The characterization of a short chain dehydrogenase/reductase (SDRx) in Comamonas testosteroni

Homologous relationship between FabG involved in fatty acid biosynthesis and SDR on chromosome II in the multi-chromosome pathogen Vibrio anguillarum

Vibrio anguillarum threatens fish and larval farming industries and human health worldwide. The identification of bacterial adaptation and responses to stress due to environmental changes is vital for establishing a response strategy for pathogenic Vibrio. Previously, short-chain dehydrogenase/reductase (SDR) was identified on chromosome II of the multichromosomal V. anguillarum. In this study, a comparison of SDR and the enzyme FabG-1b (encoded on chromosome I and responsible for the β-ketoacyl acyl carrier protein (ACP) reductase in fatty acid biosynthesis (FAS II)) showed that the amino acid sequence homology was only 33.2%; however, the core of functionality, which includes the NAD(P)-binding domain and the conserved region of the active site, the topologies predicted using sequence-based homology modeling, and the quaternary homotetramer-type structures showed a significant similarity. FabG-1b was specific to the substrates fluorinated and halogenated aliphatic ketones, aromatic ketones, and aromatic β-ketoesters and SDR toward non-fluorinated and non-halogenated aliphatic ketones, aromatic ketones, and non-aromatic β-ketoesters. This complementary catalytic efficiencies of the two enzymes on various substrates conclusively supports the hypothesis that the two enzymes are likely homologs. This is the first study to report potential paralogous enzymes FabG-1b and SDR in Vibrio. This information improves our understanding of bacterial FAS for establishing strategies to overcome infectious diseases caused by pathogenic strains and identify targets for developing new antibacterial agents.

Removal of BPA by Pseudomonas asiatica P1: Synergistic response mechanism of toxicity resistance and biodegradation

Bisphenol A (BPA) is a globally concerning toxic pollutant, and microbial degradation is considered an effective method to treat BPA contamination. However, the inherent microbial toxicity of BPA is often overlooked, particularly the microbial mechanisms of resistance and detoxification against BPA. This study found that under the toxic stress of BPA, cbb3-type cytochrome c oxidase (cbb3-Cox) in the cells of Pseudomonas asiatica P1 (P. asiatica P1) was the first to resist the toxicity. Genes such as ccoNOQPG showed significant upregulation with an average log2FC value of 3.56. Subsequently, genes that are related to metal ion binding, transport, and DNA repair were upregulated in the middle to later phase, which enhanced the metabolic functions of the strains and induced strain mutations to assist P. asiatica P1 in resisting the BPA toxicity. Meanwhile, three potential BPA degradation genes were identified, among which sdrP1 was crucial to the BPA degradation and detoxification. After genetic recombination, sdrP1 achieved a degradation rate of 92.52 % for BPA. Furthermore, through various methods such as alkyl interactions, sdrP1 exhibited oxidation and demethylation to form lower toxic intermediate products and complete the biological detoxification of BPA. This study provides a systematic analysis of the toxicity resistance, biodegradation, and detoxification processes in bacterial BPA removal, refines the mechanism of BPA biodegradation and contributes to a more comprehensive and systematic understanding of the overall process of microbial removal of toxic pollutants.

Engineering the cofactor binding site of 7α-hydroxysteroid dehydrogenase for improvement of catalytic activity, thermostability, and alteration of substrate preference

Hydroxysteroid dehydrogenases (HSDHs) are crucial for bile acid metabolism and influence the size of the bile acid pool and gut microbiota composition. HSDHs with high activity, thermostability, and substrate selectivity are the basis for constructing engineered bacteria for disease treatment. In this study, we designed mutations at the cofactor binding site involving Thr15 and Arg16 residues of HSDH St-2-2. The T15A, R16A, and R16Q mutants exhibited 7.85-, 2.50-, and 4.35-fold higher catalytic activity than the wild type, respectively, while also displaying an altered substrate preference (from taurocholic acid (TCA) to taurochenodeoxycholic acid (TCDCA)). These mutants showed lower Km and higher kcat values, indicating stronger binding to the substrate and resulting in 3190-, 3123-, and 3093-fold higher kcat/Km values for TCDCA oxidation. Furthermore, the Tm values of the T15A, R16A, and R16Q mutants were found to increase by 4.3 °C, 6.0 °C, and 7.0 °C, respectively. Molecular structure analysis indicated that reshaped internal hydrogens and surface mutations could improve catalytic activity and thermostability, and altered interactions among the catalytic triad, cofactor binding sites, and substrates could change substrate preference. This work provides valuable insights into modifying substrate preference as well as enhancing the catalytic activity and thermostability of HSDHs by targeting the cofactor binding site.

