Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae

The genus Parapedobacter was established to describe a novel genus within the family Sphingobacteriaceae and derives its name from Pedobacter, with which it is shown to be evolutionarily related. Despite this, Parapedobacter and Pedobacter do not share very high 16S rRNA gene sequence similarities....

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Main Authors: Shekhar Nagar, Chandni Talwar, Shazia Haider, Akshita Puri, Kalaiarasan Ponnusamy, Madhuri Gupta, Utkarsh Sood, Abhay Bajaj, Rup Lal, Roshan Kumar
Format: Article
Language:English
Published: Frontiers Media S.A. 2020-09-01
Series:Frontiers in Microbiology
Subjects:
Online Access:https://www.frontiersin.org/article/10.3389/fmicb.2020.01725/full
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spelling doaj-36238c4377c141b2967fc6c0d8c608d32020-11-25T03:21:55ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2020-09-011110.3389/fmicb.2020.01725544133Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family SphingobacteriaceaeShekhar Nagar0Chandni Talwar1Shazia Haider2Akshita Puri3Akshita Puri4Kalaiarasan Ponnusamy5Madhuri Gupta6Utkarsh Sood7Utkarsh Sood8Abhay Bajaj9Abhay Bajaj10Rup Lal11Rup Lal12Roshan Kumar13Roshan Kumar14Department of Zoology, University of Delhi, Delhi, IndiaDepartment of Zoology, University of Delhi, Delhi, IndiaDepartment of Biotechnology, Jaypee Institute of Information Technology, Noida, IndiaDepartment of Zoology, University of Delhi, Delhi, IndiaP.G.T.D, Zoology, R.T.M Nagpur University, Nagpur, IndiaSchool of Biotechnology, Jawaharlal Nehru University, New Delhi, IndiaDepartment of Zoology, University of Delhi, Delhi, IndiaDepartment of Zoology, University of Delhi, Delhi, IndiaThe Energy and Resources Institute, New Delhi, IndiaDepartment of Zoology, University of Delhi, Delhi, IndiaEnvironmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, IndiaDepartment of Zoology, University of Delhi, Delhi, IndiaThe Energy and Resources Institute, New Delhi, IndiaDepartment of Zoology, University of Delhi, Delhi, IndiaP.G. Department of Zoology, Magadh University, Bodh Gaya, IndiaThe genus Parapedobacter was established to describe a novel genus within the family Sphingobacteriaceae and derives its name from Pedobacter, with which it is shown to be evolutionarily related. Despite this, Parapedobacter and Pedobacter do not share very high 16S rRNA gene sequence similarities. Therefore, we hypothesized whether these substantial differences at the 16S rRNA gene level depict the true phylogeny or that these genomes have actually diverged. Thus, we performed genomic analysis of the four available genomes of Parapedobacter to better understand their phylogenomic position within family Sphingobacteriaceae. Our results demonstrated that Parapedobacter is more closely related to species of Olivibacter, as opposed to the genus Pedobacter. Further, we identified a significant class of enzymes called pectinases with potential industrial applications within the genomes of Parapedobacter luteus DSM 22899T and Parapedobacter composti DSM 22900T. These enzymes, specifically pectinesterases and pectate lyases, are presumed to have largely different catalytic activities based on very low sequence similarities to already known enzymes and thus may be exploited for industrial applications. We also determined the complete Bacteroides aerotolerance (Bat) operon (batA, batB, batC, batD, batE, hypothetical protein, moxR, and pa3071) within the genome of Parapedobacter indicus RK1T. This expands the definition of genus Parapedobacter to containing members that are able to tolerate oxygen stress using encoded oxidative stress responsive systems. By conducting a signal propagation network analysis, we determined that BatD, BatE, and hypothetical proteins are the major controlling hubs that drive the expression of Bat operon. As a key metabolic difference, we also annotated the complete iol operon within the P. indicus RK1T genome for utilization of all three stereoisomers of inositol, namely myo-inositol, scyllo-inositol, and 1D-chiro-inositol, which are abundant sources of organic phosphate found in soils. The results suggest that the genus Parapedobacter holds promising applications owing to its environmentally relevant genomic adaptations, which may be exploited in the future.https://www.frontiersin.org/article/10.3389/fmicb.2020.01725/fullParapedobacterBat operonpectinasesinositolortholog analysis
