Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae
Open Access
- 4 September 2020
- journal article
- research article
- Published by Frontiers Media SA in Frontiers in Microbiology
Abstract
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.This publication has 64 references indexed in Scilit:
- Phage-Mediated Acquisition of a Type III Secreted Effector Protein Boosts Growth of Salmonella by Nitrate RespirationmBio, 2012
- Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineageThe ISME Journal, 2011
- Prodigal: prokaryotic gene recognition and translation initiation site identificationBMC Bioinformatics, 2010
- De novo assembly of human genomes with massively parallel short read sequencingGenome Research, 2009
- Expression patterns of genes induced by oxidative stress in Porphyromonas gingivalisOral Microbiology and Immunology, 2008
- Molecular basis of the activity of the phytopathogen pectin methylesteraseThe EMBO Journal, 2007
- Crystal structure of the electron transfer complex rubredoxin–rubredoxin reductase of Pseudomonas aeruginosaProceedings of the National Academy of Sciences of the United States of America, 2007
- Identifying bacterial genes and endosymbiont DNA with GlimmerBioinformatics, 2007
- Characterization of myo -Inositol Utilization by Corynebacterium glutamicum : the Stimulon, Identification of Transporters, and Influence on l -Lysine FormationJournal of Bacteriology, 2006
- Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction NetworksGenome Research, 2003