Delving into the lifestyle of Sundarban Wetland resident, biofilm producing, halotolerant Salinicoccus roseus: a comparative genomics-based intervention

BACKGROUND

Microbial community played an essential role in ecosystem processes, be it mangrove wetland or other intertidal ecologies. Several enzymatic activities like hydrolases are effective ecological indicators of soil microbial function. So far, little is known on halophilic bacterial contribution and function on a genomic viewpoint of Indian Sundarban Wetland. Considering the above mentioned issues, the aims of this study was to understand the life style, metabolic functionalities and genomic features of the isolated bacterium, Salinicoccus roseus strain RF1H. A comparative genome-based study of S. roseus has not been reported yet. Henceforth, we have considered the inclusion of the intra-species genome comparison of S. roseus to gain insight into the high degree of variation in the genome of strain RF1H among others.

RESULTS

Salinicoccus roseus strain RF1H is a pink-red pigmented, Gram-positive and non-motile cocci. The bacterium exhibited high salt tolerance (up to 15% NaCl), antibiotic resistance, biofilm formation and secretion of extracellular hydrolytic enzymes. The circular genome was approximately 2.62978 Mb in size, encoding 574 predicted genes with GC content 49.5%. Presence of genomic elements (prophages, transposable elements, CRISPR-Cas system) represented bacterial virulence and multidrug-resistance. Furthermore, genes associated with salt tolerance, temperature adaptation and DNA repair system were distributed in 17 genomic islands. Genes related to hydrocarbon degradation manifested metabolic capability of the bacterium for potential biotechnological applications. A comparative pangenome analysis revealed two-component response regulator, modified C4-dicarboxylate transport system and osmotic stress regulated ATP-binding proteins. Presence of genes encoding arginine decarboxylase (ADC) enzyme being involved in biofilm formation was reported from the genome. In silico study revealed the protein is thermostable and made up with ~ 415 amino acids, and hydrophilic in nature. Three motifs appeared to be evolutionary conserved in all Salinicoccus sequences.

CONCLUSION

The first report of whole genome analysis of Salinicoccus roseus strain RF1H provided information of metabolic functionalities, biofilm formation, resistance mechanism and adaptation strategies to thrive in climate-change induced vulnerable spot like Sundarban. Comparative genome analysis highlighted the unique genome content that contributed the strain's adaptability. The biomolecules produced during metabolism are important sources of compounds with potential beneficial applications in pharmaceuticals.

Expression Profile of Hydroxysteroid Dehydrogenase-like 2 in Polychaete Perinereis aibuhitensis in Response to BPA

Hydroxysteroid dehydrogenases (HSDs) play an important role in the metabolism of steroids and xenobiotics. However, the function of HSDs in invertebrates is unclear. In this study, we cloned the hydroxysteroid dehydrogenase-like 2 (HSDL2) gene in Perinereis aibuhitensis, which is 1652 bp in length, encoding 400 amino acids. This sequence contains conserved short-chain dehydrogenase and sterol carrier protein-2 domain, and the alignment analysis showed its close relationship with other invertebrate HSDL2. Further, the tissue distribution analysis of the HSDL2 gene showed it is expressed strongly in the intestine. The expression level of HSDL2 after inducement with bisphenol A (BPA) was also detected both at transcriptional and translational levels. The results inferred that BPA exposure can induce HSDL2 expression, and the inductive effect was obvious in the high-concentration BPA group (100 μg/L). In summary, our results showed the detoxification function of HSDL2 in polychaetes.

Nitric oxide enhances resistance of Pleurotus eryngii to cadmium stress by alleviating oxidative damage and regulating of short-chain dehydrogenase/reductase family

The function and mechanism of nitric oxide (NO) in regulating Pleurotus eryngii biological response to cadmium (Cd) stress was evaluated by using anti-oxidation and short-chain dehydrogenase/reductase (SDR) family analysis. The fresh biomass of P. eryngii mycelia sharply decreased after treatment with 50 µM Cd; the lipid peroxidation and H₂O₂ accumulation in P. eryngii were found responsible for it. Proper exogenous supply of NO (150 µM SNP) alleviated the oxidative damage induced by Cd stress in P. eryngii, which reduced the accumulation of thiobarbituric acid reactive substances (TBARS) and H₂O₂. The activities of antioxidant enzymes (superoxide dismutase, peroxidase) were significantly increased to deal with Cd stress when treated with SNP (150 µM), and the content of proline was also closely related to NO-mediated reduction of Cd toxicity. Moreover, SDR family members were widely involved in the response to Cd stress, especially PleSCH70 gene was observed for the first time in participating in NO-mediated enhancement of Cd tolerance in P. eryngii. Taken together, this study provides new insights in understanding the tolerance mechanisms of P. eryngii to heavy metal and lays a foundation for molecular breeding of P. eryngii to improve its tolerance to environmental stress.

