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Sun J, Yan B, Chen H, Tu S, Zhang J, Chen T, Huang Q, Zhang Y, Xie L. Insight into the mechanisms of combined toxicity of cadmium and flotation agents in luminescent bacteria: Role of micro/nano particles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 940:173588. [PMID: 38823693 DOI: 10.1016/j.scitotenv.2024.173588] [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: 02/28/2024] [Revised: 05/22/2024] [Accepted: 05/26/2024] [Indexed: 06/03/2024]
Abstract
Currently, risk assessment and pollution management in mines primarily focus on toxic metals, with the flotation agents being overlooked. However, the combined effects of metals and flotation agents in mines remain largely unknown. Therefore, this study aimed to evaluate the combined effects of Cd and two organic flotation agents (ethyl xanthate (EX) and diethyldithiocarbamate (DDTC)), and the associated mechanisms. The results showed that Cd + EX and Cd + DDTC exhibited synergistic toxicity. The EC50 values for luminescent bacteria were 1.6 mg/L and 1.0 mg/L at toxicity unit ratios of 0.3 and 1, respectively. The synergistic effects were closely related with the formation of Cd(EX)2 and Cd(DDTC)2 micro/nano particles, with nano-particles exhibiting higher toxicity. We observed severe cell membrane damage and cell shrinkage of the luminescent bacteria, which were probably caused by secondary harm to cells through the released CS2 during their decomposition inside cells. In addition, these particles induced toxicity by altering cellular levels of biochemical markers and the transcriptional levels of transport proteins and lipoproteins, leading to cell membrane impairment and DNA damage. This study has demonstrated that particulates formed by Cd and flotation agents contribute to the majority of the toxicity of the binary mixture. This study helps to better understand the complex ecological risk of inorganic metals and organic flotation agents in realistic mining environments.
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Affiliation(s)
- Jiacheng Sun
- School of Environment, South China Normal University, University Town, Guangzhou 510006, China; SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Bo Yan
- School of Environment, South China Normal University, University Town, Guangzhou 510006, China; SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China.
| | - Hongxing Chen
- School of Environment, South China Normal University, University Town, Guangzhou 510006, China; SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China.
| | - Shuchen Tu
- School of Environment, South China Normal University, University Town, Guangzhou 510006, China; SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Junhao Zhang
- School of Environment, South China Normal University, University Town, Guangzhou 510006, China; SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Tao Chen
- School of Environment, South China Normal University, University Town, Guangzhou 510006, China; SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Qinzi Huang
- School of Environment, South China Normal University, University Town, Guangzhou 510006, China; SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Yuting Zhang
- School of Environment, South China Normal University, University Town, Guangzhou 510006, China; SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Lingtian Xie
- School of Environment, South China Normal University, University Town, Guangzhou 510006, China; SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
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Wang Y, Zheng C, Qiu M, Zhang L, Fang H, Yu Y. Tebuconazole promotes spread of a multidrug-resistant plasmid into soil bacteria to form new resistant bacterial strains. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172444. [PMID: 38615769 DOI: 10.1016/j.scitotenv.2024.172444] [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: 02/05/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 04/16/2024]
Abstract
The development of antibiotic resistance threatens human and environmental health. Non-antibiotic stressors, including fungicides, may contribute to the spread of antibiotic resistance genes (ARGs). We determined the promoting effects of tebuconazole on ARG dissemination using a donor, Escherichia coli MG1655, containing a multidrug-resistant fluorescent plasmid (RP4) and a recipient (E. coli HB101). The donor was then incorporated into the soil to test whether tebuconazole could accelerate the spread of RP4 into indigenous bacteria. Tebuconazole promoted the transfer of the RP4 plasmid from the donor into the recipient via overproduction of reactive oxygen species (ROS), enhancement of cell membrane permeability and regulation of related genes. The dissemination of the RP4 plasmid from the donor to soil bacteria was significantly enhanced by tebuconazole. RP4 plasmid could be propagated into more genera of bacteria in tebuconazole-contaminated soil as the exposure time increased. These findings demonstrate that the fungicide tebuconazole promotes the spread of the RP4 plasmid into indigenous soil bacteria, revealing the potential risk of tebuconazole residues enhancing the dissemination of ARGs in soil environments.
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Affiliation(s)
- Yingnan Wang
- Institute of Pesticide and Environmental Toxicology, the Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Conglai Zheng
- Institute of Pesticide and Environmental Toxicology, the Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Mengting Qiu
- Institute of Pesticide and Environmental Toxicology, the Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Luqing Zhang
- Institute of Pesticide and Environmental Toxicology, the Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hua Fang
- Institute of Pesticide and Environmental Toxicology, the Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yunlong Yu
- Institute of Pesticide and Environmental Toxicology, the Key Laboratory of Molecular Biology of Crop Pathogens and Insects, College of Agricultural and Biotechnology, Zhejiang University, Hangzhou 310058, China.
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Huang WC, Dwija IBNP, Hashimoto M, Wu JJ, Wang MC, Kao CY, Lin WH, Wang S, Teng CH. Peptidoglycan endopeptidase MepM of uropathogenic Escherichia coli contributes to competitive fitness during urinary tract infections. BMC Microbiol 2024; 24:190. [PMID: 38816687 PMCID: PMC11137974 DOI: 10.1186/s12866-024-03290-9] [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: 09/01/2023] [Accepted: 04/02/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND Urinary tract infections (UTIs) are common bacterial infections, primarily caused by uropathogenic Escherichia coli (UPEC), leading to significant health issues and economic burden. Although antibiotics have been effective in treating UPEC infections, the rise of antibiotic-resistant strains hinders their efficacy. Hence, identifying novel bacterial targets for new antimicrobial approaches is crucial. Bacterial factors required for maintaining the full virulence of UPEC are the potential target. MepM, an endopeptidase in E. coli, is involved in the biogenesis of peptidoglycan, a major structure of bacterial envelope. Given that the bacterial envelope confronts the hostile host environment during infections, MepM's function could be crucial for UPEC's virulence. This study aims to explore the role of MepM in UPEC pathogenesis. RESULTS MepM deficiency significantly impacted UPEC's survival in urine and within macrophages. Moreover, the deficiency hindered the bacillary-to-filamentous shape switch which is known for aiding UPEC in evading phagocytosis during infections. Additionally, UPEC motility was downregulated due to MepM deficiency. As a result, the mepM mutant displayed notably reduced fitness in causing UTIs in the mouse model compared to wild-type UPEC. CONCLUSIONS This study provides the first evidence of the vital role of peptidoglycan endopeptidase MepM in UPEC's full virulence for causing UTIs. MepM's contribution to UPEC pathogenesis may stem from its critical role in maintaining the ability to resist urine- and immune cell-mediated killing, facilitating the morphological switch, and sustaining motility. Thus, MepM is a promising candidate target for novel antimicrobial strategies.
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Affiliation(s)
- Wen-Chun Huang
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ida Bagus Nyoman Putra Dwija
- Department of Clinical Microbiology, Faculty of Medicine, Udayana University, Denpasar, Bali, Indonesia
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Masayuki Hashimoto
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jiunn-Jong Wu
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Ming-Cheng Wang
- Division of Nephrology, Department of Internal Medicine, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
| | - Cheng-Yen Kao
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Wei-Hung Lin
- Department of Internal Medicine, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
| | - Shuying Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Ching-Hao Teng
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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Zhang L, Yao M. Ambient particle composition and toxicity in 31 major cities in China. FUNDAMENTAL RESEARCH 2024; 4:505-515. [PMID: 38933208 PMCID: PMC11197799 DOI: 10.1016/j.fmre.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 09/24/2022] [Accepted: 10/03/2022] [Indexed: 11/07/2022] Open
Abstract
Current assessment of air quality or control effectiveness is solely based on particulate matter (PM) mass levels, without considering their toxicity differences in terms of health benefits. Here, we collected a total of 465 automobile air conditioning filters from 31 major Chinese cities to study the composition and toxicity of PM at a national scale. Dithiothreitol assay showed that normalized PM toxicity (NIOG) in different Chinese cities varied greatly from the highest 4.99 × 10-3 for Changsha to the lowest 7.72 × 10-4 for Yinchuan. NIOG values were observed to have significant correlations with annual PM10 concentration (r = -0.416, p = 0.020) and some PM components (total fungi, SO4 2- and calcium element). The concentrations of different elements and water-soluble ions in PM also varied by several orders of magnitude for 31 cities in China. Endotoxin concentrations in PM analyzed using limulus amebocyte lysate assay ranged from 2.88 EU/mg PM (Hangzhou) to 62.82 EU/mg PM (Shijiazhuang) among 31 Chinese cities. Besides, real-time qPCR revealed 10∼100-fold differences in total bacterial and fungal levels among 31 Chinese cities. The concentrations of chemical (water soluble ions and trace elements) and biological (fungi, bacteria and endotoxin) components in PM were found to be significantly correlated with some meteorological factors and gaseous pollutants such as SO2. Our results have demonstrated that PM toxicity from 31 major cities varied greatly up to 6.5 times difference; and components such as fungi and SO4 2- in PM could play important roles in the observed PM toxicity. The city-specific air pollution control strategy that integrates toxicity factors should be enacted in order to maximize health and economic co-benefits. This work also provides a comprehensive view on the overall PM pollution situation in China.
