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Deciphering the genome of polyphosphate accumulating actinobacterium Microlunatus phosphovorus.

Kawakoshi A, Nakazawa H, Fukada J, Sasagawa M, Katano Y, Nakamura S, Hosoyama A, Sasaki H, Ichikawa N, Hanada S, Kamagata Y, Nakamura K, Yamazaki S, Fujita N - DNA Res. (2012)

Bottom Line: The number of genes for polyP metabolism was greater in M. phosphovorus than in other actinobacteria; it possesses genes for four polyP kinases (ppks), two polyP-dependent glucokinases (ppgks), and three phosphate transporters (pits).Furthermore, M. phosphovorus lacks the phaABC genes for PHA synthesis and the actP gene encoding an acetate/H(+) symporter, both of which play crucial roles in anaerobic PHA accumulation in proteobacterial PAOs.Thus, while the general features of M. phosphovorus regarding aerobic polyP accumulation are similar to those of proteobacterial PAOs, its anaerobic polyP use and PHA synthesis appear to be different.

View Article: PubMed Central - PubMed

Affiliation: Biological Resource Center, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Tokyo 151-0066, Japan.

ABSTRACT
Polyphosphate accumulating organisms (PAOs) belong mostly to Proteobacteria and Actinobacteria and are quite divergent. Under aerobic conditions, they accumulate intracellular polyphosphate (polyP), while they typically synthesize polyhydroxyalkanoates (PHAs) under anaerobic conditions. Many ecological, physiological, and genomic analyses have been performed with proteobacterial PAOs, but few with actinobacterial PAOs. In this study, the whole genome sequence of an actinobacterial PAO, Microlunatus phosphovorus NM-1(T) (NBRC 101784(T)), was determined. The number of genes for polyP metabolism was greater in M. phosphovorus than in other actinobacteria; it possesses genes for four polyP kinases (ppks), two polyP-dependent glucokinases (ppgks), and three phosphate transporters (pits). In contrast, it harbours only a single ppx gene for exopolyphosphatase, although two copies of ppx are generally present in other actinobacteria. Furthermore, M. phosphovorus lacks the phaABC genes for PHA synthesis and the actP gene encoding an acetate/H(+) symporter, both of which play crucial roles in anaerobic PHA accumulation in proteobacterial PAOs. Thus, while the general features of M. phosphovorus regarding aerobic polyP accumulation are similar to those of proteobacterial PAOs, its anaerobic polyP use and PHA synthesis appear to be different.

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Schematic representation of the circular chromosome of M. phosphovorus. From the periphery toward the centre, circles indicate the scale in Mbp, ORFs predicted on the forward and reverse strands, tRNA genes, rRNA operon, G + C contents, and GC skew.
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DSS020F1: Schematic representation of the circular chromosome of M. phosphovorus. From the periphery toward the centre, circles indicate the scale in Mbp, ORFs predicted on the forward and reverse strands, tRNA genes, rRNA operon, G + C contents, and GC skew.

Mentions: The genome consisted of a single circular chromosome of 5 683 123 bp with an average G + C content of 67.3% (Fig. 1). No plasmid DNA sequence was detected. The chromosome was predicted to encode 5360 protein-coding genes, 46 transfer RNA genes, and a set of ribosomal RNA genes (16S, 23S, and 5S). Of the 5360 predicted protein-coding genes, 4887 (91%) were orthologous or had similarity to genes of known function or to hypothetical genes (E-value of <0.001), and the remaining 473 (9%) showed no significant similarity to any registered genes. After manual curation, 1999 (37%) genes could be assigned to known biological roles. Microlunatus phosphovorus harboured only a single rRNA operon, a significant finding given its relatively large genome. The general features of the M. phosphovorus genome are compared with those of 14 other actinobacterial species in Supplementary Table S1. In this comparison, target genomes were selected to represent each taxonomic rank from the genus Microlunatus stepwise to the class Actinobacteria. Supplementary Table S2 shows the distribution of ORFs in COG functional categories. No significant overrepresentation or underrepresentation of any particular functional category in M. phosphovorus was observed except that a higher percentage of ORFs was categorised as ‘function unknown’ in M. phosphovorus than in other actinobacteria.Figure 1.


