive TCA cycle suggests that mixotrophy may be possible under certain growth conditions.However, known biosynthetic pathways for several amino acids are incomplete; this suggests that I. album is dependent upon on exogenous sources of these metabolites or employs novel biosynthetic pathways.Comparisons of I. album and other members of the phylum Chlorobi suggest that the physiology of the ancestors of this phylum might have been quite different from that of modern GSB.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University University Park, PA, USA.

ABSTRACT
Prior to the recent discovery of Ignavibacterium album (I. album), anaerobic photoautotrophic green sulfur bacteria (GSB) were the only members of the bacterial phylum Chlorobi that had been grown axenically. In contrast to GSB, sequence analysis of the 3.7-Mbp genome of I. album shows that this recently described member of the phylum Chlorobi is a chemoheterotroph with a versatile metabolism. I. album lacks genes for photosynthesis and sulfur oxidation but has a full set of genes for flagella and chemotaxis. The occurrence of genes for multiple electron transfer complexes suggests that I. album is capable of organoheterotrophy under both oxic and anoxic conditions. The occurrence of genes encoding enzymes for CO(2) fixation as well as other enzymes of the reductive TCA cycle suggests that mixotrophy may be possible under certain growth conditions. However, known biosynthetic pathways for several amino acids are incomplete; this suggests that I. album is dependent upon on exogenous sources of these metabolites or employs novel biosynthetic pathways. Comparisons of I. album and other members of the phylum Chlorobi suggest that the physiology of the ancestors of this phylum might have been quite different from that of modern GSB.

No MeSH data available.


Phylogenetic distribution of BLASTP best hits of I. album proteins compared to proteins in the NCBI nr database. An e-value cut-off of 0.001 was used.
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Figure 3: Phylogenetic distribution of BLASTP best hits of I. album proteins compared to proteins in the NCBI nr database. An e-value cut-off of 0.001 was used.

Mentions: Ignavibacterium album has a single circular chromosome of 3,658,997 bp with a mol% G + C content of 34% (Figure 2). The genome includes one rRNA operon, 45 tRNA genes, and 3,195 predicted protein coding sequences (open reading frames, ORFs), and 2 ORFs with frameshift mutations encoding non-functional proteins. The 3,195 ORFs were compared to the proteins of the GenBank non-redundant protein database using BLASTP, and Figure 3 shows the distribution by phylum of the best hits from this analysis. Only ∼15% of the most similar homologs (top BLASTP hits) in the GenBank database were proteins derived from other members of the phylum Chlorobi, with these best hits often coming from Chloroherpeton thalassium. Proteins from members of the Bacteroidetes, which share a common ancestor with members of the Chlorobi (Ludwig and Klenk, 2001; Ciccarelli et al., 2006), accounted for ∼26% of the most similar homologs. The remaining proteins, accounting for nearly 60% of the proteins in the genome, were either most similar to proteins of very distantly related organisms, including members of the Proteobacteria (16.2%), Firmicutes (9.0%), or “Others” (21.4%), or had no hits in the database (12.4%). The data in Figure 3 demonstrate the relative uniqueness of I. album within the broader context of current knowledge of the comparative genomics of other members of the Chlorobi. This distribution of most similar homologs will probably change significantly when the genomes of additional, early-diverging members of the Chlorobi are characterized, especially those belonging to organisms other than GSB. It should be noted that the absence of well-characterized close relatives of I. album inevitably increases the uncertainty of inferences about its metabolism and physiology.


Complete Genome of Ignavibacterium album, a Metabolically Versatile, Flagellated, Facultative Anaerobe from the Phylum Chlorobi.

Liu Z, Frigaard NU, Vogl K, Iino T, Ohkuma M, Overmann J, Bryant DA - Front Microbiol (2012)

Phylogenetic distribution of BLASTP best hits of I. album proteins compared to proteins in the NCBI nr database. An e-value cut-off of 0.001 was used.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3362086&req=5

Figure 3: Phylogenetic distribution of BLASTP best hits of I. album proteins compared to proteins in the NCBI nr database. An e-value cut-off of 0.001 was used.
Mentions: Ignavibacterium album has a single circular chromosome of 3,658,997 bp with a mol% G + C content of 34% (Figure 2). The genome includes one rRNA operon, 45 tRNA genes, and 3,195 predicted protein coding sequences (open reading frames, ORFs), and 2 ORFs with frameshift mutations encoding non-functional proteins. The 3,195 ORFs were compared to the proteins of the GenBank non-redundant protein database using BLASTP, and Figure 3 shows the distribution by phylum of the best hits from this analysis. Only ∼15% of the most similar homologs (top BLASTP hits) in the GenBank database were proteins derived from other members of the phylum Chlorobi, with these best hits often coming from Chloroherpeton thalassium. Proteins from members of the Bacteroidetes, which share a common ancestor with members of the Chlorobi (Ludwig and Klenk, 2001; Ciccarelli et al., 2006), accounted for ∼26% of the most similar homologs. The remaining proteins, accounting for nearly 60% of the proteins in the genome, were either most similar to proteins of very distantly related organisms, including members of the Proteobacteria (16.2%), Firmicutes (9.0%), or “Others” (21.4%), or had no hits in the database (12.4%). The data in Figure 3 demonstrate the relative uniqueness of I. album within the broader context of current knowledge of the comparative genomics of other members of the Chlorobi. This distribution of most similar homologs will probably change significantly when the genomes of additional, early-diverging members of the Chlorobi are characterized, especially those belonging to organisms other than GSB. It should be noted that the absence of well-characterized close relatives of I. album inevitably increases the uncertainty of inferences about its metabolism and physiology.

Bottom Line: The occurrence of genes encoding enzymes for CO(2) fixation as well as other enzymes of the reductive TCA cycle suggests that mixotrophy may be possible under certain growth conditions.However, known biosynthetic pathways for several amino acids are incomplete; this suggests that I. album is dependent upon on exogenous sources of these metabolites or employs novel biosynthetic pathways.Comparisons of I. album and other members of the phylum Chlorobi suggest that the physiology of the ancestors of this phylum might have been quite different from that of modern GSB.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University University Park, PA, USA.

ABSTRACT
Prior to the recent discovery of Ignavibacterium album (I. album), anaerobic photoautotrophic green sulfur bacteria (GSB) were the only members of the bacterial phylum Chlorobi that had been grown axenically. In contrast to GSB, sequence analysis of the 3.7-Mbp genome of I. album shows that this recently described member of the phylum Chlorobi is a chemoheterotroph with a versatile metabolism. I. album lacks genes for photosynthesis and sulfur oxidation but has a full set of genes for flagella and chemotaxis. The occurrence of genes for multiple electron transfer complexes suggests that I. album is capable of organoheterotrophy under both oxic and anoxic conditions. The occurrence of genes encoding enzymes for CO(2) fixation as well as other enzymes of the reductive TCA cycle suggests that mixotrophy may be possible under certain growth conditions. However, known biosynthetic pathways for several amino acids are incomplete; this suggests that I. album is dependent upon on exogenous sources of these metabolites or employs novel biosynthetic pathways. Comparisons of I. album and other members of the phylum Chlorobi suggest that the physiology of the ancestors of this phylum might have been quite different from that of modern GSB.

No MeSH data available.