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Shi J, Feng Z, Song Q, Wang F, Zhang Z, Liu J, Li F, Wen A, Liu T, Ye Z, Zhang C, Das K, Wang S, Feng Y, Lin W. Structural and functional insights into transcription activation of the essential LysR-type transcriptional regulators. Protein Sci 2024; 33:e5012. [PMID: 38723180 PMCID: PMC11081524 DOI: 10.1002/pro.5012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024]
Abstract
The enormous LysR-type transcriptional regulators (LTTRs), which are diversely distributed amongst prokaryotes, play crucial roles in transcription regulation of genes involved in basic metabolic pathways, virulence and stress resistance. However, the precise transcription activation mechanism of these genes by LTTRs remains to be explored. Here, we determine the cryo-EM structure of a LTTR-dependent transcription activation complex comprising of Escherichia coli RNA polymerase (RNAP), an essential LTTR protein GcvA and its cognate promoter DNA. Structural analysis shows two N-terminal DNA binding domains of GcvA (GcvA_DBD) dimerize and engage the GcvA activation binding sites, presenting the -35 element for specific recognition with the conserved σ70R4. In particular, the versatile C-terminal domain of α subunit of RNAP directly interconnects with GcvA_DBD, σ70R4 and promoter DNA, providing more interfaces for stabilizing the complex. Moreover, molecular docking supports glycine as one potential inducer of GcvA, and single molecule photobleaching experiments kinetically visualize the occurrence of tetrameric GcvA-engaged transcription activation complex as suggested for the other LTTR homologs. Thus, a general model for tetrameric LTTR-dependent transcription activation is proposed. These findings will provide new structural and functional insights into transcription activation of the essential LTTRs.
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Affiliation(s)
- Jing Shi
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Zhenzhen Feng
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Qian Song
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Fulin Wang
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Zhipeng Zhang
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal UniversityGuangzhouGuangdongChina
- Guangdong Key Laboratory of Laser Life ScienceCollege of Biophotonics, South China Normal UniversityGuangzhouGuangdongChina
- Songshan Lake Materials LaboratoryDongguanGuangdongChina
| | - Jian Liu
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Fangfang Li
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Aijia Wen
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Tianyu Liu
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Zonghang Ye
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Chao Zhang
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Kalyan Das
- Rega Institute for Medical Research, Department of MicrobiologyImmunology and Transplantation, KU LeuvenLeuvenBelgium
| | - Shuang Wang
- Songshan Lake Materials LaboratoryDongguanGuangdongChina
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of Physics, Chinese Academy of SciencesBeijingChina
| | - Yu Feng
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Wei Lin
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and TechnologyShanghaiChina
- Nanjing Drum Tower Hospital Clinical College, Nanjing University of Chinese MedicineNanjingChina
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Chen Y, Liu F, Sha A, Xu M, Rao Z, Zhang X. Deciphering styrene oxide tolerance mechanisms in Gluconobacter oxydans mutant strain. BIORESOURCE TECHNOLOGY 2024; 401:130674. [PMID: 38642663 DOI: 10.1016/j.biortech.2024.130674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/21/2024] [Accepted: 04/05/2024] [Indexed: 04/22/2024]
Abstract
Chemical production wastewater contains large amounts of organic solvents (OSs), which pose a significant threat to the environment. In this study, a 10 g·L-1 styrene oxide tolerant strain with broad-spectrum OSs tolerance was obtained via adaptive laboratory evolution. The mechanisms underlying the high OS tolerance of tolerant strain were investigated by integrating physiological, multi-omics, and genetic engineering analyses. Physiological changes are one of the main factors responsible for the high OS tolerance in mutant strains. Moreover, the P-type ATPase GOX_RS04415 and the LysR family transcriptional regulator GOX_RS04700 were also verified as critical genes for styrene oxide tolerance. The tolerance mechanisms of OSs can be used in biocatalytic chassis cell factories to synthesize compounds and degrade environmental pollutants. This study provides new insights into the mechanisms underlying the toxicological response to OS stress and offers potential targets for enhancing the solvent tolerance of G. oxydans.
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Affiliation(s)
- Yan Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Fei Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Aobo Sha
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China.