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Affiliation(s)
- Lu Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Maosheng Yao
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
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5
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Zhang Z, Huo J, Velo J, Zhou H, Flaherty A, Saier MH. Comprehensive Characterization of fucAO Operon Activation in Escherichia coli. Int J Mol Sci 2024; 25:3946. [PMID: 38612757 PMCID: PMC11011485 DOI: 10.3390/ijms25073946] [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: 02/14/2024] [Revised: 03/26/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
Wildtype Escherichia coli cells cannot grow on L-1,2-propanediol, as the fucAO operon within the fucose (fuc) regulon is thought to be silent in the absence of L-fucose. Little information is available concerning the transcriptional regulation of this operon. Here, we first confirm that fucAO operon expression is highly inducible by fucose and is primarily attributable to the upstream operon promoter, while the fucO promoter within the 3'-end of fucA is weak and uninducible. Using 5'RACE, we identify the actual transcriptional start site (TSS) of the main fucAO operon promoter, refuting the originally proposed TSS. Several lines of evidence are provided showing that the fucAO locus is within a transcriptionally repressed region on the chromosome. Operon activation is dependent on FucR and Crp but not SrsR. Two Crp-cAMP binding sites previously found in the regulatory region are validated, where the upstream site plays a more critical role than the downstream site in operon activation. Furthermore, two FucR binding sites are identified, where the downstream site near the first Crp site is more important than the upstream site. Operon transcription relies on Crp-cAMP to a greater degree than on FucR. Our data strongly suggest that FucR mainly functions to facilitate the binding of Crp to its upstream site, which in turn activates the fucAO promoter by efficiently recruiting RNA polymerase.
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Affiliation(s)
- Zhongge Zhang
- Department of Molecular Biology, School of Biological Sciences, University of California at San Diego, 9500 Gilman Dr, La Jolla, CA 92093-0116, USA; (J.H.); (J.V.); (A.F.)
| | | | | | | | | | - Milton H. Saier
- Department of Molecular Biology, School of Biological Sciences, University of California at San Diego, 9500 Gilman Dr, La Jolla, CA 92093-0116, USA; (J.H.); (J.V.); (A.F.)
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Grzesiak J, Rogala MM, Gawor J, Kouřilová X, Obruča S. Polyhydroxyalkanoate involvement in stress-survival of two psychrophilic bacterial strains from the High Arctic. Appl Microbiol Biotechnol 2024; 108:273. [PMID: 38520566 PMCID: PMC10960890 DOI: 10.1007/s00253-024-13092-8] [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: 01/05/2024] [Revised: 02/19/2024] [Accepted: 02/25/2024] [Indexed: 03/25/2024]
Abstract
An ever-growing body of literature evidences the protective role of polyhydroxyalkanoates (PHAs) against a plethora of mostly physical stressors in prokaryotic cells. To date, most of the research done involved bacterial strains isolated from habitats not considered to be life-challenging or extremely impacted by abiotic environmental factors. Polar region microorganisms experience a multitude of damaging factors in combinations rarely seen in other of Earth's environments. Therefore, the main objective of this investigation was to examine the role of PHAs in the adaptation of psychrophilic, Arctic-derived bacteria to stress conditions. Arctic PHA producers: Acidovorax sp. A1169 and Collimonas sp. A2191, were chosen and their genes involved in PHB metabolism were deactivated making them unable to accumulate PHAs (ΔphaC) or to utilize them (Δi-phaZ) as a carbon source. Varying stressors were applied to the wild-type and the prepared mutant strains and their survival rates were assessed based on CFU count. Wild-type strains with a functional PHA metabolism were best suited to survive the freeze-thaw cycle - a common feature of polar region habitats. However, the majority of stresses were best survived by the ΔphaC mutants, suggesting that the biochemical imbalance caused by the lack of PHAs induced a permanent cell-wide stress response thus causing them to better withstand the stressor application. Δi-phaZ mutants were superior in surviving UV irradiation, hinting that PHA granule presence in bacterial cells is beneficial despite it being biologically inaccessible. Obtained data suggests that the ability to metabolize PHA although important for survival, probably is not the most crucial mechanism in the stress-resistance strategies arsenal of cold-loving bacteria. KEY POINTS: • PHA metabolism helps psychrophiles survive freezing • PHA-lacking psychrophile mutants cope better with oxidative and heat stresses • PHA granule presence enhances the UV resistance of psychrophiles.
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Affiliation(s)
- Jakub Grzesiak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland.
| | - Małgorzata Marta Rogala
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Jan Gawor
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Xenie Kouřilová
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
| | - Stanislav Obruča
- Department of Food Chemistry and Biotechnology, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00, Brno, Czech Republic
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Banta AB, Myers KS, Ward RD, Cuellar RA, Place M, Freeh CC, Bacon EE, Peters JM. A Targeted Genome-scale Overexpression Platform for Proteobacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582922. [PMID: 38496613 PMCID: PMC10942329 DOI: 10.1101/2024.03.01.582922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Targeted, genome-scale gene perturbation screens using Clustered Regularly Interspaced Short Palindromic Repeats interference (CRISPRi) and activation (CRISPRa) have revolutionized eukaryotic genetics, advancing medical, industrial, and basic research. Although CRISPRi knockdowns have been broadly applied in bacteria, options for genome-scale overexpression face key limitations. Here, we develop a facile approach for genome-scale gene overexpression in bacteria we call, "CRISPRtOE" (CRISPR transposition and OverExpression). We create a platform for comprehensive gene targeting using CRISPR-associated transposition (CAST) and show that transposition occurs at a higher frequency in non-transcribed DNA. We then demonstrate that CRISPRtOE can upregulate gene expression in Proteobacteria with medical and industrial relevance by integrating synthetic promoters of varying strength upstream of target genes. Finally, we employ CRISPRtOE screening at the genome-scale in Escherichia coli, recovering known antibiotic targets and genes with unexplored roles in antibiotic function. We envision that CRISPRtOE will be a valuable overexpression tool for antibiotic mode of action, industrial strain optimization, and gene function discovery in bacteria.
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Affiliation(s)
- Amy B Banta
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Kevin S Myers
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Ryan D Ward
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Rodrigo A Cuellar
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael Place
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Claire C Freeh
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Emily E Bacon
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Jason M Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA
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8
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Sui X, Wang J, Zhao Z, Liu B, Liu M, Liu M, Shi C, Feng X, Fu Y, Shi D, Li S, Qi Q, Xian M, Zhao G. Phenolic compounds induce ferroptosis-like death by promoting hydroxyl radical generation in the Fenton reaction. Commun Biol 2024; 7:199. [PMID: 38368473 PMCID: PMC10874397 DOI: 10.1038/s42003-024-05903-5] [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: 11/05/2023] [Accepted: 02/08/2024] [Indexed: 02/19/2024] Open
Abstract
Phenolic compounds are industrially versatile chemicals, also the most ubiquitous pollutants. Recently, biosynthesis and biodegradation of phenols has attracted increasing attention, while phenols' toxicity is a major issue. Here, we evolved phloroglucinol-tolerant Escherichia coli strains via adaptive evolution, and three mutations (ΔsodB, ΔclpX and fetAB overexpression) prove of great assistance in the tolerance improvement. We discover that phloroglucinol complexes with iron and promotes the generation of hydroxyl radicals in Fenton reaction, which leads to reducing power depletion, lipid peroxidation, and ferroptosis-like cell death of E. coli. Besides phloroglucinol, various phenols can trigger ferroptosis-like death in diverse organisms, from bacteria to mammalian cells. Furthermore, repressing this ferroptosis-like death improves phloroglucinol production and phenol degradation by corresponding strains respectively, showing great application potential in microbial degradation or production of desired phenolic compounds, and phloroglucinol-induced ferroptosis suppresses tumor growth in mice, indicating phloroglucinol as a promising drug for cancer treatment.
