Comparative Genomic Analysis of Stenotrophomonas maltophilia Strain W18 Reveals Its Adaptative Genomic Features for Degrading Polycyclic Aromatic Hydrocarbons.

Polycyclic aromatic hydrocarbons (PAHs) are hazardous pollutants that are ubiquitous in the environment. Numerous bacteria have evolved to have degrading genes or pathways to degrade PAHs. Stenotrophomonas maltophilia strain W18 was found to be able to degrade PAHs. Including 43 other complete genome sequences of S. maltophilia strains, we performed a comparative genomic analysis of 44 S. maltophilia strains by running OrthoFinder. A KEGG pathway enrichment analysis of environmental and clinical isolates of S. maltophilia revealed that environmental isolates tended to enhance gene functions such as "energy metabolism," "amino acid metabolism," "xenobiotic biodegradation and metabolism," and "folding, sorting, and degradation." The pangenome of the 44 S. maltophilia strains was open, while the core genome was estimated to reach a steady plateau. Based on gene annotations, we inferred that most of the degradation potential came from the core genome of S. maltophilia, while character genes and accessory genes also contributed to the degradation ability of S. maltophilia W18. The genes expression level of core genes, character genes and accessory genes were proved by RT-qPCR experiment, and accessory genes encoding alcohol dehydrogenase were upregulated most compared with genes with similar functions. We performed a credible comparative genomic analysis of S. maltophilia strains. S. maltophilia W18 was set as a model PAH-degrading bacterium of this species in this study, which would provide guidance for understanding and predicting the degradation mechanisms of other PAH-degrading S. maltophilia strains lacking complete genome data or waiting to be determined. IMPORTANCE This study provided the latest comparative genomic analysis on Stenotrophomonas maltophilia strains and focused on analyzing their genomic features that allow them to adapt to natural environments. In this study, we set S. maltophilia W18 as a typical PAH-degrading strain of this species. By discussing the genomic adaptative features of degrading PAH, we can predict genomic adaptative features of other S. maltophilia PAH-degrading strains since the core function of this species is stable. The gene functions of how S. maltophilia environmental isolates are enhanced for adaptation to various natural environments compared with clinical isolates have been revealed. Combined with a pangenome analysis and RT-qPCR results, we have proved that core genes, character genes, and accessory genes are all involved in PAH degradation. Accessory genes encoding alcohol dehydrogenase were upregulated most compared with core and character genes with similar functions, which suggests that PAH metabolization potential might be enhanced by horizontal gene transfer.

Tween 20 regulate the function and structure of transmembrane proteins of Bacillus cereus: Promoting transmembrane transport of fluoranthene.

Polycyclic aromatic hydrocarbons (PAHs) are degraded by the highly efficient degrading bacterium Bacillus cereus. Transmembrane transport is highly important in PAH degradation by bacteria. Surfactants are the key substances that promote PAH adsorption, uptake and transmembrane transport by Bacillus cereus. In this study, the isobaric tags for relative and absolute quantitation (iTRAQ) approach was used for high-throughput screening of key functional proteins during transmembrane fluoranthene transport by Bacillus cereus treated with Tween 20. In addition, SWISS-MODEL was used to simulate the tertiary structures of key transmembrane proteins and analyze how Tween 20 promotes transmembrane transport. Transmembrane fluoranthene transport into Bacillus cereus requires transmembrane proteins and energy. Tween 20 was observed to improve bacterial motility and transmembrane protein expression. The interior of representative transmembrane proteins is mostly composed of hydrophobic ß-sheets while amphipathic α-helices are primarily distributed at their periphery. The primary reason for this configuration may be α-helices promote the aggregation of surfactants and the phospholipid bilayer and the ß-sheets promote surfactant insertion into the phospholipid bilayer to enhance PAH transport into Bacillus cereus. Investigating the effect of Tween 20 on Bacillus cereus transmembrane proteins during transmembrane fluoranthene transport is important for understanding the mechanism of PAH degradation by microorganisms.

A study on the degradation efficiency of fluoranthene and the transmembrane protein mechanism of Rhodococcus sp. BAP-1 based on iTRAQ.

Based on previous studies that examined the whole proteome of Rhodococcus sp. BAP-1 during the degradation of polycyclic aromatic hydrocarbons (PAHs), transmembrane proteins have a large role in the degradation of fluoranthene. To further study the specific functions and mechanisms of transmembrane proteins from Rhodococcus sp. BAP-1 involved in the degradation process of fluoranthene, the degradation of PAHs and the membrane permeability were determined. In addition, the isobaric tags for relative and absolute quantization (iTRAQ) method were used to conduct a proteomics analysis of Rhodococcus sp. BAP-1 after exposure to fluoranthene for 1 d, 3 d, and 6 d. The results showed that the degradation rate was the highest on the first and sixth days, and the membrane permeability was also the highest on the sixth day. The iTRAQ analysis results showed 18, 29, and 48 upregulated proteins and 111, 97, and 21 downregulated proteins in the 1 d group vs control group, 3 d group vs control group, and 6 d group vs control group samples respectively. According to a Clusters of Orthologous Groups of proteins (COG) analysis, amino acid transport and metabolism are the most important functions. According to functional analysis from the gene ontology (GO) database, the oxidation-reduction process is the most important biological process; transporter activity is the main molecular function; and transmembrane proteins are the most important in the cell composition. This study combined the degradation rate, membrane permeability and transmembrane protein functions to analyze the functions and mechanisms of transmembrane proteins from Rhodococcus sp. BAP-1, which are involved in the degradation of fluoranthene at the protein level, and this study provides a solid foundation for further research on the metabolic processes of bacteria.