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Zhang L, Fu Y, Xu Q, Chen X, Xie Y, Zhang B, Lin X. Quantitative proteomics reveals the complex regulatory networks of LTTR-type regulators in pleiotropic functions of Aeromonas hydrophila. Int J Biol Macromol 2024; 270:132315. [PMID: 38740149 DOI: 10.1016/j.ijbiomac.2024.132315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
LysR-type transcriptional regulators (LTTRs) are ubiquitously distributed and abundant transcriptional regulators in prokaryotes, playing pivotal roles in diverse physiological processes. Nonetheless, despite their prevalence, the intricate functionalities and physiological implications of this protein family remain incompletely elucidated. In this study, we employed a comprehensive approach to deepen our understanding of LTTRs by generating a collection of 20 LTTR gene-deletion strains in Aeromonas hydrophila, accounting for 42.6 % of the predicted total LTTR repertoire, and subjected them to meticulous assessment of their physiological phenotypes. Leveraging quantitative proteomics, we conducted a comparative analysis of protein expression variations between six representative mutants and the wild-type strain. Subsequent bioinformatics analysis unveiled the involvement of these LTTRs in modulating a wide array of biological processes, notably including two-component regulatory systems (TCSs) and intracellular central metabolism. Moreover, employing subsequent microbiological methodologies, we experimentally verified the direct involvement of at least six LTTRs in the regulation of galactose metabolism. Importantly, through ELISA and competitive ELISA assays, we demonstrated the competitive binding capabilities of these LTTRs with the promoter of the α-galactosidase gene AHA_1897 and identified that four LTTRs (XapR, YidZ, YeeY, and AHA_1805) do not engage in competitive binding with other LTTRs. Overall, our comprehensive findings not only provide fundamental insights into the regulatory mechanisms governing crucial physiological functions of bacteria through LTTR family proteins but also uncover an intricate and interactive regulatory network mediated by LTTRs.
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Affiliation(s)
- Lishan Zhang
- College of JunCao Science and Ecology, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuying Fu
- School of Safety and Environment, Fujian Chuanzheng Communications College, Fuzhou, Fujian Province 350007, China
| | - Qiaozhen Xu
- College of JunCao Science and Ecology, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin Chen
- College of JunCao Science and Ecology, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuyue Xie
- College of JunCao Science and Ecology, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Binghui Zhang
- College of JunCao Science and Ecology, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Tobacco Science, Fujian Provincial Tobacco Company, Fuzhou 350003, China
| | - Xiangmin Lin
- College of JunCao Science and Ecology, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fujian Province University, Fuzhou 350002, China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Ashikur Rahman M, Akter S, Ashrafudoulla M, Anamul Hasan Chowdhury M, Uddin Mahamud AGMS, Hong Park S, Ha SD. Insights into the mechanisms and key factors influencing biofilm formation by Aeromonas hydrophila in the food industry: A comprehensive review and bibliometric analysis. Food Res Int 2024; 175:113671. [PMID: 38129021 DOI: 10.1016/j.foodres.2023.113671] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 12/23/2023]
Abstract
Biofilm formation by Aeromonas hydrophila in the food industry poses significant challenges to food safety and quality. Therefore, this comprehensive review aimed to provide insights into the mechanisms and key factors influencing A. hydrophila biofilm formation. It explores the molecular processes involved in initial attachment, microcolony formation, and biofilm maturation; moreover, it concurrently examines the impact of intrinsic factors, including quorum sensing, cyclic-di-GMP, the efflux pump, and antibiotic resistance, as well as environmental conditions, such as temperature, nutrient availability, and osmotic pressure, on biofilm architecture and resilience. Furthermore, the article highlights the potential of bibliometric analysis as a promising method for conceptualizing the research landscape of and identifying knowledge gaps in A. hydrophila biofilm research. The findings underscore the requirement for focused interventions that prevent biofilm development and raise food sector safety. The consolidation of current information and incorporation of bibliometric analysis enhances existing understanding of A. hydrophila biofilm formation and offers insights for future research and control strategies within a food industry context.
