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Jiang Z, Lu J, Tong Y, Yang H, Feng S. Enhancement of acid tolerance of Escherichia coli by introduction of molecule chaperone CbpA from extremophile. World J Microbiol Biotechnol 2023; 39:158. [PMID: 37046107 DOI: 10.1007/s11274-023-03613-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/08/2023] [Indexed: 04/14/2023]
Abstract
Molecular chaperone CbpA from extreme acidophile Acidithiobacillus caldus was applied to improve acid tolerance of Escherichia coli via CRISPR/Cas9. Cell growth and viability of plasmid complementary strain indicated the importance of cbpAAc for bacteria acid tolerance. With in situ gene replacement by CRISPR/Cas9 system, colony formation unit (CFU) of genome recombinant strain BL21-ΔcbpA/AccbpA showed 7.7 times higher cell viability than deficient strain BL21-ΔcbpA and 2.3 times higher than wild type. Cell morphology observation using Field Emission Scanning Electron Microscopy (FESEM) revealed cell breakage of BL21-ΔcbpA and significant recovery of BL21-ΔcbpA/AccbpA. The intracellular ATP level of all strains gradually decreased along with the increased stress time. Particularly, the value of recombinant strain was 56.0% lower than that of deficient strain after 5 h, indicating that the recombinant strain consumed a lot of energy to resist acid stress. The arginine concentration in BL21-ΔcbpA/AccbpA was double that of BL21-ΔcbpA, while the aspartate and glutamate contents were 14.8% and 6.2% higher, respectively, compared to that of wild type. Moreover, RNA-Seq analysis examined 93 genes down-regulated in BL21-ΔcbpA compared to wild type strain, while 123 genes were up-regulated in BL21-ΔcbpA/AccbpA compared to BL21-ΔcbpA, with an emphasis on energy metabolism, transport, and cell components. Finally, the working model in response to acid stress of cbpA from A. caldus was developed. This study constructed a recombinant strain resistant to acid stress and also provided a reference for enhancing microorganisms' robustness to various conditions.
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Affiliation(s)
- Zhenming Jiang
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Jie Lu
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Yanjun Tong
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, China
| | - Hailin Yang
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Shoushuai Feng
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.
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Sulfite altered permanganate pretreatment effects on the volatile fatty acid production during sludge anaerobic fermentation. Sep Purif Technol 2023. [DOI: 10.1016/j.seppur.2022.122514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Tian K, Yu Y, Qiu Q, Sun X, Meng F, Bi Y, Gu J, Wang Y, Zhang F, Huo H. Mechanisms of BPA Degradation and Toxicity Resistance in Rhodococcus equi. Microorganisms 2022; 11:microorganisms11010067. [PMID: 36677360 PMCID: PMC9862853 DOI: 10.3390/microorganisms11010067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/05/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022] Open
Abstract
Bisphenol A (BPA) pollution poses an increasingly serious problem. BPA has been detected in a variety of environmental media and human tissues. Microbial degradation is an effective method of environmental BPA remediation. However, BPA is also biotoxic to microorganisms. In this study, Rhodococcus equi DSSKP-R-001 (R-001) was used to degrade BPA, and the effects of BPA on the growth metabolism, gene expression patterns, and toxicity-resistance mechanisms of Rhodococcus equi were analyzed. The results showed that R-001 degraded 51.2% of 5 mg/L BPA and that 40 mg/L BPA was the maximum BPA concentration tolerated by strain R-001. Cytochrome P450 monooxygenase and multicopper oxidases played key roles in BPA degradation. However, BPA was toxic to strain R-001, exhibiting nonlinear inhibitory effects on the growth and metabolism of this bacterium. R-001 bacterial biomass, total protein content, and ATP content exhibited V-shaped trends as BPA concentration increased. The toxic effects of BPA included the downregulation of R-001 genes related to glycolysis/gluconeogenesis, pentose phosphate metabolism, and glyoxylate and dicarboxylate metabolism. Genes involved in aspects of the BPA-resistance response, such as base excision repair, osmoprotectant transport, iron-complex transport, and some energy metabolisms, were upregulated to mitigate the loss of energy associated with BPA exposure. This study helped to clarify the bacterial mechanisms involved in BPA biodegradation and toxicity resistance, and our results provide a theoretical basis for the application of strain R-001 in BPA pollution treatments.
