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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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Molecular phylogenetic analyses of the (A) polyP kinase family (PPK1, PPK2 and PAP) in bacteria, (B) exopolyphosphatase family (PPX1 and PPX2) in actinobacteria, (C) glucokinase family (PPGK and GK) in prokaryotes, with some eukaryotes, and (D) phosphate transporters (Pit) in actinobacteria and proteobacteria. Trees were constructed using the distance matrix method in ClustalX. Amino acid sequences deduced from nucleotide sequences were used as operational taxonomic units (OTUs) for the analyses. All topologies agreed with those of maximum parsimony analyses in PHYLIP. The numbers on interior nodes are bootstrap percentages. Single and double asterisks indicate OTUs in which the polyP-synthetic or degradative reaction is dominant, respectively, and the abbreviation ‘U. C.’ indicates a cluster for which the function has yet to be characterised.
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DSS020F2: Molecular phylogenetic analyses of the (A) polyP kinase family (PPK1, PPK2 and PAP) in bacteria, (B) exopolyphosphatase family (PPX1 and PPX2) in actinobacteria, (C) glucokinase family (PPGK and GK) in prokaryotes, with some eukaryotes, and (D) phosphate transporters (Pit) in actinobacteria and proteobacteria. Trees were constructed using the distance matrix method in ClustalX. Amino acid sequences deduced from nucleotide sequences were used as operational taxonomic units (OTUs) for the analyses. All topologies agreed with those of maximum parsimony analyses in PHYLIP. The numbers on interior nodes are bootstrap percentages. Single and double asterisks indicate OTUs in which the polyP-synthetic or degradative reaction is dominant, respectively, and the abbreviation ‘U. C.’ indicates a cluster for which the function has yet to be characterised.

Mentions: Four putative PPK genes were identified in the M. phosphovorus genome; a single ppk1 (MLP_47700) and three ppk2 (MLP_05750, MLP_50300, and MLP_23310) homologues. The number of ppk homologues in M. phosphovorus was relatively large; usually 1–4 ppk homologues exist in an actinobacterial genome (Table 1). Based on the similarity of deduced amino acid sequences, one of the M. phosphovorus PPK2s (MLP_05750) was of the C. glutamicum type (63% identity), whereas the other (MLP_50300) was of the Myc. tuberculosis type (78% identity; Fig. 2a). The third ppk2 homologue (MLP_23310) was relatively similar to both ppk2 and pap, but was located in a distinct cluster of undetermined function (Fig. 2a).Table 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)

Molecular phylogenetic analyses of the (A) polyP kinase family (PPK1, PPK2 and PAP) in bacteria, (B) exopolyphosphatase family (PPX1 and PPX2) in actinobacteria, (C) glucokinase family (PPGK and GK) in prokaryotes, with some eukaryotes, and (D) phosphate transporters (Pit) in actinobacteria and proteobacteria. Trees were constructed using the distance matrix method in ClustalX. Amino acid sequences deduced from nucleotide sequences were used as operational taxonomic units (OTUs) for the analyses. All topologies agreed with those of maximum parsimony analyses in PHYLIP. The numbers on interior nodes are bootstrap percentages. Single and double asterisks indicate OTUs in which the polyP-synthetic or degradative reaction is dominant, respectively, and the abbreviation ‘U. C.’ indicates a cluster for which the function has yet to be characterised.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSS020F2: Molecular phylogenetic analyses of the (A) polyP kinase family (PPK1, PPK2 and PAP) in bacteria, (B) exopolyphosphatase family (PPX1 and PPX2) in actinobacteria, (C) glucokinase family (PPGK and GK) in prokaryotes, with some eukaryotes, and (D) phosphate transporters (Pit) in actinobacteria and proteobacteria. Trees were constructed using the distance matrix method in ClustalX. Amino acid sequences deduced from nucleotide sequences were used as operational taxonomic units (OTUs) for the analyses. All topologies agreed with those of maximum parsimony analyses in PHYLIP. The numbers on interior nodes are bootstrap percentages. Single and double asterisks indicate OTUs in which the polyP-synthetic or degradative reaction is dominant, respectively, and the abbreviation ‘U. C.’ indicates a cluster for which the function has yet to be characterised.
Mentions: Four putative PPK genes were identified in the M. phosphovorus genome; a single ppk1 (MLP_47700) and three ppk2 (MLP_05750, MLP_50300, and MLP_23310) homologues. The number of ppk homologues in M. phosphovorus was relatively large; usually 1–4 ppk homologues exist in an actinobacterial genome (Table 1). Based on the similarity of deduced amino acid sequences, one of the M. phosphovorus PPK2s (MLP_05750) was of the C. glutamicum type (63% identity), whereas the other (MLP_50300) was of the Myc. tuberculosis type (78% identity; Fig. 2a). The third ppk2 homologue (MLP_23310) was relatively similar to both ppk2 and pap, but was located in a distinct cluster of undetermined function (Fig. 2a).Table 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