Phylogenetic Relationships and Potential Functional Attributes of the GenusParapedobacter: A Member of FamilySphingobacteriaceae

Abstract

The genusParapedobacterwas established to describe a novel genus within the familySphingobacteriaceaeand derives its name fromPedobacter, with which it is shown to be evolutionarily related. Despite this,ParapedobacterandPedobacterdo 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 ofParapedobacterto better understand their phylogenomic position within familySphingobacteriaceae. Our results demonstrated thatParapedobacteris more closely related to species ofOlivibacter, as opposed to the genusPedobacter. Further, we identified a significant class of enzymes called pectinases with potential industrial applications within the genomes ofParapedobacter luteusDSM 22899(T)andParapedobacter compostiDSM 22900(T). 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 completeBacteroidesaerotolerance (Bat) operon (batA, batB, batC, batD, batE, hypothetical protein,moxR, andpa3071) within the genome ofParapedobacter indicusRK1(T). This expands the definition of genusParapedobacterto 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 completeioloperon within theP.indicusRK1(T)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 genusParapedobacterholds promising applications owing to its environmentally relevant genomic adaptations, which may be exploited in the future.