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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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Oxford University Press
2016
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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. |
format | Online Article Text |
id | pubmed-5010890 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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