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Affiliation(s)
- Md Ashikur Rahman
- School of Food Science and Technology, Chung-Ang University, Anseong-Si, Republic of Korea; Bangladesh Fisheries Research Institute, Bangladesh
| | - Shirin Akter
- School of Food Science and Technology, Chung-Ang University, Anseong-Si, Republic of Korea; Department of Fisheries and Marine Bioscience, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Md Ashrafudoulla
- School of Food Science and Technology, Chung-Ang University, Anseong-Si, Republic of Korea
| | | | | | - Si Hong Park
- Food Science and Technology, Oregon State University, Corvallis, OR, USA
| | - Sang-Do Ha
- School of Food Science and Technology, Chung-Ang University, Anseong-Si, Republic of Korea.
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Li Z, Li W, Lu J, Liu Z, Lin X, Liu Y. Quantitative Proteomics Analysis Reveals the Effect of a MarR Family Transcriptional Regulator AHA_2124 on Aeromonas hydrophila. BIOLOGY 2023; 12:1473. [PMID: 38132299 PMCID: PMC10740729 DOI: 10.3390/biology12121473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
The transcriptional regulators of the MarR family play an important role in diverse bacterial physiologic functions, whereas their effect and intrinsic regulatory mechanism on the aquatic pathogenic bacterium Aeromonas hydrophila are, clearly, still unknown. In this study, we firstly constructed a deletion strain of AHA_2124 (ΔAHA_2124) of a MarR family transcriptional regulator in Aeromonas hydrophila ATCC 7966 (wild type), and found that the deletion of AHA_2124 caused significantly enhanced hemolytic activity, extracellular protease activity, and motility when compared with the wild type. The differentially abundant proteins (DAPs) were compared by using data-independent acquisition (DIA), based on a quantitative proteomics technology, between the ΔAHA_2124 strain and wild type, and there were 178 DAPs including 80 proteins up-regulated and 98 proteins down-regulated. The bioinformatics analysis showed that the deletion of gene AHA_2124 led to some changes in the abundance of proteins related to multiple biological processes, such as translation, peptide transport, and oxidation and reduction. These results provided a theoretical basis for better exploring the regulatory mechanism of the MarR family transcriptional regulators of Aeromonas hydrophila on bacterial physiological functions.
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Affiliation(s)
- Zhen Li
- Zhangzhou Health Vocational College, Zhangzhou 363000, China;
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.L.); (X.L.)
| | - Wanxin Li
- School of Public Health, Fujian Medical University, Fuzhou 350122, China;
| | - Jinlian Lu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.L.); (X.L.)
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ziqiu Liu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.L.); (X.L.)
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiangmin Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.L.); (X.L.)
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanling Liu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.L.); (X.L.)
- National Engineering Research Center of Juncao Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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6
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Yousefi M, Hoseini SM, Abdel Rahman AN, Vatnikov YA, Kulikov EV, Kharlitskaya EV, Seleznev SB. Effects of Dietary Limonene Supplementation on Growth Performance and Immunological Parameters of Common Carp, Cyprinus carpio, Challenged by Aeromonas hydrophila. Animals (Basel) 2023; 13:3197. [PMID: 37893921 PMCID: PMC10603678 DOI: 10.3390/ani13203197] [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: 08/23/2023] [Revised: 09/01/2023] [Accepted: 09/15/2023] [Indexed: 10/29/2023] Open
Abstract
This study examined the impact of dietary limonene treatment on the growth performance, immune response, and disease resistance of common carp, Cyprinus carpio. The fish were fed with either a control diet (CTL; no limonene supplementation) or four experimental diets containing 50 (50 L), 100 (100 L), 200 (200 L), and 400 (400 L) mg/kg limonene over a 70-day period, followed by Aeromonas hydrophila challenge. The 200 L treatment resulted in a significant decrease in FCR compared to the CTL treatment. The highest post-challenge mortality was associated with the CTL treatment (62.7%), while the 200 L treatment had the lowest mortality (30.7%). Before the challenge, dietary limonene significantly increased humoral and skin mucosal immune parameters compared to the CTL treatment. The highest leukocyte, lymphocyte counts, skin mucosal protease activity, and intestinal lactic acid bacteria were observed in the 200 L treatment before the challenge. The highest plasma lysozyme activity was observed in the 400 L treatment, whereas the highest skin mucosal lysozyme and peroxidase activities were observed in the 100 L and 200 L treatments before the challenge. There were no significant differences in the blood neutrophil, monocyte, and eosinophil counts, humoral alternative complement activity, skin mucosal alkaline phosphatase activity, and the intestinal total viable bacteria among the treatments before the challenge. After the challenge, the 200 L treatment exhibited the highest leukocyte, neutrophil, and monocyte count, skin mucosal immune parameters, and intestinal lactic acid bacteria, whereas the highest blood eosinophil count was observed in the 100 L, 200 L, and 400 L treatments. At this time, the lowest blood lymphocyte counts were observed in the 100 L and 200 L, but the lowest intestinal total viable bacteria were observed in the 100 L, 200 L, and 400 L treatments. Based on these findings, dietary limonene at 200 mg/kg is ideal for common carp to promote feed efficiency, innate immunity boosting, and resistance against A. hydrophila.