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Affiliation(s)
- Kejian Tian
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun 130117, China
| | - Yue Yu
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun 130117, China
| | - Qing Qiu
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun 130117, China
| | - Xuejian Sun
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun 130117, China
| | - Fanxing Meng
- Jilin Province Water Resources and Hydropower Consultative Company of P.R. China, Changchun 130021, China
| | - Yuanping Bi
- School of Life Sciences, Northeast Normal University, No. 5268, Renmin Main Street, Changchun 130024, China
| | - Jinming Gu
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun 130117, China
| | - Yibing Wang
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun 130117, China
| | - Fenglin Zhang
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun 130117, China
| | - Hongliang Huo
- School of Environment, Northeast Normal University, No. 2555 Jingyue Avenue, Changchun 130117, China
- Jilin Province Laboratory of Water Pollution Treatment and Resource Engineering, Changchun 130117, China
- Northeast China Low Carbon Water Pollution Treatment and Green Development Engineering Research Center, Changchun 130117, China
- Correspondence:
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Yan H, Li J, Meng J, Li J, Jha AK, Zhang Y, Wang X, Fan Y. Insight into the effect of N-acyl-homoserine lactones-mediated quorum sensing on the microbial social behaviors in a UASB with the regulation of alkalinity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 800:149413. [PMID: 34384968 DOI: 10.1016/j.scitotenv.2021.149413] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
N-acyl-homoserine lactones (AHLs)-mediated quorum sensing (QS) has been reported as the inducers of microbial social behaviors in anaerobic digestion (AD) processes. However, it is not well understood that how to intentionally change the secretion of AHLs by conventional engineering control such as the regulation of alkalinity. The present research investigated the effect of endogenous AHLs-mediated QS on the microbial social behaviors in an upflow anaerobic sludge bed (UASB) reactor with the influent alkalinity decreased from 2800 mg/L to 700 mg/L by stages. The results showed that the alkalinity of 1800-2200 mg/L was more favorable for the AD in the UASB, with an excellent specific methanogenic activity (SMA) and better microbial aggregation statuses. The alkalinity out of the favorable alkalinity range would decrease the SMA with the accumulation of VFAs in the reactor. It was found that signal molecule C4-HSL was always the dominant AHL in the UASB along with the decrease of influent alkalinity, while 3-oxo-C6-HSL, 3-oxo-C12-HSL and C14-HSL were remarkably improved only within the favorable range of alkalinity. Pearson correlation concluded that the dominant signal molecule C4-HSL was the specific AHL in enhancing the synthesis of extracellular polysaccharide and the metabolism of acidogens. The co-occurrence network revealed that Mesotoga, Sulfurospirillum and Methanoregula were the key hubs in the microbial interaction network, and the AHLs-mediated QS indirectly facilitated the methanogenic metabolism. The present work provided a revealing insight into the effect of AHLs-mediated QS on the microbial social behaviors in AD process with the regulation of alkalinity.
