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Insights Into the Phylogenetic Distribution, Diversity, Structural Attributes, and Substrate Specificity of Putative Cyanobacterial Orthocaspases
The functionality of caspase homologs in prokaryotic cell execution has been perceived, yet the dimensions of their metabolic pertinence are still cryptic. Here, a detailed in silico study on putative cyanobacterial caspase homologs, termed orthocaspases, in a sequenced genome of 132 strains was per...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8283722/ https://www.ncbi.nlm.nih.gov/pubmed/34276616 http://dx.doi.org/10.3389/fmicb.2021.682306 |
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author | Bhattacharjee, Samujjal Kharwar, Surbhi Mishra, Arun Kumar |
author_facet | Bhattacharjee, Samujjal Kharwar, Surbhi Mishra, Arun Kumar |
author_sort | Bhattacharjee, Samujjal |
collection | PubMed |
description | The functionality of caspase homologs in prokaryotic cell execution has been perceived, yet the dimensions of their metabolic pertinence are still cryptic. Here, a detailed in silico study on putative cyanobacterial caspase homologs, termed orthocaspases, in a sequenced genome of 132 strains was performed. We observed that 473 putative orthocaspases were distributed among 62% cyanobacterial strains subsumed within all the taxonomical orders. However, high diversity among these orthocaspases was also evident as the conventional histidine–cysteine (HC) dyad was present only in 72.03% of orthocaspases (wild-type), whereas the rest 28.18% were pseudo-variants having substituted the catalytic dyad. Besides, the presence of various accessory functional domains with Peptidase C14 probably suggested the multifunctionality of the orthocaspases. Moreover, the early origin and emergence of wild-type orthocaspases were conferred by their presence in Gloeobacter; however, the complex phylogeny displayed by these caspase-homologs perhaps suggested horizontal a gene transfer for their acquisition. However, morpho-physiological advancements and larger genome size favored the acquisition of orthocaspases. Moreover, the conserved caspase hemoglobinase fold not only in the wild-type but also in the pseudo-orthocaspases in Nostoc sp. PCC 7120 ascertained the least effect of catalytic motifs in the protein tertiary structure. Further, the 100-ns molecular dynamic simulation and molecular mechanics/generalized born surface area exhibited stable binding of arginylarginine dipeptide with wild-type orthocaspase of Nostoc sp. PCC 7120, displaying arginine-P1 specificity of wild-type orthocaspases. This study deciphered the distribution, diversity, domain architecture, structure, and basic substrate specificity of putative cyanobacterial orthocaspases, which may aid in functional investigations in the future. |
format | Online Article Text |
id | pubmed-8283722 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-82837222021-07-17 Insights Into the Phylogenetic Distribution, Diversity, Structural Attributes, and Substrate Specificity of Putative Cyanobacterial Orthocaspases Bhattacharjee, Samujjal Kharwar, Surbhi Mishra, Arun Kumar Front Microbiol Microbiology The functionality of caspase homologs in prokaryotic cell execution has been perceived, yet the dimensions of their metabolic pertinence are still cryptic. Here, a detailed in silico study on putative cyanobacterial caspase homologs, termed orthocaspases, in a sequenced genome of 132 strains was performed. We observed that 473 putative orthocaspases were distributed among 62% cyanobacterial strains subsumed within all the taxonomical orders. However, high diversity among these orthocaspases was also evident as the conventional histidine–cysteine (HC) dyad was present only in 72.03% of orthocaspases (wild-type), whereas the rest 28.18% were pseudo-variants having substituted the catalytic dyad. Besides, the presence of various accessory functional domains with Peptidase C14 probably suggested the multifunctionality of the orthocaspases. Moreover, the early origin and emergence of wild-type orthocaspases were conferred by their presence in Gloeobacter; however, the complex phylogeny displayed by these caspase-homologs perhaps suggested horizontal a gene transfer for their acquisition. However, morpho-physiological advancements and larger genome size favored the acquisition of orthocaspases. Moreover, the conserved caspase hemoglobinase fold not only in the wild-type but also in the pseudo-orthocaspases in Nostoc sp. PCC 7120 ascertained the least effect of catalytic motifs in the protein tertiary structure. Further, the 100-ns molecular dynamic simulation and molecular mechanics/generalized born surface area exhibited stable binding of arginylarginine dipeptide with wild-type orthocaspase of Nostoc sp. PCC 7120, displaying arginine-P1 specificity of wild-type orthocaspases. This study deciphered the distribution, diversity, domain architecture, structure, and basic substrate specificity of putative cyanobacterial orthocaspases, which may aid in functional investigations in the future. Frontiers Media S.A. 2021-07-02 /pmc/articles/PMC8283722/ /pubmed/34276616 http://dx.doi.org/10.3389/fmicb.2021.682306 Text en Copyright © 2021 Bhattacharjee, Kharwar and Mishra. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Bhattacharjee, Samujjal Kharwar, Surbhi Mishra, Arun Kumar Insights Into the Phylogenetic Distribution, Diversity, Structural Attributes, and Substrate Specificity of Putative Cyanobacterial Orthocaspases |
title | Insights Into the Phylogenetic Distribution, Diversity, Structural Attributes, and Substrate Specificity of Putative Cyanobacterial Orthocaspases |
title_full | Insights Into the Phylogenetic Distribution, Diversity, Structural Attributes, and Substrate Specificity of Putative Cyanobacterial Orthocaspases |
title_fullStr | Insights Into the Phylogenetic Distribution, Diversity, Structural Attributes, and Substrate Specificity of Putative Cyanobacterial Orthocaspases |
title_full_unstemmed | Insights Into the Phylogenetic Distribution, Diversity, Structural Attributes, and Substrate Specificity of Putative Cyanobacterial Orthocaspases |
title_short | Insights Into the Phylogenetic Distribution, Diversity, Structural Attributes, and Substrate Specificity of Putative Cyanobacterial Orthocaspases |
title_sort | insights into the phylogenetic distribution, diversity, structural attributes, and substrate specificity of putative cyanobacterial orthocaspases |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8283722/ https://www.ncbi.nlm.nih.gov/pubmed/34276616 http://dx.doi.org/10.3389/fmicb.2021.682306 |
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