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Affiliation(s)
- Morteza Yousefi
- Department of Veterinary Medicine, RUDN University, Miklukho-Maklaya St., 117198 Moscow, Russia; (Y.A.V.); (E.V.K.); (E.V.K.); (S.B.S.)
| | - Seyyed Morteza Hoseini
- Inland Waters Aquatics Resources Research Center, Iranian Fisheries Sciences Research Institute, Agricultural Research, Education and Extension Organization, Gorgan 4916687631, Iran
| | - Afaf N. Abdel Rahman
- Department of Aquatic Animal Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig P.O. Box 44511, Egypt;
| | - Yury Anatolyevich Vatnikov
- Department of Veterinary Medicine, RUDN University, Miklukho-Maklaya St., 117198 Moscow, Russia; (Y.A.V.); (E.V.K.); (E.V.K.); (S.B.S.)
| | - Evgeny Vladimirovich Kulikov
- Department of Veterinary Medicine, RUDN University, Miklukho-Maklaya St., 117198 Moscow, Russia; (Y.A.V.); (E.V.K.); (E.V.K.); (S.B.S.)
| | - Elena Valentinovna Kharlitskaya
- Department of Veterinary Medicine, RUDN University, Miklukho-Maklaya St., 117198 Moscow, Russia; (Y.A.V.); (E.V.K.); (E.V.K.); (S.B.S.)
| | - Sergey Borisovich Seleznev
- Department of Veterinary Medicine, RUDN University, Miklukho-Maklaya St., 117198 Moscow, Russia; (Y.A.V.); (E.V.K.); (E.V.K.); (S.B.S.)
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Qin T, Chen K, Xi B, Pan L, Xie J, Lu L, Liu K. In Vitro Antibiofilm Activity of Resveratrol against Aeromonas hydrophila. Antibiotics (Basel) 2023; 12:antibiotics12040686. [PMID: 37107048 PMCID: PMC10135085 DOI: 10.3390/antibiotics12040686] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Aeromonas hydrophila is a Gram-negative bacterium that widely exists in various aquatic environments and causes septicemia in fish and humans. Resveratrol, a natural polyterpenoid product, has potential chemo-preventive and antibacterial properties. In this study, we investigated the effect of resveratrol on A. hydrophila biofilm formation and motility. The results demonstrated that resveratrol, at sub-MIC levels, can significantly inhibit the biofilm formation of A. hydrophila, and the biofilm was decreased with increasing concentrations. The motility assay showed that resveratrol could diminish the swimming and swarming motility of A. hydrophila. Transcriptome analyses (RNA-seq) showed that A. hydrophila treated with 50 and 100 μg/mL resveratrol, respectively, presented 230 and 308 differentially expressed genes (DEGs), including 90 or 130 upregulated genes and 130 or 178 downregulated genes. Among them, genes related to flagellar, type IV pilus and chemotaxis were significantly repressed. In addition, mRNA of virulence factors OmpA, extracellular proteases, lipases and T6SS were dramatically suppressed. Further analysis revealed that the major DEGs involved in flagellar assembly and bacterial chemotaxis pathways could be regulated by cyclic-di-guanosine monophosphate (c-di-GMP)- and LysR-Type transcriptional regulator (LTTR)-dependent quorum sensing (QS) systems. Overall, our results indicate that resveratrol can inhibit A. hydrophila biofilm formation by disturbing motility and QS systems, and can be used as a promising candidate drug against motile Aeromonad septicemia.
