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Phenotypic and Genomic Properties of Chitinispirillum alkaliphilum gen. nov., sp. nov., A Haloalkaliphilic Anaerobic Chitinolytic Bacterium Representing a Novel Class in the Phylum Fibrobacteres.

Sorokin DY, Rakitin AL, Gumerov VM, Beletsky AV, Sinninghe Damsté JS, Mardanov AV, Ravin NV - Front Microbiol (2016)

Bottom Line: The chitinolytic activity was associated with cells.Analysis of the 4.4 Mb draft genome identified pathways for chitin utilization, particularly, secreted chitinases linked to the cell surface, as well as genes for the hydrolysis of other polysaccharides and fermentation of sugars, while the genes needed for aerobic and anaerobic respiration were absent.The phylogenetic analysis using 16S rRNA gene and ribosomal proteins indicated that ACht6-1 forms a novel deep lineage at the class level within the bacterial candidate division TG3.

View Article: PubMed Central - PubMed

Affiliation: Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of SciencesMoscow, Russia; Department of Biotechnology, Delft University of TechnologyDelft, Netherlands.

ABSTRACT
Anaerobic enrichment from sediments of hypersaline alkaline lakes in Wadi el Natrun (Egypt) with chitin resulted in the isolation of a fermentative haloalkaliphilic bacterium, strain ACht6-1, growing exclusively with insoluble chitin as the substrate in a sodium carbonate-based medium at pH 8.5-10.5 and total Na(+) concentrations from 0.4 to 1.75 M. The isolate had a Gram-negative cell wall and formed lipid cysts in old cultures. The chitinolytic activity was associated with cells. Analysis of the 4.4 Mb draft genome identified pathways for chitin utilization, particularly, secreted chitinases linked to the cell surface, as well as genes for the hydrolysis of other polysaccharides and fermentation of sugars, while the genes needed for aerobic and anaerobic respiration were absent. Adaptation to a haloalkaliphilic lifestyle was reflected by the gene repertoire encoding sodium rather than proton-dependent membrane-bound ion pumps, including the Rnf-type complex, oxaloacetate decarboxylase, V-type ATPase, and pyrophosphatase. The phylogenetic analysis using 16S rRNA gene and ribosomal proteins indicated that ACht6-1 forms a novel deep lineage at the class level within the bacterial candidate division TG3. Based on phylogenetic, phenotypic and genomic analyses, the novel chitinolytic bacterium is described as Chitinispirillum alkaliphilum gen. nov., sp. nov., within a novel class Chitinispirillia that could be included into the phylum Fibrobacteres.

No MeSH data available.


Related in: MedlinePlus

Chitin degradation in ACht6-1.(A) Schematic representation of domain structure of the GH18, GH19, and GH20 family hydrolases from ACht6-1. C, ChiC chitin-binding domain; Por, Por secretion system C-terminal sorting domain; GH, glycoside hydrolase catalytic domain; S, signal peptide. Domain localization is shown according to results of BLASTP searches against NCBI’s conserved domain database. The bar at the bottom of the figure showed coordinates of the amino acid residues in the predicted proteins. (B) Predicted pathways for degradation, transport and metabolism of chitin by strain ACht6-1. Enzymes are given gene identifiers from ACht6-1 when possible. Abbreviations: OM, outer membrane; PP, periplasm; CP, cytoplasm.
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Figure 4: Chitin degradation in ACht6-1.(A) Schematic representation of domain structure of the GH18, GH19, and GH20 family hydrolases from ACht6-1. C, ChiC chitin-binding domain; Por, Por secretion system C-terminal sorting domain; GH, glycoside hydrolase catalytic domain; S, signal peptide. Domain localization is shown according to results of BLASTP searches against NCBI’s conserved domain database. The bar at the bottom of the figure showed coordinates of the amino acid residues in the predicted proteins. (B) Predicted pathways for degradation, transport and metabolism of chitin by strain ACht6-1. Enzymes are given gene identifiers from ACht6-1 when possible. Abbreviations: OM, outer membrane; PP, periplasm; CP, cytoplasm.

Mentions: The phenotypic hallmark of ACht6-1 is its ability to utilize as a growth substrate insoluble chitin, but not soluble chito-oligomers or N-acetyl glucosamine, or any other polymers. The predicted chitin degradation pathway of ACht6-1 (summarized in Figure 4) is mostly similar to that found in Chv. alkaliphilus (Sorokin et al., 2014), in spite of limited sequence similarity of the enzymes involved.