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Affiliation(s)
- Xinyue Sui
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Jichao Wang
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Zhiqiang Zhao
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Miaomiao Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
| | - Min Liu
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Cong Shi
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Xinjun Feng
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Yingxin Fu
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Dayong Shi
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Shengying Li
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Mo Xian
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Guang Zhao
- State Key Laboratory of Microbial Technology and Institute of Microbial Technology, Shandong University, Qingdao, China.
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.
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9
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Li C, Wei Z, He X, He H, Liu Y, Zuo Y, Xiao H, Wang Y, Shen X, Zhu L. OxyR-regulated T6SS functions in coordination with siderophore to resist oxidative stress. Microbiol Spectr 2024; 12:e0323123. [PMID: 38189330 PMCID: PMC10846153 DOI: 10.1128/spectrum.03231-23] [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: 08/30/2023] [Accepted: 12/02/2023] [Indexed: 01/09/2024] Open
Abstract
The formation of reactive oxygen species is harmful and can destroy intracellular macromolecules such as lipids, proteins, and DNA, even leading to bacterial death. To cope with this situation, microbes have evolved a variety of sophisticated mechanisms, including antioxidant enzymes, siderophores, and the type VI secretion system (T6SS). However, the mechanism of oxidative stress resistance in Cupriavidus pinatubonensis is unclear. In this study, we identified Reut_A2805 as an OxyR ortholog in C. pinatubonensis, which positively regulated the expression of T6SS1 by directly binding to its operon promoter region. The study revealed that OxyR-regulated T6SS1 combats oxidative stress by importing iron into bacterial cells. Moreover, the T6SS1-mediated outer membrane vesicles-dependent iron acquisition pathway played a crucial role in the oxidative stress resistance process. Finally, our study demonstrated that the T6SS1 and siderophore systems in C. pinatubonensis exhibit different responses in combating oxidative stress under low-iron conditions, providing a comprehensive understanding of how bacterial iron acquisition systems function in diverse conditions.IMPORTANCEThe ability to eliminate reactive oxygen species is crucial for bacterial survival. Continuous formation of hydroperoxides can damage metalloenzymes, disrupt DNA integrity, and even result in cell death. While various mechanisms have been identified in other bacterial species to combat oxidative stress, the specific mechanism of oxidative stress resistance in C. pinatubonensis remains unclear. The importance of this study is that we elucidate the mechanism that OxyR-regulated T6SS1 combats oxidative stress by importing iron with the help of bacterial outer membrane vesicle. Moreover, the study highlights the contrasting responses of T6SS1- and siderophore-mediated iron acquisition systems to oxidative stress. This study provides a comprehensive understanding of bacterial iron acquisition and its role in oxidative stress resistance in C. pinatubonensis under low-iron conditions.
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Affiliation(s)
- Changfu Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhiyan Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinquan He
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Haiyang He
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuqi Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuxin Zuo
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - He Xiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xihui Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Lingfang Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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10
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Tulin G, Figueroa NR, Checa SK, Soncini FC. The multifarious MerR family of transcriptional regulators. Mol Microbiol 2024; 121:230-242. [PMID: 38105009 DOI: 10.1111/mmi.15212] [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: 08/10/2023] [Revised: 11/28/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023]
Abstract
The MerR family of transcriptional regulators includes a variety of bacterial cytoplasmic proteins that respond to a wide range of signals, including toxins, metal ions, and endogenous metabolites. Its best-characterized members share similar structural and functional features with the family founder, the mercury sensor MerR, although most of them do not respond to metal ions. The group of "canonical" MerR homologs displays common molecular mechanisms for controlling the transcriptional activation of their target genes in response to inducer signals. This includes the recognition of distinctive operator sequences located at suboptimal σ70 -dependent promoters. Interestingly, an increasing number of proteins assigned to the MerR family based on their DNA-binding domain do not match in structure, sequence, or mode of action with any of the canonical MerR-like regulators. Here, we analyzed several members of the family, including this last group. Based on a phylogenetic analysis, and similarities in structural/functional features and position of their target operators relative to the promoter elements, we propose to assign these "atypical/divergent" MerR regulators to a phylogenetically separated group. These atypical/divergent homologs represent a new class of transcriptional regulators with novel regulatory mechanisms.
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Affiliation(s)
- Gonzalo Tulin
- Instituto de Biología Molecular y Celular de Rosario, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Nicolás R Figueroa
- Centro de Estudios Fotosintéticos y Bioquímicos, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Susana K Checa
- Instituto de Biología Molecular y Celular de Rosario, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Fernando C Soncini
- Instituto de Biología Molecular y Celular de Rosario, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
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11
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Verbeelen T, Fernandez CA, Nguyen TH, Gupta S, Aarts R, Tabury K, Leroy B, Wattiez R, Vlaeminck SE, Leys N, Ganigué R, Mastroleo F. Whole transcriptome analysis highlights nutrient limitation of nitrogen cycle bacteria in simulated microgravity. NPJ Microgravity 2024; 10:3. [PMID: 38200027 PMCID: PMC10781756 DOI: 10.1038/s41526-024-00345-z] [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: 09/20/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024] Open
Abstract
Regenerative life support systems (RLSS) will play a vital role in achieving self-sufficiency during long-distance space travel. Urine conversion into a liquid nitrate-based fertilizer is a key process in most RLSS. This study describes the effects of simulated microgravity (SMG) on Comamonas testosteroni, Nitrosomonas europaea, Nitrobacter winogradskyi and a tripartite culture of the three, in the context of nitrogen recovery for the Micro-Ecological Life Support System Alternative (MELiSSA). Rotary cell culture systems (RCCS) and random positioning machines (RPM) were used as SMG analogues. The transcriptional responses of the cultures were elucidated. For CO2-producing C. testosteroni and the tripartite culture, a PermaLifeTM PL-70 cell culture bag mounted on an in-house 3D-printed holder was applied to eliminate air bubble formation during SMG cultivation. Gene expression changes indicated that the fluid dynamics in SMG caused nutrient and O2 limitation. Genes involved in urea hydrolysis and nitrification were minimally affected, while denitrification-related gene expression was increased. The findings highlight potential challenges for nitrogen recovery in space.
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Affiliation(s)
- Tom Verbeelen
- Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400, Mol, Belgium
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Celia Alvarez Fernandez
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Thanh Huy Nguyen
- Department of Proteomics and Microbiology, University of Mons, Av. Du Champs de Mars 6, 7000, Mons, Belgium
| | - Surya Gupta
- Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400, Mol, Belgium
| | - Raf Aarts
- Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400, Mol, Belgium
| | - Kevin Tabury
- Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400, Mol, Belgium
| | - Baptiste Leroy
- Department of Proteomics and Microbiology, University of Mons, Av. Du Champs de Mars 6, 7000, Mons, Belgium
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, University of Mons, Av. Du Champs de Mars 6, 7000, Mons, Belgium
| | - Siegfried E Vlaeminck
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
- Centre for Advanced Process Technology for Urban REsource Recovery (CAPTURE), Frieda Saeysstraat 1, 9052, Ghent, Belgium
| | - Natalie Leys
- Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400, Mol, Belgium
| | - Ramon Ganigué
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
- Centre for Advanced Process Technology for Urban REsource Recovery (CAPTURE), Frieda Saeysstraat 1, 9052, Ghent, Belgium
| | - Felice Mastroleo
- Nuclear Medical Applications, Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400, Mol, Belgium.