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Affiliation(s)
- Han Yan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jianzheng Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Jia Meng
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jiuling Li
- Advanced Water Management Centre, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Avinash Kumar Jha
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yafei Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xin Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yiyang Fan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
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Short-Chain Fatty Acids Alter Metabolic and Virulence Attributes of Borrelia burgdorferi. Infect Immun 2018; 86:IAI.00217-18. [PMID: 29891543 DOI: 10.1128/iai.00217-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 06/06/2018] [Indexed: 12/22/2022] Open
Abstract
Borrelia burgdorferi responds to a variety of host-derived factors and appropriately alters its gene expression for adaptation under different host-specific conditions. We previously showed that various levels of acetate, a short-chain fatty acid (SCFA), altered the protein profile of B. burgdorferi In this study, we determined the effects of other physiologically relevant SCFAs in the regulation of metabolic/virulence-associated proteins using mutant borrelial strains. No apparent increase in the synthesis of outer surface protein C (OspC) was noted when a carbon storage regulator A (csrA of B. burgdorferi, or csrABb ) mutant (mt) was propagated within dialysis membrane chambers implanted within rat peritoneal cavity, while the parental wild type (wt; B31-A3 strain) and csrABb cis-complemented strain (ct) had increased OspC with a reciprocal reduction in OspA levels. Growth rates of wt, mt, ct, 7D (csrABb mutant lacking 7 amino acids at the C terminus), and 8S (csrABb with site-specific changes altering its RNA-binding properties) borrelial strains were similar in the presence of acetate. Increased levels of propionate and butyrate reduced the growth rates of all strains tested, with mt and 8S exhibiting profound growth deficits at higher concentrations of propionate. Transcriptional levels of rpoS and ospC were elevated on supplementation of SCFAs compared to those of untreated spirochetes. Immunoblot analysis revealed elevated levels of RpoS, OspC, and DbpA with increased levels of SCFAs. Physiological levels of SCFAs prevalent in select human and rodent fluids were synergistic with mammalian host temperature and pH to increase the levels of aforementioned proteins, which could impact the colonization of B. burgdorferi during the mammalian phase of infection.
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Wang H, Zeng Y, Guo C, Bao Y, Lu G, Reinfelder JR, Dang Z. Bacterial, archaeal, and fungal community responses to acid mine drainage-laden pollution in a rice paddy soil ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 616-617:107-116. [PMID: 29107775 DOI: 10.1016/j.scitotenv.2017.10.224] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/17/2017] [Accepted: 10/21/2017] [Indexed: 05/21/2023]
Abstract
Lacking sufficient clean water, the paddy soils along the Hengshi River have suffered from long-term acid mine drainage (AMD) contamination. The impacted cropland is too heavily contaminated to grow food safely. The microbial communities inhabiting the environment play pivotal roles in the crop growth, health, and ecological services. In this study, the bacterial, archaeal, and fungal communities in the impacted paddy soil were examined using high-throughput Illumina MiSeq sequencing. The results showed that AMD irrigation considerably enriched the bacterial phylum Acidobacteria and the archaeal phylum Crenarchaeota, while the fungal community was more stable. The abundances of Acidobacteria and Crenarchaeota were significantly positively correlated with the AMD-related environmental factors of pH and heavy metals (Cu, Pb, and Zn). In the most contaminated samples, communities were dominated by the bacteria Candidatus Solibacter and Candidatus Koribacter from the Acidobacteria family. Functional gene profile analysis demonstrated that the energy metabolic processes of the microbial communities, especially C/N related pathways, have adjusted and are well-adapted to tolerating AMD contamination. The present study described the structural and functional differentiation of microbial communities in the rice paddy soil under AMD irrigation. The results are useful for the development of bioremediation strategies using native microbes in the cleanup and biorestoration of AMD-contaminated agriculture soil.
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Affiliation(s)
- Han Wang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Yufei Zeng
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Chuling Guo
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou 510006, PR China.
| | - Yanping Bao
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; Department of Environmental Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Guining Lu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou 510006, PR China
| | - John R Reinfelder
- Department of Environmental Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou 510006, PR China.
