Complete Genome of the Starch-Degrading Myxobacteria Sandaracinus amylolyticus DSM 53668(T)

Myxobacteria are members of δ-proteobacteria and are typified by large genomes, well-coordinated social behavior, gliding motility, and starvation-induced fruiting body formation. Here, we report the 10.33 Mb whole genome of a starch-degrading myxobacterium Sandaracinus amylolyticus DSM 53668(T) tha...

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Autores principales: Sharma, Gaurav, Khatri, Indu, Subramanian, Srikrishna
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5010890/
https://www.ncbi.nlm.nih.gov/pubmed/27358428
http://dx.doi.org/10.1093/gbe/evw151
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author Sharma, Gaurav
Khatri, Indu
Subramanian, Srikrishna
author_facet Sharma, Gaurav
Khatri, Indu
Subramanian, Srikrishna
author_sort Sharma, Gaurav
collection PubMed
description Myxobacteria are members of δ-proteobacteria and are typified by large genomes, well-coordinated social behavior, gliding motility, and starvation-induced fruiting body formation. Here, we report the 10.33 Mb whole genome of a starch-degrading myxobacterium Sandaracinus amylolyticus DSM 53668(T) that encodes 8,962 proteins, 56 tRNA, and two rRNA operons. Phylogenetic analysis, in silico DNA-DNA hybridization and average nucleotide identity reveal its divergence from other myxobacterial species and support its taxonomic characterization into a separate family Sandaracinaceae, within the suborder Sorangiineae. Sequence similarity searches using the Carbohydrate-active enzymes (CAZyme) database help identify the enzyme repertoire of S. amylolyticus involved in starch, agar, chitin, and cellulose degradation. We identified 16 α-amylases and two γ-amylases in the S. amylolyticus genome that likely play a role in starch degradation. While many of the amylases are seen conserved in other δ-proteobacteria, we notice several novel amylases acquired via horizontal transfer from members belonging to phylum Deinococcus-Thermus, Acidobacteria, and Cyanobacteria. No agar degrading enzyme(s) were identified in the S. amylolyticus genome. Interestingly, several putative β-glucosidases and endoglucanases proteins involved in cellulose degradation were identified. However, the absence of cellobiohydrolases/exoglucanases corroborates with the lack of cellulose degradation by this bacteria.
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spelling pubmed-50108902016-09-06 Complete Genome of the Starch-Degrading Myxobacteria Sandaracinus amylolyticus DSM 53668(T) Sharma, Gaurav Khatri, Indu Subramanian, Srikrishna Genome Biol Evol Genome Report Myxobacteria are members of δ-proteobacteria and are typified by large genomes, well-coordinated social behavior, gliding motility, and starvation-induced fruiting body formation. Here, we report the 10.33 Mb whole genome of a starch-degrading myxobacterium Sandaracinus amylolyticus DSM 53668(T) that encodes 8,962 proteins, 56 tRNA, and two rRNA operons. Phylogenetic analysis, in silico DNA-DNA hybridization and average nucleotide identity reveal its divergence from other myxobacterial species and support its taxonomic characterization into a separate family Sandaracinaceae, within the suborder Sorangiineae. Sequence similarity searches using the Carbohydrate-active enzymes (CAZyme) database help identify the enzyme repertoire of S. amylolyticus involved in starch, agar, chitin, and cellulose degradation. We identified 16 α-amylases and two γ-amylases in the S. amylolyticus genome that likely play a role in starch degradation. While many of the amylases are seen conserved in other δ-proteobacteria, we notice several novel amylases acquired via horizontal transfer from members belonging to phylum Deinococcus-Thermus, Acidobacteria, and Cyanobacteria. No agar degrading enzyme(s) were identified in the S. amylolyticus genome. Interestingly, several putative β-glucosidases and endoglucanases proteins involved in cellulose degradation were identified. However, the absence of cellobiohydrolases/exoglucanases corroborates with the lack of cellulose degradation by this bacteria. Oxford University Press 2016-06-29 /pmc/articles/PMC5010890/ /pubmed/27358428 http://dx.doi.org/10.1093/gbe/evw151 Text en © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Genome Report
Sharma, Gaurav
Khatri, Indu
Subramanian, Srikrishna
Complete Genome of the Starch-Degrading Myxobacteria Sandaracinus amylolyticus DSM 53668(T)
title Complete Genome of the Starch-Degrading Myxobacteria Sandaracinus amylolyticus DSM 53668(T)
title_full Complete Genome of the Starch-Degrading Myxobacteria Sandaracinus amylolyticus DSM 53668(T)
title_fullStr Complete Genome of the Starch-Degrading Myxobacteria Sandaracinus amylolyticus DSM 53668(T)
title_full_unstemmed Complete Genome of the Starch-Degrading Myxobacteria Sandaracinus amylolyticus DSM 53668(T)
title_short Complete Genome of the Starch-Degrading Myxobacteria Sandaracinus amylolyticus DSM 53668(T)
title_sort complete genome of the starch-degrading myxobacteria sandaracinus amylolyticus dsm 53668(t)
topic Genome Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5010890/
https://www.ncbi.nlm.nih.gov/pubmed/27358428
http://dx.doi.org/10.1093/gbe/evw151
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