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12
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Maunders EA, Giles MW, Ganio K, Cunningham BA, Bennett-Wood V, Cole GB, Ng D, Lai CC, Neville SL, Moraes TF, McDevitt CA, Tan A. Zinc acquisition and its contribution to Klebsiella pneumoniae virulence. Front Cell Infect Microbiol 2024; 13:1322973. [PMID: 38249299 PMCID: PMC10797113 DOI: 10.3389/fcimb.2023.1322973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/08/2023] [Indexed: 01/23/2024] Open
Abstract
Klebsiella pneumoniae is a World Health Organization priority pathogen and a significant clinical concern for infections of the respiratory and urinary tracts due to widespread and increasing resistance to antimicrobials. In the absence of a vaccine, there is an urgent need to identify novel targets for therapeutic development. Bacterial pathogens, including K. pneumoniae, require the d-block metal ion zinc as an essential micronutrient, which serves as a cofactor for ~6% of the proteome. During infection, zinc acquisition necessitates the use of high affinity uptake systems to overcome niche-specific zinc limitation and host-mediated nutritional immunity. Here, we report the identification of ZnuCBA and ZniCBA, two ATP-binding cassette permeases that are highly conserved in Klebsiella species and contribute to K. pneumoniae AJ218 zinc homeostasis, and the high-resolution structure of the zinc-recruiting solute-binding protein ZniA. The Znu and Zni permeases appear functionally redundant with abrogation of both systems required to reduce K. pneumoniae zinc accumulation. Disruption of both systems also exerted pleiotropic effects on the homeostasis of other d-block elements. Zinc limitation perturbed K. pneumoniae cell morphology and compromised resistance to stressors, such as salt and oxidative stress. The mutant strain lacking both systems showed significantly impaired virulence in acute lung infection models, highlighting the necessity of zinc acquisition in the virulence and pathogenicity of K. pneumoniae.
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Affiliation(s)
- Eve A. Maunders
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Matthew W. Giles
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Katherine Ganio
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Bliss A. Cunningham
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Vicki Bennett-Wood
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Gregory B. Cole
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Dixon Ng
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Christine C. Lai
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Stephanie L. Neville
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Trevor F. Moraes
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Aimee Tan
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
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13
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Lee SM, Le HT, Taizhanova A, Nong LK, Park JY, Lee EJ, Palsson BO, Kim D. Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution. Front Microbiol 2024; 14:1271121. [PMID: 38239730 PMCID: PMC10794520 DOI: 10.3389/fmicb.2023.1271121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/01/2023] [Indexed: 01/22/2024] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a common foodborne pathogen which is frequently used as the reference strain for Salmonella. Investigating the sigma factor network and protomers is crucial to understand the genomic and transcriptomic properties of the bacterium. Its promoters were identified using various methods such as dRNA-seq, ChIP-chip, or ChIP-Seq. However, validation using ChIP-exo, which exhibits higher-resolution performance compared to conventional ChIP, has not been conducted to date. In this study, using the representative strain S. Typhimurium LT2 (LT2), the ChIP-exo experiment was conducted to accurately determine the binding sites of catalytic RNA polymerase subunit RpoB and major sigma factors (RpoD, RpoN, RpoS, and RpoE) during exponential phase. Integrated with the results of RNA-Seq, promoters and sigmulons for the sigma factors and their association with RpoB have been discovered. Notably, the overlapping regions among binding sites of each alternative sigma factor were found. Furthermore, comparative analysis with Escherichia coli str. K-12 substr. MG1655 (MG1655) revealed conserved binding sites of RpoD and RpoN across different species. In the case of small RNAs (sRNAs), 50 sRNAs observed their expression during the exponential growth of LT2. Collectively, the integration of ChIP-exo and RNA-Seq enables genome-scale promoter mapping with high resolution and facilitates the characterization of binding events of alternative sigma factors, enabling a comprehensive understanding of the bacterial sigma factor network and condition-specific active promoters.
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Affiliation(s)
- Sang-Mok Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Hoa Thi Le
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Assiya Taizhanova
- Department of Genetic Engineering and Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, Republic of Korea
| | - Linh Khanh Nong
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Joon Young Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Eun-Jin Lee
- Department of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, United States
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
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14
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Schumacher K, Gelhausen R, Kion-Crosby W, Barquist L, Backofen R, Jung K. Ribosome profiling reveals the fine-tuned response of Escherichia coli to mild and severe acid stress. mSystems 2023; 8:e0103723. [PMID: 37909716 PMCID: PMC10746267 DOI: 10.1128/msystems.01037-23] [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: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Bacteria react very differently to survive in acidic environments, such as the human gastrointestinal tract. Escherichia coli is one of the extremely acid-resistant bacteria and has a variety of acid-defense mechanisms. Here, we provide the first genome-wide overview of the adaptations of E. coli K-12 to mild and severe acid stress at both the transcriptional and translational levels. Using ribosome profiling and RNA sequencing, we uncover novel adaptations to different degrees of acidity, including previously hidden stress-induced small proteins and novel key transcription factors for acid defense, and report mRNAs with pH-dependent differential translation efficiency. In addition, we distinguish between acid-specific adaptations and general stress response mechanisms using denoising autoencoders. This workflow represents a powerful approach that takes advantage of next-generation sequencing techniques and machine learning to systematically analyze bacterial stress responses.
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Affiliation(s)
- Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Rick Gelhausen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Willow Kion-Crosby
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Würzburg, Germany
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
- University of Würzburg, Faculty of Medicine, Würzburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
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15
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Chubiz LM. The Mar, Sox, and Rob Systems. EcoSal Plus 2023; 11:eesp00102022. [PMID: 37220096 PMCID: PMC10729928 DOI: 10.1128/ecosalplus.esp-0010-2022] [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: 09/14/2022] [Accepted: 03/03/2023] [Indexed: 01/28/2024]
Abstract
Environments inhabited by Enterobacteriaceae are diverse and often stressful. This is particularly true for Escherichia coli and Salmonella during host association in the gastrointestinal systems of animals. There, E. coli and Salmonella must survive exposure to various antimicrobial compounds produced or ingested by their host. A myriad of changes to cellular physiology and metabolism are required to achieve this feat. A central regulatory network responsible for sensing and responding to intracellular chemical stressors like antibiotics are the Mar, Sox, and Rob systems found throughout the Enterobacteriaceae. Each of these distinct regulatory networks controls expression of an overlapping set of downstream genes whose collective effects result in increased resistance to a wide array of antimicrobial compounds. This collection of genes is known as the mar-sox-rob regulon. This review will provide an overview of the mar-sox-rob regulon and molecular architecture of the Mar, Sox, and Rob systems.
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Affiliation(s)
- Lon M. Chubiz
- Department of Biology, University of Missouri–St. Louis, St. Louis, Missouri, USA
- Biochemistry and Biotechnology Program, University of Missouri–St. Louis, St. Louis, Missouri, USA
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16
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Wang NE, Courcelle EJ, Coltman SM, Spolek RL, Courcelle J, Courcelle CT. Manganese transporters regulate the resumption of replication in hydrogen peroxide-stressed Escherichia coli. Biometals 2023; 36:1361-1376. [PMID: 37493920 DOI: 10.1007/s10534-023-00523-8] [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: 04/18/2023] [Accepted: 07/06/2023] [Indexed: 07/27/2023]
Abstract
Following hydrogen peroxide treatment, ferrous iron (Fe2+) is oxidized to its ferric form (Fe3+), stripping it from and inactivating iron-containing proteins. Many mononuclear iron enzymes can be remetallated by manganese to restore function, while other enzymes specifically utilize manganese as a cofactor, having redundant activities that compensate for iron-depleted counterparts. DNA replication relies on one or more iron-dependent protein(s) as synthesis abates in the presence of hydrogen peroxide and requires manganese in the medium to resume. Here, we show that manganese transporters regulate the ability to resume replication following oxidative challenge in Escherichia coli. The absence of the primary manganese importer, MntH, impairs the ability to resume replication; whereas deleting the manganese exporter, MntP, or transporter regulator, MntR, dramatically increases the rate of recovery. Unregulated manganese import promoted recovery even in the absence of Fur, which maintains iron homeostasis. Similarly, replication was not restored in oxyR mutants, which cannot upregulate manganese import following hydrogen peroxide stress. Taken together, the results define a central role for manganese transport in restoring replication following oxidative stress.
