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Enantioselective Utilization of D-Amino Acids by Deep-Sea Microorganisms.

Kubota T, Kobayashi T, Nunoura T, Maruyama F, Deguchi S - Front Microbiol (2016)

Bottom Line: Microorganisms that utilize various D-amino acids (DAAs) were successfully isolated from deep-sea sediments.In contrast, the Nautella strains isolated from shallow-sea grew only with L-Val.No significant differences were found among the strains in the genome sequences including genes possibly related to DAA metabolisms.

View Article: PubMed Central - PubMed

Affiliation: Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan.

ABSTRACT
Microorganisms that utilize various D-amino acids (DAAs) were successfully isolated from deep-sea sediments. The isolates were phylogenetically assigned to Alphaproteobacteria, Gammmaproteobacteria, and Bacilli. Some of the isolates exhibited high enantioselective degradation activities to various DAAs. In particular, the Alphaproteobacteria Nautella sp. strain A04V exhibited robust growth in minimal medium supplemented with D-Val as a sole carbon and nitrogen source, whereas its growth was poor on minimal medium supplemented with L-Val instead of D-Val. Its growth was facilitated most when racemic mixtures of valine were used. In contrast, the Nautella strains isolated from shallow-sea grew only with L-Val. No significant differences were found among the strains in the genome sequences including genes possibly related to DAA metabolisms.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree based on the 16S rRNA gene sequences of D-amino acid-degrading isolates from deep-sea sediments. Thermotoga maritima MSB-8 was used as an outgroup. The phylogenetic tree was constructed using the neighbor-joining method (Saitou and Nei, 1987). The accession numbers of the sequences are shown in parentheses. Numbers at each node indicate the bootstrap value based on 1000 replicates. Strains obtained in this study are shown in bold and the first letter of the strain number indicates the screening medium used: DAM (A) or DBM (B). Figures following the strain numbers are identifiers employed in this study.
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Figure 1: Phylogenetic tree based on the 16S rRNA gene sequences of D-amino acid-degrading isolates from deep-sea sediments. Thermotoga maritima MSB-8 was used as an outgroup. The phylogenetic tree was constructed using the neighbor-joining method (Saitou and Nei, 1987). The accession numbers of the sequences are shown in parentheses. Numbers at each node indicate the bootstrap value based on 1000 replicates. Strains obtained in this study are shown in bold and the first letter of the strain number indicates the screening medium used: DAM (A) or DBM (B). Figures following the strain numbers are identifiers employed in this study.

Mentions: Partial nucleotide sequences (0.8–1.4 kb) of the 16S rRNA genes of the 28 isolates showed that 17 strains belonged to Alphaproteobacteria, 5 strains belonged to Gammaproteobacteria, and 6 strains belonged to Bacilli (Figure 1). There were no significant relationships between the taxonomic diversity of the DAA-degrading bacteria and the two types of screening media used for their enrichment and isolation.


Enantioselective Utilization of D-Amino Acids by Deep-Sea Microorganisms.

Kubota T, Kobayashi T, Nunoura T, Maruyama F, Deguchi S - Front Microbiol (2016)

Phylogenetic tree based on the 16S rRNA gene sequences of D-amino acid-degrading isolates from deep-sea sediments. Thermotoga maritima MSB-8 was used as an outgroup. The phylogenetic tree was constructed using the neighbor-joining method (Saitou and Nei, 1987). The accession numbers of the sequences are shown in parentheses. Numbers at each node indicate the bootstrap value based on 1000 replicates. Strains obtained in this study are shown in bold and the first letter of the strain number indicates the screening medium used: DAM (A) or DBM (B). Figures following the strain numbers are identifiers employed in this study.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4836201&req=5

Figure 1: Phylogenetic tree based on the 16S rRNA gene sequences of D-amino acid-degrading isolates from deep-sea sediments. Thermotoga maritima MSB-8 was used as an outgroup. The phylogenetic tree was constructed using the neighbor-joining method (Saitou and Nei, 1987). The accession numbers of the sequences are shown in parentheses. Numbers at each node indicate the bootstrap value based on 1000 replicates. Strains obtained in this study are shown in bold and the first letter of the strain number indicates the screening medium used: DAM (A) or DBM (B). Figures following the strain numbers are identifiers employed in this study.
Mentions: Partial nucleotide sequences (0.8–1.4 kb) of the 16S rRNA genes of the 28 isolates showed that 17 strains belonged to Alphaproteobacteria, 5 strains belonged to Gammaproteobacteria, and 6 strains belonged to Bacilli (Figure 1). There were no significant relationships between the taxonomic diversity of the DAA-degrading bacteria and the two types of screening media used for their enrichment and isolation.

Bottom Line: Microorganisms that utilize various D-amino acids (DAAs) were successfully isolated from deep-sea sediments.In contrast, the Nautella strains isolated from shallow-sea grew only with L-Val.No significant differences were found among the strains in the genome sequences including genes possibly related to DAA metabolisms.

View Article: PubMed Central - PubMed

Affiliation: Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan.

ABSTRACT
Microorganisms that utilize various D-amino acids (DAAs) were successfully isolated from deep-sea sediments. The isolates were phylogenetically assigned to Alphaproteobacteria, Gammmaproteobacteria, and Bacilli. Some of the isolates exhibited high enantioselective degradation activities to various DAAs. In particular, the Alphaproteobacteria Nautella sp. strain A04V exhibited robust growth in minimal medium supplemented with D-Val as a sole carbon and nitrogen source, whereas its growth was poor on minimal medium supplemented with L-Val instead of D-Val. Its growth was facilitated most when racemic mixtures of valine were used. In contrast, the Nautella strains isolated from shallow-sea grew only with L-Val. No significant differences were found among the strains in the genome sequences including genes possibly related to DAA metabolisms.

No MeSH data available.


Related in: MedlinePlus