Phenotypic and Genomic Properties of Chitinispirillum alkaliphilum gen. nov., sp. nov., A Haloalkaliphilic Anaerobic Chitinolytic Bacterium Representing a Novel Class in the Phylum Fibrobacteres.

Sorokin DY, Rakitin AL, Gumerov VM, Beletsky AV, Sinninghe Damsté JS, Mardanov AV, Ravin NV - Front Microbiol (2016)

Chitin degradation in ACht6-1.(A) Schematic representation of domain structure of the GH18, GH19, and GH20 family hydrolases from ACht6-1. C, ChiC chitin-binding domain; Por, Por secretion system C-terminal sorting domain; GH, glycoside hydrolase catalytic domain; S, signal peptide. Domain localization is shown according to results of BLASTP searches against NCBI’s conserved domain database. The bar at the bottom of the figure showed coordinates of the amino acid residues in the predicted proteins. (B) Predicted pathways for degradation, transport and metabolism of chitin by strain ACht6-1. Enzymes are given gene identifiers from ACht6-1 when possible. Abbreviations: OM, outer membrane; PP, periplasm; CP, cytoplasm.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4814513&req=5

Figure 4: Chitin degradation in ACht6-1.(A) Schematic representation of domain structure of the GH18, GH19, and GH20 family hydrolases from ACht6-1. C, ChiC chitin-binding domain; Por, Por secretion system C-terminal sorting domain; GH, glycoside hydrolase catalytic domain; S, signal peptide. Domain localization is shown according to results of BLASTP searches against NCBI’s conserved domain database. The bar at the bottom of the figure showed coordinates of the amino acid residues in the predicted proteins. (B) Predicted pathways for degradation, transport and metabolism of chitin by strain ACht6-1. Enzymes are given gene identifiers from ACht6-1 when possible. Abbreviations: OM, outer membrane; PP, periplasm; CP, cytoplasm.
Mentions: The phenotypic hallmark of ACht6-1 is its ability to utilize as a growth substrate insoluble chitin, but not soluble chito-oligomers or N-acetyl glucosamine, or any other polymers. The predicted chitin degradation pathway of ACht6-1 (summarized in Figure 4) is mostly similar to that found in Chv. alkaliphilus (Sorokin et al., 2014), in spite of limited sequence similarity of the enzymes involved.

Bottom Line: The chitinolytic activity was associated with cells.Analysis of the 4.4 Mb draft genome identified pathways for chitin utilization, particularly, secreted chitinases linked to the cell surface, as well as genes for the hydrolysis of other polysaccharides and fermentation of sugars, while the genes needed for aerobic and anaerobic respiration were absent.The phylogenetic analysis using 16S rRNA gene and ribosomal proteins indicated that ACht6-1 forms a novel deep lineage at the class level within the bacterial candidate division TG3.

View Article: PubMed Central - PubMed

Affiliation: Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of SciencesMoscow, Russia; Department of Biotechnology, Delft University of TechnologyDelft, Netherlands.

ABSTRACT
Anaerobic enrichment from sediments of hypersaline alkaline lakes in Wadi el Natrun (Egypt) with chitin resulted in the isolation of a fermentative haloalkaliphilic bacterium, strain ACht6-1, growing exclusively with insoluble chitin as the substrate in a sodium carbonate-based medium at pH 8.5-10.5 and total Na(+) concentrations from 0.4 to 1.75 M. The isolate had a Gram-negative cell wall and formed lipid cysts in old cultures. The chitinolytic activity was associated with cells. Analysis of the 4.4 Mb draft genome identified pathways for chitin utilization, particularly, secreted chitinases linked to the cell surface, as well as genes for the hydrolysis of other polysaccharides and fermentation of sugars, while the genes needed for aerobic and anaerobic respiration were absent. Adaptation to a haloalkaliphilic lifestyle was reflected by the gene repertoire encoding sodium rather than proton-dependent membrane-bound ion pumps, including the Rnf-type complex, oxaloacetate decarboxylase, V-type ATPase, and pyrophosphatase. The phylogenetic analysis using 16S rRNA gene and ribosomal proteins indicated that ACht6-1 forms a novel deep lineage at the class level within the bacterial candidate division TG3. Based on phylogenetic, phenotypic and genomic analyses, the novel chitinolytic bacterium is described as Chitinispirillum alkaliphilum gen. nov., sp. nov., within a novel class Chitinispirillia that could be included into the phylum Fibrobacteres.

No MeSH data available.


Related in: MedlinePlus