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Affiliation(s)
- Natalie E Wang
- Department of Biology, Portland State University, Portland, OR, 97201, USA
| | | | - Samantha M Coltman
- Department of Biology, Portland State University, Portland, OR, 97201, USA
| | - Raymond L Spolek
- Department of Biology, Portland State University, Portland, OR, 97201, USA
| | - Justin Courcelle
- Department of Biology, Portland State University, Portland, OR, 97201, USA.
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17
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Pieper LM, Spanogiannopoulos P, Volk RF, Miller CJ, Wright AT, Turnbaugh PJ. The global anaerobic metabolism regulator fnr is necessary for the degradation of food dyes and drugs by Escherichia coli. mBio 2023; 14:e0157323. [PMID: 37642463 PMCID: PMC10653809 DOI: 10.1128/mbio.01573-23] [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: 06/21/2023] [Accepted: 07/06/2023] [Indexed: 08/31/2023] Open
Abstract
IMPORTANCE This work has broad relevance due to the ubiquity of dyes containing azo bonds in food and drugs. We report that azo dyes can be degraded by human gut bacteria through both enzymatic and nonenzymatic mechanisms, even from a single gut bacterial species. Furthermore, we revealed that environmental factors, oxygen, and L-Cysteine control the ability of E. coli to degrade azo dyes due to their impacts on bacterial transcription and metabolism. These results open up new opportunities to manipulate the azoreductase activity of the gut microbiome through the manipulation of host diet, suggest that azoreductase potential may be altered in patients suffering from gastrointestinal disease, and highlight the importance of studying bacterial enzymes for drug metabolism in their natural cellular and ecological context.
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Affiliation(s)
- Lindsey M. Pieper
- Department of Microbiology & Immunology, University of California, San Francisco, California, USA
| | - Peter Spanogiannopoulos
- Department of Microbiology & Immunology, University of California, San Francisco, California, USA
| | - Regan F. Volk
- Department of Microbiology & Immunology, University of California, San Francisco, California, USA
| | - Carson J. Miller
- Biological Sciences Group, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Aaron T. Wright
- Biological Sciences Group, Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Biology, Baylor University, Waco, Texas, USA
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | - Peter J. Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, California, USA
- Chan Zuckerberg Biohub-San Francisco, San Francisco, California, USA
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18
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Gurunathan S, Kim JH. Bacterial extracellular vesicles: Emerging nanoplatforms for biomedical applications. Microb Pathog 2023; 183:106308. [PMID: 37595812 DOI: 10.1016/j.micpath.2023.106308] [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: 05/12/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023]
Abstract
Bacterial extracellular vesicles (BEVs) are nanosized lipid bilayers generated from membranes that are filled with components derived from bacteria. BEVs are important for the physiology, pathogenicity, and interactions between bacteria and their hosts as well. BEVs represent an important mechanism of transport and interaction between cells. Recent advances in biomolecular nanotechnology have enabled the desired properties to be engineered on the surface of BEVs and decoration with desired and diverse biomolecules and nanoparticles, which have potential biomedical applications. BEVs have been the focus of various fields, including nanovaccines, therapeutic agents, and drug delivery vehicles. In this review, we delineate the fundamental aspects of BEVs, including their biogenesis, cargo composition, function, and interactions with host cells. We comprehensively summarize the factors influencing the biogenesis of BEVs. We further highlight the importance of the isolation, purification, and characterization of BEVs because they are essential processes for potential benefits related to host-microbe interactions. In addition, we address recent advancements in BEVs in biomedical applications. Finally, we provide conclusions and future perspectives as well as highlight the remaining challenges of BEVs for different biomedical applications.
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Affiliation(s)
- Sangiliyandi Gurunathan
- Department of Biotechnology, Rathinam College of Arts and Science, Rathinam Techzone Campus, Eachanari, Coimbatore, 641 021, Tamil Nadu, India.
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Seoul, 05029, Korea.
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19
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Han Y, Li W, Filko A, Li J, Zhang F. Genome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli. Nat Commun 2023; 14:5757. [PMID: 37717013 PMCID: PMC10505187 DOI: 10.1038/s41467-023-41572-4] [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: 12/07/2022] [Accepted: 09/08/2023] [Indexed: 09/18/2023] Open
Abstract
Elucidating genome-scale regulatory networks requires a comprehensive collection of gene expression profiles, yet measuring gene expression responses for every transcription factor (TF)-gene pair in living prokaryotic cells remains challenging. Here, we develop pooled promoter responses to TF perturbation sequencing (PPTP-seq) via CRISPR interference to address this challenge. Using PPTP-seq, we systematically measure the activity of 1372 Escherichia coli promoters under single knockdown of 183 TF genes, illustrating more than 200,000 possible TF-gene responses in one experiment. We perform PPTP-seq for E. coli growing in three different media. The PPTP-seq data reveal robust steady-state promoter activities under most single TF knockdown conditions. PPTP-seq also enables identifications of, to the best of our knowledge, previously unknown TF autoregulatory responses and complex transcriptional control on one-carbon metabolism. We further find context-dependent promoter regulation by multiple TFs whose relative binding strengths determined promoter activities. Additionally, PPTP-seq reveals different promoter responses in different growth media, suggesting condition-specific gene regulation. Overall, PPTP-seq provides a powerful method to examine genome-wide transcriptional regulatory networks and can be potentially expanded to reveal gene expression responses to other genetic elements.
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Affiliation(s)
- Yichao Han
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri, USA
| | - Wanji Li
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri, USA
| | - Alden Filko
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri, USA
| | - Jingyao Li
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri, USA
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missouri, USA.
- Division of Biological and Biomedical Sciences, Washington University in St. Louis, Saint Louis, Missouri, USA.
- Institute of Materials Science and Engineering, Washington University in St. Louis, Saint Louis, Missouri, USA.
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20
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Yang SK, Jeong S, Baek I, Choi JI, Lim S, Jung JH. Deionococcus proteotlycius Genomic Library Exploration Enhances Oxidative Stress Resistance and Poly-3-hydroxybutyrate Production in Recombinant Escherichia coli. Microorganisms 2023; 11:2135. [PMID: 37763980 PMCID: PMC10538107 DOI: 10.3390/microorganisms11092135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
Cell growth is inhibited by abiotic stresses during industrial processes, which is a limitation of microbial cell factories. Microbes with robust phenotypes are critical for its maximizing the yield of the target products in industrial biotechnology. Currently, there are several reports on the enhanced production of industrial metabolite through the introduction of Deinococcal genes into host cells, which confers cellular robustness. Deinococcus is known for its unique genetic function thriving in extreme environments such as radiation, UV, and oxidants. In this study, we established that Deinococcus proteolyticus showed greater resistance to oxidation and UV-C than commonly used D. radiodurans. By screening the genomic library of D. proteolyticus, we isolated a gene (deipr_0871) encoding a response regulator, which not only enhanced oxidative stress, but also promoted the growth of the recombinant E. coli strain. The transcription analysis indicated that the heterologous expression of deipr_0871 upregulated oxidative-stress-related genes such as ahpC and sodA, and acetyl-CoA-accumulation-associated genes via soxS regulon. Deipr_0871 was applied to improve the production of the valuable metabolite, poly-3-hydroxybutyrate (PHB), in the synthetic E. coli strain, which lead to the remarkably higher PHB than the control strain. Therefore, the stress tolerance gene from D. proteolyticus should be used in the modification of E. coli for the production of PHB and other biomaterials.
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Affiliation(s)
- Seul-Ki Yang
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea (S.L.)
- Graduate School of Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Soyoung Jeong
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea (S.L.)
- Department of Food and Animal Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Inwoo Baek
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea (S.L.)
| | - Jong-il Choi
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju 61186, Republic of Korea;
| | - Sangyong Lim
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea (S.L.)
- Department of Radiation Science and Technology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Jong-Hyun Jung
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea (S.L.)