collection DOAJ
language English
format Article
sources DOAJ
author Shekhar Nagar
Chandni Talwar
Shazia Haider
Akshita Puri
Akshita Puri
Kalaiarasan Ponnusamy
Madhuri Gupta
Utkarsh Sood
Utkarsh Sood
Abhay Bajaj
Abhay Bajaj
Rup Lal
Rup Lal
Roshan Kumar
Roshan Kumar
spellingShingle Shekhar Nagar
Chandni Talwar
Shazia Haider
Akshita Puri
Akshita Puri
Kalaiarasan Ponnusamy
Madhuri Gupta
Utkarsh Sood
Utkarsh Sood
Abhay Bajaj
Abhay Bajaj
Rup Lal
Rup Lal
Roshan Kumar
Roshan Kumar
Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae
Frontiers in Microbiology
Parapedobacter
Bat operon
pectinases
inositol
ortholog analysis
author_facet Shekhar Nagar
Chandni Talwar
Shazia Haider
Akshita Puri
Akshita Puri
Kalaiarasan Ponnusamy
Madhuri Gupta
Utkarsh Sood
Utkarsh Sood
Abhay Bajaj
Abhay Bajaj
Rup Lal
Rup Lal
Roshan Kumar
Roshan Kumar
author_sort Shekhar Nagar
title Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae
title_short Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae
title_full Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae
title_fullStr Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae
title_full_unstemmed Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae
title_sort phylogenetic relationships and potential functional attributes of the genus parapedobacter: a member of family sphingobacteriaceae
publisher Frontiers Media S.A.
series Frontiers in Microbiology
issn 1664-302X
publishDate 2020-09-01
description The genus Parapedobacter was established to describe a novel genus within the family Sphingobacteriaceae and derives its name from Pedobacter, with which it is shown to be evolutionarily related. Despite this, Parapedobacter and Pedobacter do not share very high 16S rRNA gene sequence similarities. Therefore, we hypothesized whether these substantial differences at the 16S rRNA gene level depict the true phylogeny or that these genomes have actually diverged. Thus, we performed genomic analysis of the four available genomes of Parapedobacter to better understand their phylogenomic position within family Sphingobacteriaceae. Our results demonstrated that Parapedobacter is more closely related to species of Olivibacter, as opposed to the genus Pedobacter. Further, we identified a significant class of enzymes called pectinases with potential industrial applications within the genomes of Parapedobacter luteus DSM 22899T and Parapedobacter composti DSM 22900T. These enzymes, specifically pectinesterases and pectate lyases, are presumed to have largely different catalytic activities based on very low sequence similarities to already known enzymes and thus may be exploited for industrial applications. We also determined the complete Bacteroides aerotolerance (Bat) operon (batA, batB, batC, batD, batE, hypothetical protein, moxR, and pa3071) within the genome of Parapedobacter indicus RK1T. This expands the definition of genus Parapedobacter to containing members that are able to tolerate oxygen stress using encoded oxidative stress responsive systems. By conducting a signal propagation network analysis, we determined that BatD, BatE, and hypothetical proteins are the major controlling hubs that drive the expression of Bat operon. As a key metabolic difference, we also annotated the complete iol operon within the P. indicus RK1T genome for utilization of all three stereoisomers of inositol, namely myo-inositol, scyllo-inositol, and 1D-chiro-inositol, which are abundant sources of organic phosphate found in soils. The results suggest that the genus Parapedobacter holds promising applications owing to its environmentally relevant genomic adaptations, which may be exploited in the future.
topic Parapedobacter
Bat operon
pectinases
inositol
ortholog analysis
url https://www.frontiersin.org/article/10.3389/fmicb.2020.01725/full
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