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Ma Z, Li NA, Ning C, Liu Y, Guo Y, Ji C, Zhu X, Meng Q, Xia X, Zhang X, Cai X, Cai K, Jun Q. A Novel LysR Family Factor STM0859 is Associated with The Responses of Salmonella Typhimurium to Environmental Stress and Biofilm Formation. Pol J Microbiol 2022; 70:479-487. [PMID: 35003279 PMCID: PMC8702606 DOI: 10.33073/pjm-2021-045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/04/2021] [Indexed: 12/01/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Typhimurium (ST) is an intracellularly parasitic bacterium. This zoonotic pathogen causes food poisoning and thus imposes a severe threat to food safety. Here, to understand the regulatory roles of the novel transcription factor STM0859 on the response of ST to environmental stress and biofilm formation, the STM0859 gene-deficient strain and the complementation strain ΔSTM0859/STM0859 were generated, respectively. Then, its capacity of responding to environmental stresses and biofilm (BF) formation ability under different stresses, including acid, alkali, high salt, cholate, and oxidative stresses was tested. We further analyzed the interaction between the STM0859 protein and the promoter of the acid stress response-related gene rcsB by performing an electrophoresis mobility shift assay (EMSA). The results showed that acid resistance and BF formation capacities of ST-ΔSTM0859 strain were significantly weaker, as compared with those of Salmonella Typhimurium SL1344 (ST-SL1344) wild strain (p < 0.01). Quantitative qRT-PCR analysis showed that the expression levels of acid stress and BF formation-related genes, rcsB and rpoS, of ST-ΔSTM0859 strain were significantly reduced at the transcription levels, while the transcription levels of these genes were fully restored in complementation strain ST-ΔSTM0859/STM0859. The results of EMSA showed that STM0859 was capable of binding the promoter DNA fragments of the rcsB gene, suggesting that STM0859 can promote the transcription of the rcsB gene through interaction with its promoter, thereby exerting an indirectly regulatory role on the adaptive responses to acid stress and BF formation of ST. This study provided new insights into the regulatory mechanisms of the LysR family factors on the tolerances of ST under adverse environmental stresses.
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Affiliation(s)
- Zhongmei Ma
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - N A Li
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Chengcheng Ning
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Yucheng Liu
- Institute of Animal Science and Veterinary Research, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Yun Guo
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Chunhui Ji
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Xiaozhen Zhu
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Qingling Meng
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Xianzhu Xia
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Xingxing Zhang
- Institute of Animal Science and Veterinary Research, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Xuepeng Cai
- State Key Lab of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Kuojun Cai
- Center for Animal Disease Prevention and Control, Urumqi, China
| | - Qiao Jun
- College of Animal Science and Technology, Shihezi University, Shihezi, China
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9
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Microbial Lipopeptide-Producing Strains and Their Metabolic Roles under Anaerobic Conditions. Microorganisms 2021; 9:microorganisms9102030. [PMID: 34683351 PMCID: PMC8540375 DOI: 10.3390/microorganisms9102030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 01/17/2023] Open
Abstract
The lipopeptide produced by microorganisms is one of the representative biosurfactants and is characterized as a series of structural analogues of different families. Thirty-four families covering about 300 lipopeptide compounds have been reported in the last decades, and most of the reported lipopeptides produced by microorganisms were under aerobic conditions. The lipopeptide-producing strains under anaerobic conditions have attracted much attention from both the academic and industrial communities, due to the needs and the challenge of their applications in anaerobic environments, such as in oil reservoirs and in microbial enhanced oil recovery (MEOR). In this review, the fifty-eight reported bacterial strains, mostly isolated from oil reservoirs and dominated by the species Bacillus subtilis, producing lipopeptide biosurfactants, and the species Pseudomonas aeruginosa, producing glycolipid biosurfactants under anaerobic conditions were summarized. The metabolic pathway and the non-ribosomal peptide synthetases (NRPSs) of the strain Bacillus subtilis under anaerobic conditions were analyzed, which is expected to better understand the key mechanisms of the growth and production of lipopeptide biosurfactants of such kind of bacteria under anaerobic conditions, and to expand the industrial application of anaerobic biosurfactant-producing bacteria.