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21
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Shin J, Rychel K, Palsson BO. Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome. Cell Rep 2023; 42:112619. [PMID: 37285268 DOI: 10.1016/j.celrep.2023.112619] [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: 12/07/2022] [Revised: 04/27/2023] [Accepted: 05/22/2023] [Indexed: 06/09/2023] Open
Abstract
Vibrio natriegens regulates natural competence through the TfoX and QstR transcription factors, which are involved in external DNA capture and transport. However, the extensive genetic and transcriptional regulatory basis for competency remains unknown. We used a machine-learning approach to decompose Vibrio natriegens's transcriptome into 45 groups of independently modulated sets of genes (iModulons). Our findings show that competency is associated with the repression of two housekeeping iModulons (iron metabolism and translation) and the activation of six iModulons; including TfoX and QstR, a novel iModulon of unknown function, and three housekeeping iModulons (representing motility, polycations, and reactive oxygen species [ROS] responses). Phenotypic screening of 83 gene deletion strains demonstrates that loss of iModulon function reduces or eliminates competency. This database-iModulon-discovery cycle unveils the transcriptomic basis for competency and its relationship to housekeeping functions. These results provide the genetic basis for systems biology of competency in this organism.
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Affiliation(s)
- Jongoh Shin
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Kevin Rychel
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
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22
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Abstract
Oxidative stress is an important and pervasive physical stress encountered by all kingdoms of life, including bacteria. In this review, we briefly describe the nature of oxidative stress, highlight well-characterized protein-based sensors (transcription factors) of reactive oxygen species that serve as standards for molecular sensors in oxidative stress, and describe molecular studies that have explored the potential of direct RNA sensitivity to oxidative stress. Finally, we describe the gaps in knowledge of RNA sensors-particularly regarding the chemical modification of RNA nucleobases. RNA sensors are poised to emerge as an essential layer of understanding and regulating dynamic biological pathways in oxidative stress responses in bacteria and, thus, also represent an important frontier of synthetic biology.
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Affiliation(s)
- Ryan Buchser
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Phillip Sweet
- Integrative Life Sciences Program, University of Texas at Austin, Austin, Texas, USA
| | - Aparna Anantharaman
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Lydia Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA;
- Integrative Life Sciences Program, University of Texas at Austin, Austin, Texas, USA
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23
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Rodionova IA, Lim HG, Rodionov DA, Hutchison Y, Dalldorf C, Gao Y, Monk J, Palsson BO. CyuR is a Dual Regulator for L-Cysteine Dependent Antimicrobial Resistance in Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541025. [PMID: 37292663 PMCID: PMC10245726 DOI: 10.1101/2023.05.16.541025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Hydrogen sulfide (H 2 S), mainly produced from L-cysteine (Cys), renders bacteria highly resistant to oxidative stress. This mitigation of oxidative stress was suggested to be an important survival mechanism to achieve antimicrobial resistance (AMR) in many pathogenic bacteria. CyuR (known as DecR or YbaO) is a recently characterized Cys-dependent transcription regulator, responsible for the activation of the cyuAP operon and generation of hydrogen sulfide from Cys. Despite its potential importance, the regulatory network of CyuR remains poorly understood. In this study, we investigated the roles of the CyuR regulon in a Cys-dependent AMR mechanism in E. coli strains. We found: 1) Cys metabolism has a significant role in AMR and its effect is conserved in many E. coli strains, including clinical isolates; 2) CyuR negatively controls the expression of mdlAB encoding a transporter that exports antibiotics such as cefazolin and vancomycin; 3) CyuR binds to a DNA sequence motif 'GAAwAAATTGTxGxxATTTsyCC' in the absence of Cys, confirmed by an in vitro binding assay; and 4) CyuR may regulate 25 additional genes as suggested by in silico motif scanning and transcriptome sequencing. Collectively, our findings expanded the understanding of the biological roles of CyuR relevant to antibiotic resistance associated with Cys.
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24
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Song J, Zhang H, Wu Z, Qiu M, Zhan X, Zheng C, Shi N, Zhang Q, Zhang L, Yu Y, Fang H. A novel bidirectional regulation mechanism of mancozeb on the dissemination of antibiotic resistance. JOURNAL OF HAZARDOUS MATERIALS 2023; 455:131559. [PMID: 37163893 DOI: 10.1016/j.jhazmat.2023.131559] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/06/2023] [Accepted: 05/01/2023] [Indexed: 05/12/2023]
Abstract
The high abundance of antibiotic resistance genes (ARGs) in the fungicide residual environment, posing a threat to the environment and human health, raises the question of whether and how fungicide promotes the prevalence and dissemination of antibiotic resistance. Here, we reported a novel mechanism underlying bidirectional regulation of a typical heavy-metal-containing fungicide mancozeb on the horizontal transfer of ARGs. Our findings revealed that mancozeb exposure significantly exerted oxidative and osmotic stress on the microbes and facilitated plasmid-mediated ARGs transfer, but its metallic portions (Mn and Zn) were potentially utilized as essential ions by microbes for metalating enzymes to deal with cellular stress and thus reduce the transfer. The results of transcriptome analysis with RT-qPCR confirmed that the expression levels of cellular stress responses and conjugation related genes were drastically altered. It can be concluded mancozeb bidirectionally regulated the ARGs dissemination which may be attributed to the diverse effects on the microbes by its different portions. This novel mechanism provides an updated understanding of neglected fungicide-triggered ARGs dissemination and crucial insight for comprehensive risk assessment of fungicides.
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Affiliation(s)
- Jiajin Song
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Houpu Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China
| | - Zishan Wu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Mengting Qiu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiuping Zhan
- Shanghai Agricultural Technology Extension Service Center, Shanghai 201103, China
| | - Conglai Zheng
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Nan Shi
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States
| | - Qianke Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Luqing Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Yunlong Yu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Hua Fang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China.
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25
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Bang I, Lee SM, Park S, Park JY, Nong LK, Gao Y, Palsson BO, Kim D. Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling. Brief Bioinform 2023; 24:7005164. [PMID: 36702751 DOI: 10.1093/bib/bbad024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/02/2023] [Accepted: 01/08/2023] [Indexed: 01/28/2023] Open
Abstract
Recognizing binding sites of DNA-binding proteins is a key factor for elucidating transcriptional regulation in organisms. ChIP-exo enables researchers to delineate genome-wide binding landscapes of DNA-binding proteins with near single base-pair resolution. However, the peak calling step hinders ChIP-exo application since the published algorithms tend to generate false-positive and false-negative predictions. Here, we report the development of DEOCSU (DEep-learning Optimized ChIP-exo peak calling SUite), a novel machine learning-based ChIP-exo peak calling suite. DEOCSU entails the deep convolutional neural network model which was trained with curated ChIP-exo peak data to distinguish the visualized data of bona fide peaks from false ones. Performance validation of the trained deep-learning model indicated its high accuracy, high precision and high recall of over 95%. Applying the new suite to both in-house and publicly available ChIP-exo datasets obtained from bacteria, eukaryotes and archaea revealed an accurate prediction of peaks containing canonical motifs, highlighting the versatility and efficiency of DEOCSU. Furthermore, DEOCSU can be executed on a cloud computing platform or the local environment. With visualization software included in the suite, adjustable options such as the threshold of peak probability, and iterable updating of the pre-trained model, DEOCSU can be optimized for users' specific needs.
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Affiliation(s)
- Ina Bang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Sang-Mok Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Seojoung Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Joon Young Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Linh Khanh Nong
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Ye Gao
- Department of Bioengineering, University of California San Diego, La Jolla CA 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla CA 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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26
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Park J, Lee SM, Ebrahim A, Scott-Nevros Z, Kim J, Yang L, Sastry A, Seo S, Palsson BO, Kim D. Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli. NAR Genom Bioinform 2023; 5:lqad006. [PMID: 36685725 PMCID: PMC9853098 DOI: 10.1093/nargab/lqad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/07/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023] Open
Abstract
The establishment of experimental conditions for transcriptional regulator network (TRN) reconstruction in bacteria continues to be impeded by the limited knowledge of activating conditions for transcription factors (TFs). Here, we present a novel genome-scale model-driven workflow for designing experimental conditions, which optimally activate specific TFs. Our model-driven workflow was applied to elucidate transcriptional regulation under nitrogen limitation by Nac and NtrC, in Escherichia coli. We comprehensively predict alternative nitrogen sources, including cytosine and cytidine, which trigger differential activation of Nac using a model-driven workflow. In accordance with the prediction, genome-wide measurements with ChIP-exo and RNA-seq were performed. Integrative data analysis reveals that the Nac and NtrC regulons consist of 97 and 43 genes under alternative nitrogen conditions, respectively. Functional analysis of Nac at the transcriptional level showed that Nac directly down-regulates amino acid biosynthesis and restores expression of tricarboxylic acid (TCA) cycle genes to alleviate nitrogen-limiting stress. We also demonstrate that both TFs coherently modulate α-ketoglutarate accumulation stress due to nitrogen limitation by co-activating amino acid and diamine degradation pathways. A systems-biology approach provided a detailed and quantitative understanding of both TF's roles and how nitrogen and carbon metabolic networks respond complementarily to nitrogen-limiting stress.