Cloning and identification of a new repressor of 3,17β-Hydroxysteroid dehydrogenase of Comamonas testosteroni

BACKGROUND

3,17β-hydroxysteroid dehydrogenase (3,17β-HSD) is a key enzyme in the metabolic pathway for steroid compounds catabolism in Comamonas testosteroni. Tetracycline repressor (TetR) family, repressors existing in most microorganisms, may play key roles in regulating the expression of 3,17β-HSD. Previous reports showed that three tetR genes are located in the contig58 of C. testosteroni ATCC 11996 (GenBank: AHIL01000049.1), among which the first tetR gene encoded a potential repressor of 3,17β-HSD by sensing environmental signals. However, whether the other proposed tetR genes act as repressors of 3,17β-HSD are still unknown.

METHODS AND RESULTS

In the present study, we cloned the second tetR gene and analyzed the regulatory mechanism of the protein on 3,17β-HSD using electrophoretic mobility shift assay (EMSA), gold nanoparticles (AuNPs)-based assay, and loss-of-function analysis. The results showed that the second tetR gene was 660-bp, encoding a 26 kD protein, which could regulate the expression of 3,17β-HSD gene via binding to the conserved consensus sequences located 1100-bp upstream of the 3,17β-HSD gene. Furthermore, the mutant strain of C. testosteroni with the second tetR gene knocked-out mutant expresses good biological genetic stability, and the expression of 3,17β-HSD in the mutant strain is slightly higher than that in the wild type under testosterone induction.

CONCLUSIONS

The second tetR gene acts as a negative regulator in 3,17β-HSD expression, and the mutant has potential application in bioremediation of steroids contaminated environment.

Bioremediation of various aromatic and emerging pollutants by Bacillus cereus sp. isolated from petroleum sludge

The accumulation of toxic chemical constituents in sludge and wastewater has fuelled an interest in investigating efficient and eco-friendly wastewater remediation approaches. In this study, a set of bacterial samples were isolated from petroleum sludge and tested for their ability to degrade different aromatic pollutants, including azo dyes and emerging pollutants. Although exhibiting differential specificity, all bacterial isolates were able to degrade different classes of aromatic dyes efficiently. Ribosomal 16S rRNA sequencing of the 12 bacterial isolates showed that they belonged to two different bacterial genera: Bacillus cereus and Pseudomonas guariconensis. Of these 12 strains, MA1 (B. cereus) was the most promising and was chosen for further optimization and biochemical studies. The optimum culture and remediation conditions for MA1 was found to be at pH 7, with 100 ppm dye concentration, and under aerobic condition. In addition to efficiently degrading various aromatic dyes (e.g. Congo Red, Reactive Black 5, PBS, and Toluidine Blue), MA1 was also found to be capable of degrading various emerging pollutants (e.g. prometryn, fluometuron and sulfamethoxazole). Preliminary transcriptome analysis shows that MA1 grown on media containing a mixture of aromatic dyes appears to differentially express a number of genes. Data shown here strongly suggests that petroleum sludge is a rich reservoir of bacteria with powerful remediation abilities.

Expanding the Application Range of Microbial Oxidoreductases by an Alcohol Dehydrogenase from Comamonas testosteroni with a Broad Substrate Spectrum and pH Profile

Alcohol dehydrogenases catalyse the conversion of a large variety of ketone substrates to the corresponding chiral products. Due to their high regio- and stereospecificity, they are key components in a wide range of industrial applications. A novel alcohol dehydrogenase from Comamonas testosteroni (CtADH) was identified in silico, recombinantly expressed and purified, enzymatically and biochemically investigated as well as structurally characterized. These studies revealed a broad pH profile and an extended substrate spectrum with the highest activity for compounds containing halogens as substituents and a moderate activity for bulky–bulky ketones. Biotransformations with selected ketones—performed with a coupled regeneration system for the co-substrate NADPH—resulted in conversions of more than 99% with all tested substrates and with excellent enantioselectivity for the corresponding S-alcohol products. CtADH/NADPH/substrate complexes modelled on the basis of crystal structures of CtADH and its closest homologue suggested preliminary hints to rationalize the enzyme’s substrate preferences

Suitability of Immobilized Systems for Microbiological Degradation of Endocrine Disrupting Compounds

The rising pollution of the environment with endocrine disrupting compounds has increased interest in searching for new, effective bioremediation methods. Particular attention is paid to the search for microorganisms with high degradation potential and the possibility of their use in the degradation of endocrine disrupting compounds. Increasingly, immobilized microorganisms or enzymes are used in biodegradation systems. This review presents the main sources of endocrine disrupting compounds and identifies the risks associated with their presence in the environment. The main pathways of degradation of these compounds by microorganisms are also presented. The last part is devoted to an overview of the immobilization methods used for the purposes of enabling the use of biocatalysts in environmental bioremediation.