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Murthy AMV, Mathivanan S, Chittori S, Savithri HS, Murthy MRN. Structures of substrate- and nucleotide-bound propionate kinase from Salmonella typhimurium: substrate specificity and phosphate-transfer mechanism. ACTA ACUST UNITED AC 2015; 71:1640-8. [PMID: 26249345 DOI: 10.1107/s1399004715009992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/22/2015] [Indexed: 11/11/2022]
Abstract
Kinases are ubiquitous enzymes that are pivotal to many biochemical processes. There are contrasting views on the phosphoryl-transfer mechanism in propionate kinase, an enzyme that reversibly transfers a phosphoryl group from propionyl phosphate to ADP in the final step of non-oxidative catabolism of L-threonine to propionate. Here, X-ray crystal structures of propionate- and nucleotide-bound Salmonella typhimurium propionate kinase are reported at 1.8-2.0 Å resolution. Although the mode of nucleotide binding is comparable to those of other members of the ASKHA superfamily, propionate is bound at a distinct site deeper in the hydrophobic pocket defining the active site. The propionate carboxyl is at a distance of ∼ 5 Å from the γ-phosphate of the nucleotide, supporting a direct in-line transfer mechanism. The phosphoryl-transfer reaction is likely to occur via an associative SN2-like transition state that involves a pentagonal bipyramidal structure with the axial positions occupied by the nucleophile of the substrate and the O atom between the β- and the γ-phosphates, respectively. The proximity of the strictly conserved His175 and Arg236 to the carboxyl group of the propionate and the γ-phosphate of ATP suggests their involvement in catalysis. Moreover, ligand binding does not induce global domain movement as reported in some other members of the ASKHA superfamily. Instead, residues Arg86, Asp143 and Pro116-Leu117-His118 that define the active-site pocket move towards the substrate and expel water molecules from the active site. The role of Ala88, previously proposed to be the residue determining substrate specificity, was examined by determining the crystal structures of the propionate-bound Ala88 mutants A88V and A88G. Kinetic analysis and structural data are consistent with a significant role of Ala88 in substrate-specificity determination. The active-site pocket-defining residues Arg86, Asp143 and the Pro116-Leu117-His118 segment are also likely to contribute to substrate specificity.
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Affiliation(s)
| | - Subashini Mathivanan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Sagar Chittori
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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Chittori S, Savithri HS, Murthy MRN. Structural and mechanistic investigations on Salmonella typhimurium acetate kinase (AckA): identification of a putative ligand binding pocket at the dimeric interface. BMC STRUCTURAL BIOLOGY 2012; 12:24. [PMID: 23031654 PMCID: PMC3475010 DOI: 10.1186/1472-6807-12-24] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 09/24/2012] [Indexed: 01/23/2023]
Abstract
Background Bacteria such as Escherichia coli and Salmonella typhimurium can utilize acetate as the sole source of carbon and energy. Acetate kinase (AckA) and phosphotransacetylase (Pta), key enzymes of acetate utilization pathway, regulate flux of metabolites in glycolysis, gluconeogenesis, TCA cycle, glyoxylate bypass and fatty acid metabolism. Results Here we report kinetic characterization of S. typhimurium AckA (StAckA) and structures of its unliganded (Form-I, 2.70 Å resolution) and citrate-bound (Form-II, 1.90 Å resolution) forms. The enzyme showed broad substrate specificity with kcat/Km in the order of acetate > propionate > formate. Further, the Km for acetyl-phosphate was significantly lower than for acetate and the enzyme could catalyze the reverse reaction (i.e. ATP synthesis) more efficiently. ATP and Mg2+ could be substituted by other nucleoside 5′-triphosphates (GTP, UTP and CTP) and divalent cations (Mn2+ and Co2+), respectively. Form-I StAckA represents the first structural report of an unliganded AckA. StAckA protomer consists of two domains with characteristic βββαβαβα topology of ASKHA superfamily of proteins. These domains adopt an intermediate conformation compared to that of open and closed forms of ligand-bound Methanosarcina thermophila AckA (MtAckA). Spectroscopic and structural analyses of StAckA further suggested occurrence of inter-domain motion upon ligand-binding. Unexpectedly, Form-II StAckA structure showed a drastic change in the conformation of residues 230–300 compared to that of Form-I. Further investigation revealed electron density corresponding to a citrate molecule in a pocket located at the dimeric interface of Form-II StAckA. Interestingly, a similar dimeric interface pocket lined with largely conserved residues could be identified in Form-I StAckA as well as in other enzymes homologous to AckA suggesting that ligand binding at this pocket may influence the function of these enzymes. Conclusions The biochemical and structural characterization of StAckA reported here provides insights into the biochemical specificity, overall fold, thermal stability, molecular basis of ligand binding and inter-domain motion in AckA family of enzymes. Dramatic conformational differences observed between unliganded and citrate-bound forms of StAckA led to identification of a putative ligand-binding pocket at the dimeric interface of StAckA with implications for enzymatic function.
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Affiliation(s)
- Sagar Chittori
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
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