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Affiliation(s)
- Joon Young Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sang-Mok Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Ali Ebrahim
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zoe K Scott-Nevros
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jaehyung Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Laurence Yang
- Department of Chemical Engineering, Queen's University, Kingston, Canada
| | - Anand Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, and Interdisciplinary Program in Bioengineering, and Institute of Chemical Processes, and Bio-MAX Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
- The Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, 6 Kogle Alle, Hørsholm, Denmark
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
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27
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Čapek J, Večerek B. Why is manganese so valuable to bacterial pathogens? Front Cell Infect Microbiol 2023; 13:943390. [PMID: 36816586 PMCID: PMC9936198 DOI: 10.3389/fcimb.2023.943390] [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: 05/13/2022] [Accepted: 01/04/2023] [Indexed: 02/05/2023] Open
Abstract
Apart from oxygenic photosynthesis, the extent of manganese utilization in bacteria varies from species to species and also appears to depend on external conditions. This observation is in striking contrast to iron, which is similar to manganese but essential for the vast majority of bacteria. To adequately explain the role of manganese in pathogens, we first present in this review that the accumulation of molecular oxygen in the Earth's atmosphere was a key event that linked manganese utilization to iron utilization and put pressure on the use of manganese in general. We devote a large part of our contribution to explanation of how molecular oxygen interferes with iron so that it enhances oxidative stress in cells, and how bacteria have learned to control the concentration of free iron in the cytosol. The functioning of iron in the presence of molecular oxygen serves as a springboard for a fundamental understanding of why manganese is so valued by bacterial pathogens. The bulk of this review addresses how manganese can replace iron in enzymes. Redox-active enzymes must cope with the higher redox potential of manganese compared to iron. Therefore, specific manganese-dependent isoenzymes have evolved that either lower the redox potential of the bound metal or use a stronger oxidant. In contrast, redox-inactive enzymes can exchange the metal directly within the individual active site, so no isoenzymes are required. It appears that in the physiological context, only redox-inactive mononuclear or dinuclear enzymes are capable of replacing iron with manganese within the same active site. In both cases, cytosolic conditions play an important role in the selection of the metal used. In conclusion, we summarize both well-characterized and less-studied mechanisms of the tug-of-war for manganese between host and pathogen.
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Affiliation(s)
- Jan Čapek
- *Correspondence: Jan Čapek, ; Branislav Večerek,
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28
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VanArsdale E, Navid A, Chu MJ, Halvorsen TM, Payne GF, Jiao Y, Bentley WE, Yung MC. Electrogenetic signaling and information propagation for controlling microbial consortia via programmed lysis. Biotechnol Bioeng 2023; 120:1366-1381. [PMID: 36710487 DOI: 10.1002/bit.28337] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023]
Abstract
To probe signal propagation and genetic actuation in microbial consortia, we have coopted the components of both redox and quorum sensing (QS) signaling into a communication network for guiding composition by "programming" cell lysis. Here, we use an electrode to generate hydrogen peroxide as a redox cue that determines consortia composition. The oxidative stress regulon of Escherichia coli, OxyR, is employed to receive and transform this signal into a QS signal that coordinates the lysis of a subpopulation of cells. We examine a suite of information transfer modalities including "monoculture" and "transmitter-receiver" models, as well as a series of genetic circuits that introduce time-delays for altering information relay, thereby expanding design space. A simple mathematical model aids in developing communication schemes that accommodate the transient nature of redox signals and the "collective" attributes of QS signals. We suggest this platform methodology will be useful in understanding and controlling synthetic microbial consortia for a variety of applications, including biomanufacturing and biocontainment.
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Affiliation(s)
- Eric VanArsdale
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, USA.,Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, USA.,Fischell Institute of Biomedical Devices, University of Maryland, College Park, Maryland, USA
| | - Ali Navid
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California, USA
| | - Monica J Chu
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, USA.,Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, USA.,Fischell Institute of Biomedical Devices, University of Maryland, College Park, Maryland, USA
| | - Tiffany M Halvorsen
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California, USA
| | - Gregory F Payne
- Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, USA.,Fischell Institute of Biomedical Devices, University of Maryland, College Park, Maryland, USA
| | - Yongqin Jiao
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, USA.,Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, USA.,Fischell Institute of Biomedical Devices, University of Maryland, College Park, Maryland, USA
| | - Mimi C Yung
- Lawrence Livermore National Laboratory, Biosciences and Biotechnology Division, Livermore, California, USA
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29
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Cheng JH, Zou S, Ma J, Sun DW. Toxic reactive oxygen species stresses for reconfiguring central carbon metabolic fluxes in foodborne bacteria: Sources, mechanisms and pathways. Crit Rev Food Sci Nutr 2023; 63:1806-1821. [PMID: 36688292 DOI: 10.1080/10408398.2023.2169245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The toxic reactive oxygen species (toxROS) is the reactive oxygen species (ROS) beyond the normal concentration of cells, which has inactivation and disinfection effects on foodborne bacteria. However, foodborne bacteria can adapt and survive by physicochemical regulation of antioxidant systems, especially through central carbon metabolism (CCM), which is a significant concern for food safety. It is thus necessary to study the antioxidant regulation mechanisms of CCM in foodborne bacteria under toxROS stresses. Therefore, the purpose of this review is to provide an update and comprehensive overview of the reconfiguration of CCM fluxes in foodborne bacteria that respond to different toxROS stresses. In this review, two key types of toxROS including exogenous toxROS (exo-toxROS) and endogenous toxROS (endo-toxROS) are introduced. Exo-toxROS are produced by disinfectants, such as H2O2 and HOCl, or during food non-thermal processing such as ultraviolet (UV/UVA), cold plasma (CP), ozone (O3), electrolyzed water (EW), pulsed electric field (PEF), pulsed light (PL), and electron beam (EB) processing. Endo-toxROS are generated by bioreagents such as antibiotics (aminoglycosides, quinolones, and β-lactams). Three main pathways for CCM in foodborne bacteria under the toxROS stress are also highlighted, which are glycolysis (EMP), pentose phosphate pathway (PPP), and tricarboxylic acid cycle (TCA). In addition, energy metabolisms throughout these pathways are discussed. Finally, challenges and future work in this area are suggested. It is hoped that this review should be beneficial in providing insights for future research on bacterial antioxidant CCM defence under both exo-toxROS stresses and endo-toxROS stresses.