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Miao Y, Wang Y, Huang D, Lin X, Lin Z, Lin X. Profile of protein lysine propionylation in Aeromonas hydrophila and its role in enzymatic regulation. Biochem Biophys Res Commun 2021; 562:1-8. [PMID: 34030039 DOI: 10.1016/j.bbrc.2021.05.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 05/16/2021] [Indexed: 11/18/2022]
Abstract
Protein lysine propionylation (Kpr) modification is a novel post-translational modification (PTM) of prokaryotic cells that was recently discovered; however, it is not clear how this modification regulates bacterial life. In this study, the protein Kpr modification profile in Aeromonas hydrophila was identified by high specificity antibody-based affinity enrichment combined with high resolution LC MS/MS. A total of 98 lysine-propionylated peptides with 59 Kpr proteins were identified, most of which were associated with energy metabolism, transcription and translation processes. To further understand the role of Kpr modified proteins, the K168 site on malate dehydrogenase (MDH) and K608 site on acetyl-coenzyme A synthetase (AcsA) were subjected to site-directed mutation to arginine (R) and glutamine (Q) to simulate deacylation and propionylation, respectively. Subsequent measurement of the enzymatic activity showed that the K168 site of Kpr modification on MDH may negatively regulate the MDH enzymatic activity while also affecting the survival of mdh derivatives when using glucose as the carbon source, whereas Kpr modification of K608 of AcsA does not. Overall, the results of this study indicate that protein Kpr modification plays an important role in bacterial biological functions, especially those involved in the activity of metabolic enzymes.
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Affiliation(s)
- Yuxuan Miao
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Yuqian Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Dongping Huang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Xiaoke Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Zhenping Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China
| | - Xiangmin Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, PR China; Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, PR China; Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China.
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11
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Amino Acid k-mer Feature Extraction for Quantitative Antimicrobial Resistance (AMR) Prediction by Machine Learning and Model Interpretation for Biological Insights. BIOLOGY 2020; 9:biology9110365. [PMID: 33126516 PMCID: PMC7694136 DOI: 10.3390/biology9110365] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 12/31/2022]
Abstract
Machine learning algorithms can learn mechanisms of antimicrobial resistance from the data of DNA sequence without any a priori information. Interpreting a trained machine learning algorithm can be exploited for validating the model and obtaining new information about resistance mechanisms. Different feature extraction methods, such as SNP calling and counting nucleotide k-mers have been proposed for presenting DNA sequences to the model. However, there are trade-offs between interpretability, computational complexity and accuracy for different feature extraction methods. In this study, we have proposed a new feature extraction method, counting amino acid k-mers or oligopeptides, which provides easier model interpretation compared to counting nucleotide k-mers and reaches the same or even better accuracy in comparison with different methods. Additionally, we have trained machine learning algorithms using different feature extraction methods and compared the results in terms of accuracy, model interpretability and computational complexity. We have built a new feature selection pipeline for extraction of important features so that new AMR determinants can be discovered by analyzing these features. This pipeline allows the construction of models that only use a small number of features and can predict resistance accurately.
