Evolution of Phosphotriesterases (PTEs): How bacteria can acquire new degradative functions

The promiscuity of enzymes has often been considered a vestige activity based on the broad substrate spectrum of their progenitors. As such, divergent enzymes can be used as a fingerprint to track their evolutionary history. In the presence of structural mimics of active site or binding site ligands and assisted by mutations in the associated binding site, this promiscuity contributes to acquisition of new catalytic functions. This phenomenon is often referred to as substrate-assisted gain-of-function and helps soil microbes to thrive on re-calcitrant xenobiotic molecules, hitherto unfamiliar to the microbial world. This review describes the evolution of organophosphorous hydrolases, which potentially and originally functioned as quorum-sensing ‘quenching’ lactonases and highlights their remarkable horizontal mobility within diverse bacterial species

TonB-Dependent Transporters in Sphingomonads: Unraveling Their Distribution and Function in Environmental Adaptation

TonB-dependent transport system plays a critical role in the transport of nutrients across the energy-deprived outer membrane of Gram-negative bacteria. It contains a specialized outer membrane TonB-dependent transporter (TBDT) and energy generating (ExbB/ExbD) and transducing (TonB) inner membrane multi-protein complex, called TonB complex. Very few TonB complex protein-coding sequences exist in the genomes of Gram-negative bacteria. Interestingly, the TBDT coding alleles are phenomenally high, especially in the genomes of bacteria surviving in complex and stressful environments. Sphingomonads are known to survive in highly polluted environments using rare, recalcitrant, and toxic substances as their sole source of carbon. Naturally, they also contain a huge number of TBDTs in the outer membrane. Out of them, only a few align with the well-characterized TBDTs. The functions of the remaining TBDTs are not known. Predictions made based on genome context and expression pattern suggest their involvement in the transport of xenobiotic compounds across the outer membrane

The Organophosphate degradation (opd) island-borne esterase-induced metabolic diversion in Escherichia coli and its influence on p-nitrophenol degradation

In previous studies of the organophosphate degradation gene cluster we showed that expression of an open reading frame (orf306) present within the cluster in E. coli allowed growth on p-nitrophenol (PNP) as sole carbon source. We have now shown that expression of orf306 in E. coli causes a dramatic up-regulation in genes coding for alternative carbon catabolism. The propionate, glyoxylate and Methyl Citrate Cycle (MCC) pathway-specific enzymes are up regulated, along with hca (phenyl propionate) and mhp (hydroxy phenyl propionate) degradation operons. These hca and mhp operons play a key role in degradation of PNP, enabling E. coli to grow using it as sole carbon source. Supporting growth experiments, PNP degradation products entered central metabolic pathways and got incorporated into the carbon backbone. The protein and RNA samples isolated from E. coli (pSDP10) cells grown in C14 labelled PNP indicated incorporation of C14 carbon suggesting Orf306-dependent assimilation of PNP in E. coli cells

Genome-guided insights reveal organophosphate-degrading Brevundimonas diminuta as Sphingopyxis wildii and define its versatile metabolic capabilities and environmental adaptations

The complete genome sequence of Brevundimonas diminuta represented a chromosome (∼4.15 Mb) and two plasmids (pCMS1 and pCMS2) with sizes of 65,908 and 30,654 bp, respectively. The sequence of the genome showed no significant similarity with the known bacterial genome sequences, instead showed weak similarity with the members of different genera of family, Sphingomonadaceae. Contradicting existing taxonomic position, the core genome-guided phylogenetic tree placed B. diminuta in the genus Sphingopyxis and showed sufficient genome-to-genome distance warranting a new species name. Reflecting the strains ability to grow in harsh environments, the genome-contained genetic repertoire required for mineralization of several recalcitrant man-made aromatic compounds