Bioinformatics Analysis and Characterization of Highly Efficient Polyvinyl Alcohol (PVA)-Degrading Enzymes from the Novel PVA Degrader Stenotrophomonas rhizophila QL-P4

Abstract

Polyvinyl alcohol (PVA) is used widely in industry, and associated environmental pollution is a serious problem. Herein, we report a novel, efficient PVA degrader, QL-P4, isolated from fallen leaves from a virgin forest in the Qinling Mountains. The complete genome was obtained using single-molecule real-time (SMRT) technology and corrected using Illumina sequencing. Bioinformatics analysis revealed eight PVA/vinyl alcohol oligomer (OVA)-degrading genes. Of these, seven genes were predicted to be involved in the classic intracellular PVA/OVA degradation pathway, and one (BAY15_3292) was identified as a novel PVA oxidase. Five PVA/OVA-degrading enzymes were purified and characterized. One of these, BAY15_1712, a PVA dehydrogenase (PVADH), displayed high catalytic efficiency toward PVA and OVA substrate. All reported PVADHs only have PVA-degrading ability. Most importantly, we discovered a novel PVA oxidase (BAY15_3292) that exhibited higher PVA-degrading efficiency than the reported PVADHs. Further investigation indicated that BAY15_3292 plays a crucial role in PVA degradation in QL-P4. Knocking out BAY15_3292 resulted in a significant decline in PVA-degrading activity in QL-P4. Interestingly, we found that BAY15_3292 possesses exocrine activity, which distinguishes it from classic PVADHs. Transparent circle experiments further proved that BAY15_3292 greatly affects extracellular PVA degradation in QL-P4. The exocrine characteristics of BAY15_3292 facilitate its potential application to PVA bioremediation. In addition, we report three new efficient secondary alcohol dehydrogenases (SADHs) with OVA-degrading ability in QL-P4; in contrast, only one OVA-degrading SADH was reported previously. With the widespread application of PVA in industry, PVA-related environmental pollution is an increasingly serious issue. Because PVA is difficult to degrade, it accumulates in aquatic environments and causes chronic toxicity to aquatic organisms. Biodegradation of PVA, as an economical and environment-friendly method, has attracted much interest. To date, effective and applicable PVA-degrading bacteria/enzymes have not been reported. Herein, we report a new efficient PVA degrader ( QL-P4) that has five PVA/OVA-degrading enzymes with high catalytic efficiency, among which BAY15_1712 is the only reported PVADH with both PVA- and OVA-degrading abilities. Importantly, we discovered a novel PVA oxidase (BAY15_3292) that is not only more efficient than other reported PVA-degrading PVADHs but also has exocrine activity. Overall, our findings provide new insight into PVA-degrading pathways in microorganisms and suggest QL-P4 and its enzymes have the potential for application to PVA bioremediation to reduce or eliminate PVA-related environmental pollution.

Application of different types of CRISPR/Cas-based systems in bacteria

“…[ 46 ], B. subtilis [ 47 ], Corynebacterium glutamicum [ 48 – 50 ], Clostridium beijerinckii [ 51 ], Streptomyces sp. [ 52 , 53 ], Clostridium difficile [ 54 ], Clostridium saccharoperbutylacetonicum N1–4 [ 55 ], and Clostridium autoethanogenum [ 56 ], have all been successfully engineered in recent years (Table 2 ).…”

Analysis of endometrial lavage microbiota reveals an increased relative abundance of the plastic-degrading bacteria Bacillus pseudofirmus and Stenotrophomonas rhizophila in women with endometrial cancer/endometrial hyperplasia

“…Since the uterine cavity harbors a diversity of microorganisms, we hypothesized that the extent of increases or decreases in the relative proportion of certain bacteria may affect the risk of malignant endometrial transformation. We were surprised to observe that the key dysbiosis occurring in the endometrial lavage uid collected from patients with EH/EC had an increase in the relative abundance of Bacillus pseudo rmus and Stenotrophomonas rhizophila -two plastic-degrading bacteria [19][20][21][22].…”

Comparative Genomics of Stenotrophomonas maltophilia and Stenotrophomonas rhizophila Revealed Characteristic Features of Both Species

“…To date, only a few strains of this species have been sequenced. One of them is S. rhizophila QL-P4, which is a strain that efficiently degrades polyvinyl alcohol [ 15 ]. Extensive abilities of xenobiotic degradation are widespread in the Stenotrophomonas genus and many strains of both S. maltophilia and S. rhizophila were reported as being excellent degraders [ 16 ].…”