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12
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Fu Y, Zhang L, Wang G, Lin Y, Ramanathan S, Yang G, Lin W, Lin X. The LysR-Type Transcriptional Regulator YeeY Plays Important Roles in the Regulatory of Furazolidone Resistance in Aeromonas hydrophila. Front Microbiol 2020; 11:577376. [PMID: 33013815 PMCID: PMC7509050 DOI: 10.3389/fmicb.2020.577376] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/19/2020] [Indexed: 12/18/2022] Open
Abstract
Aeromonas hydrophila is an aquatic pathogen of freshwater fish. The emergence of widespread antimicrobial-resistance strains of this pathogen has caused increasing rates of fish infections. Our previous research reported that A. hydrophila yeeY, a LysR-type transcriptional regulator (LTTR), negatively regulated furazolidone (FZ) resistance. Although, it’s intrinsic regulatory mechanism is still unclear. In this study, a data-independent acquisition (DIA) quantitative proteomics method was used to compare the differentially expressed proteins (DEPs) between the ΔyeeY and wild-type strain under FZ treatment. When compared to the control, a total of 594 DEPs were identified in ΔyeeY. Among which, 293 and 301 proteins were substantially increased and decreased in abundance, respectively. Bioinformatics analysis showed that several biological pathways such as the secretion system and protein transport were mainly involved in FZ resistance. Subsequently, the antibiotics susceptibility assays of several gene deletion strains identified from the proteomics results showed that YeeY may regulate some important genes such as cysD, AHA_2766, AHA_3195, and AHA_4275, which affects the FZ resistance in A. hydrophila. Furthermore, 34 antimicrobial resistance genes (ARGs) from the bacterial drug resistance gene database (CARD) were found to be directly or indirectly regulated by YeeY. A subsequent assay of several ARGs mutants showed that ΔAHA_3222 increased the susceptibility of A. hydrophila to FZ, while ΔcysN and ΔAHA_3753 decreased the susceptibility rate. Finally, the chromatin immunoprecipitation (ChIP) PCR and an electrophoretic mobility shift assay (EMSA) have revealed that the genes such as AHA_3222 and AHA_4275 were directly and transcriptionally regulated by YeeY. Taken together, our findings demonstrated that YeeY may participate in antimicrobial resistance of A. hydrophila to FZ, which provides a new target for the development of novel antimicrobial agents in the future.
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Affiliation(s)
- Yuying Fu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Lishan Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Guibin Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yuexu Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Srinivasan Ramanathan
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Guidi Yang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Xiangmin Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China.,Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, China
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13
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da Cruz Nizer WS, Inkovskiy V, Overhage J. Surviving Reactive Chlorine Stress: Responses of Gram-Negative Bacteria to Hypochlorous Acid. Microorganisms 2020; 8:E1220. [PMID: 32796669 PMCID: PMC7464077 DOI: 10.3390/microorganisms8081220] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 07/30/2020] [Accepted: 08/09/2020] [Indexed: 01/29/2023] Open
Abstract
Sodium hypochlorite (NaOCl) and its active ingredient, hypochlorous acid (HOCl), are the most commonly used chlorine-based disinfectants. HOCl is a fast-acting and potent antimicrobial agent that interacts with several biomolecules, such as sulfur-containing amino acids, lipids, nucleic acids, and membrane components, causing severe cellular damage. It is also produced by the immune system as a first-line of defense against invading pathogens. In this review, we summarize the adaptive responses of Gram-negative bacteria to HOCl-induced stress and highlight the role of chaperone holdases (Hsp33, RidA, Cnox, and polyP) as an immediate response to HOCl stress. We also describe the three identified transcriptional regulators (HypT, RclR, and NemR) that specifically respond to HOCl. Besides the activation of chaperones and transcriptional regulators, the formation of biofilms has been described as an important adaptive response to several stressors, including HOCl. Although the knowledge on the molecular mechanisms involved in HOCl biofilm stimulation is limited, studies have shown that HOCl induces the formation of biofilms by causing conformational changes in membrane properties, overproducing the extracellular polymeric substance (EPS) matrix, and increasing the intracellular concentration of cyclic-di-GMP. In addition, acquisition and expression of antibiotic resistance genes, secretion of virulence factors and induction of the viable but nonculturable (VBNC) state has also been described as an adaptive response to HOCl. In general, the knowledge of how bacteria respond to HOCl stress has increased over time; however, the molecular mechanisms involved in this stress response is still in its infancy. A better understanding of these mechanisms could help understand host-pathogen interactions and target specific genes and molecules to control bacterial spread and colonization.
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Affiliation(s)
| | | | - Joerg Overhage
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada; (W.S.d.C.N.); (V.I.)
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14
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Proteomics analysis reveals the effect of Aeromonas hydrophila sirtuin CobB on biological functions. J Proteomics 2020; 225:103848. [DOI: 10.1016/j.jprot.2020.103848] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 05/09/2020] [Accepted: 05/24/2020] [Indexed: 02/07/2023]
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