Deciphering the genome of polyphosphate accumulating actinobacterium Microlunatus phosphovorus.

Kawakoshi A, Nakazawa H, Fukada J, Sasagawa M, Katano Y, Nakamura S, Hosoyama A, Sasaki H, Ichikawa N, Hanada S, Kamagata Y, Nakamura K, Yamazaki S, Fujita N - DNA Res. (2012)

Schematic representation of the circular chromosome of M. phosphovorus. From the periphery toward the centre, circles indicate the scale in Mbp, ORFs predicted on the forward and reverse strands, tRNA genes, rRNA operon, G + C contents, and GC skew.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3473371&req=5

DSS020F1: Schematic representation of the circular chromosome of M. phosphovorus. From the periphery toward the centre, circles indicate the scale in Mbp, ORFs predicted on the forward and reverse strands, tRNA genes, rRNA operon, G + C contents, and GC skew.
Mentions: The genome consisted of a single circular chromosome of 5 683 123 bp with an average G + C content of 67.3% (Fig. 1). No plasmid DNA sequence was detected. The chromosome was predicted to encode 5360 protein-coding genes, 46 transfer RNA genes, and a set of ribosomal RNA genes (16S, 23S, and 5S). Of the 5360 predicted protein-coding genes, 4887 (91%) were orthologous or had similarity to genes of known function or to hypothetical genes (E-value of <0.001), and the remaining 473 (9%) showed no significant similarity to any registered genes. After manual curation, 1999 (37%) genes could be assigned to known biological roles. Microlunatus phosphovorus harboured only a single rRNA operon, a significant finding given its relatively large genome. The general features of the M. phosphovorus genome are compared with those of 14 other actinobacterial species in Supplementary Table S1. In this comparison, target genomes were selected to represent each taxonomic rank from the genus Microlunatus stepwise to the class Actinobacteria. Supplementary Table S2 shows the distribution of ORFs in COG functional categories. No significant overrepresentation or underrepresentation of any particular functional category in M. phosphovorus was observed except that a higher percentage of ORFs was categorised as ‘function unknown’ in M. phosphovorus than in other actinobacteria.Figure 1.

Bottom Line: The number of genes for polyP metabolism was greater in M. phosphovorus than in other actinobacteria; it possesses genes for four polyP kinases (ppks), two polyP-dependent glucokinases (ppgks), and three phosphate transporters (pits).Furthermore, M. phosphovorus lacks the phaABC genes for PHA synthesis and the actP gene encoding an acetate/H(+) symporter, both of which play crucial roles in anaerobic PHA accumulation in proteobacterial PAOs.Thus, while the general features of M. phosphovorus regarding aerobic polyP accumulation are similar to those of proteobacterial PAOs, its anaerobic polyP use and PHA synthesis appear to be different.

View Article: PubMed Central - PubMed

Affiliation: Biological Resource Center, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Tokyo 151-0066, Japan.

ABSTRACT
Polyphosphate accumulating organisms (PAOs) belong mostly to Proteobacteria and Actinobacteria and are quite divergent. Under aerobic conditions, they accumulate intracellular polyphosphate (polyP), while they typically synthesize polyhydroxyalkanoates (PHAs) under anaerobic conditions. Many ecological, physiological, and genomic analyses have been performed with proteobacterial PAOs, but few with actinobacterial PAOs. In this study, the whole genome sequence of an actinobacterial PAO, Microlunatus phosphovorus NM-1(T) (NBRC 101784(T)), was determined. The number of genes for polyP metabolism was greater in M. phosphovorus than in other actinobacteria; it possesses genes for four polyP kinases (ppks), two polyP-dependent glucokinases (ppgks), and three phosphate transporters (pits). In contrast, it harbours only a single ppx gene for exopolyphosphatase, although two copies of ppx are generally present in other actinobacteria. Furthermore, M. phosphovorus lacks the phaABC genes for PHA synthesis and the actP gene encoding an acetate/H(+) symporter, both of which play crucial roles in anaerobic PHA accumulation in proteobacterial PAOs. Thus, while the general features of M. phosphovorus regarding aerobic polyP accumulation are similar to those of proteobacterial PAOs, its anaerobic polyP use and PHA synthesis appear to be different.

Show MeSH
Related in: MedlinePlus