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Affiliation(s)
- Jun-Hu Cheng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, China.,Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou, China
| | - Sang Zou
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, China.,Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou, China
| | - Ji Ma
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, China.,Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou, China
| | - Da-Wen Sun
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China.,Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, China.,Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou, China.,Food Refrigeration and Computerized Food Technology (FRCFT), Agriculture and Food Science Centre, University College Dublin, National University of Ireland, Dublin 4, Ireland
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30
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Plasma-Generated Nitric Oxide Water Mediates Environmentally Transmitted Pathogenic Bacterial Inactivation via Intracellular Nitrosative Stress. Int J Mol Sci 2023; 24:ijms24031901. [PMID: 36768225 PMCID: PMC9915551 DOI: 10.3390/ijms24031901] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/17/2022] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Over time, the proportion of resistant bacteria will increase. This is a major concern. Therefore, effective and biocompatible therapeutic strategies against these bacteria are urgently needed. Non-thermal plasma has been exhaustively characterized for its antibacterial activity. This study aims to investigate the inactivation efficiency and mechanisms of plasma-generated nitric oxide water (PG-NOW) on pathogenic water, air, soil, and foodborne Gram-negative and Gram-positive bacteria. Using a colony-forming unit assay, we found that PG-NOW treatment effectively inhibited the growth of bacteria. Moreover, the intracellular nitric oxide (NO) accumulation was evaluated by 4-amino-5-methylamino-2',7'-dichlorofluorescein diacetate (DAF-FM DA) staining. The reduction of viable cells unambiguously indicates the anti-microbial effect of PG-NOW. The soxR and soxS genes are associated with nitrosative stress, and oxyR regulation corresponds to oxidative stress in bacterial cells. To support the nitrosative effect mediated by PG-NOW, we have further assessed the soxRS and oxyR gene expressions after treatment. Accordingly, soxRS expression was enhanced, whereas the oxyR expression was decreased following PG-NOW treatment. The disruption of cell morphology was observed using scanning electron microscopy (SEM) analysis. In conclusion, our findings furnish evidence of an initiation point for the further progress and development of PG-NOW-based antibacterial treatments.
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31
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Roth M, Goodall ECA, Pullela K, Jaquet V, François P, Henderson IR, Krause KH. Transposon-Directed Insertion-Site Sequencing Reveals Glycolysis Gene gpmA as Part of the H2O2 Defense Mechanisms in Escherichia coli. Antioxidants (Basel) 2022; 11:antiox11102053. [PMID: 36290776 PMCID: PMC9598634 DOI: 10.3390/antiox11102053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
Hydrogen peroxide (H2O2) is a common effector of defense mechanisms against pathogenic infections. However, bacterial factors involved in H2O2 tolerance remain unclear. Here we used transposon-directed insertion-site sequencing (TraDIS), a technique allowing the screening of the whole genome, to identify genes implicated in H2O2 tolerance in Escherichia coli. Our TraDIS analysis identified 10 mutants with fitness defect upon H2O2 exposure, among which previously H2O2-associated genes (oxyR, dps, dksA, rpoS, hfq and polA) and other genes with no known association with H2O2 tolerance in E. coli (corA, rbsR, nhaA and gpmA). This is the first description of the impact of gpmA, a gene involved in glycolysis, on the susceptibility of E. coli to H2O2. Indeed, confirmatory experiments showed that the deletion of gpmA led to a specific hypersensitivity to H2O2 comparable to the deletion of the major H2O2 scavenger gene katG. This hypersensitivity was not due to an alteration of catalase function and was independent of the carbon source or the presence of oxygen. Transcription of gpmA was upregulated under H2O2 exposure, highlighting its role under oxidative stress. In summary, our TraDIS approach identified gpmA as a member of the oxidative stress defense mechanism in E. coli.
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Affiliation(s)
- Myriam Roth
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
- Correspondence:
| | - Emily C. A. Goodall
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Karthik Pullela
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Vincent Jaquet
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
- READS Unit, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Patrice François
- Genomic Research Laboratory, Infectious Diseases Service, University Hospitals of Geneva, University Medical Center, Michel-Servet 1, 1211 Geneva, Switzerland
| | - Ian R. Henderson
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Karl-Heinz Krause
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
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Bacterial Transcription Factors Bind to Coding Regions and Regulate Internal Cryptic Promoters. mBio 2022; 13:e0164322. [PMID: 36200779 PMCID: PMC9600179 DOI: 10.1128/mbio.01643-22] [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] [Indexed: 11/20/2022] Open
Abstract
Transcription factors (TFs) regulate transcription by binding to the specific sequences at the promoter region. However, the mechanisms and functions of TFs binding within the coding sequences (CDS) remain largely elusive in prokaryotes. To this end, we collected 409 data sets for bacterial TFs, including 104 chromatin immunoprecipitation sequencing (ChIP-seq) assays and 305 data sets from the systematic evolution of ligands by exponential enrichment (SELEX) in seven model bacteria. Interestingly, these TFs displayed the same binding capabilities for both coding and intergenic regions. Subsequent biochemical and genetic experiments demonstrated that several TFs bound to the coding regions and regulated the transcription of the binding or adjacent genes. Strand-specific RNA sequencing revealed that these CDS-binding TFs regulated the activity of the cryptic promoters, resulting in the altered transcription of the corresponding antisense RNA. TF RhpR hindered the transcriptional elongation of a subgenic transcript within a CDS. A ChIP-seq and Ribo-seq coanalysis revealed that RhpR influenced the translational efficiency of binding genes. Taken together, the present study reveals three regulatory mechanisms of CDS-bound TFs within individual genes, operons, and antisense RNAs, which demonstrate the variability of the regulatory mechanisms of TFs and expand upon the complexity of bacterial transcriptomes.
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Tang H, Liu Z, Hu B, Zhu L. Effects of iron mineral adhesion on bacterial conjugation: Interfering the transmission of antibiotic resistance genes through an interfacial process. JOURNAL OF HAZARDOUS MATERIALS 2022; 435:128889. [PMID: 35472548 DOI: 10.1016/j.jhazmat.2022.128889] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/02/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
Bacterial conjugation is one of the most prominent ways for antibiotic resistance genes (ARGs) transmission in the environment. Interfacial interactions between natural colloidal minerals and bacteria can alter the effective contact of bacteria, thereby affecting ARGs conjugation. Understanding the impact of iron minerals, a core component of colloidal minerals, on ARGs conjugation can help assess and intervene in the risk of ARGs transmission. With three selected iron minerals perturbation experiments, it was found that the conjugative transfer of plasmid that carried kanamycin resistance gene was 1.35 - 3.91-fold promoted by low concentrations of iron minerals (i.e., 5 - 100 mg L-1), but inhibited at high concentrations (i.e., 1000 - 2000 mg L-1) as 0.10 - 0.22-fold. Conjugation occurrence was highly relevant to the number of bacteria adhering per unit mass of mineral, thus switch in the adhesion modes of mineral-bacterial determined whether the conjugate transfer of ARGs was facilitated or inhibited. In addition, a unified model was formularized upon the physicochemical and physiological effects of adhesion on conjugation, and it can be used in estimating the critical inhibitory concentration of different iron minerals on conjugation. Our findings indicate natural colloidal minerals have great potential for applications in preventing the environmental propagation of ARGs through interfacial interactions.
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Affiliation(s)
- Huiming Tang
- Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou 310058, China
| | - Zishu Liu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Baolan Hu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lizhong Zhu
- Department of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou 310058, China.
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Hancock SJ, Lo AW, Ve T, Day CJ, Tan L, Mendez AA, Phan MD, Nhu NTK, Peters KM, Richards AC, Fleming BA, Chang C, Ngu DHY, Forde BM, Haselhorst T, Goh KGK, Beatson SA, Jennings MP, Mulvey MA, Kobe B, Schembri MA. Ucl fimbriae regulation and glycan receptor specificity contribute to gut colonisation by extra-intestinal pathogenic Escherichia coli. PLoS Pathog 2022; 18:e1010582. [PMID: 35700218 PMCID: PMC9236248 DOI: 10.1371/journal.ppat.1010582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 06/27/2022] [Accepted: 05/09/2022] [Indexed: 11/25/2022] Open
Abstract
Extra-intestinal pathogenic Escherichia coli (ExPEC) belong to a critical priority group of antibiotic resistant pathogens. ExPEC establish gut reservoirs that seed infection of the urinary tract and bloodstream, but the mechanisms of gut colonisation remain to be properly understood. Ucl fimbriae are attachment organelles that facilitate ExPEC adherence. Here, we investigated cellular receptors for Ucl fimbriae and Ucl expression to define molecular mechanisms of Ucl-mediated ExPEC colonisation of the gut. We demonstrate differential expression of Ucl fimbriae in ExPEC sequence types associated with disseminated infection. Genome editing of strains from two common sequence types, F11 (ST127) and UTI89 (ST95), identified a single nucleotide polymorphism in the ucl promoter that changes fimbriae expression via activation by the global stress-response regulator OxyR, leading to altered gut colonisation. Structure-function analysis of the Ucl fimbriae tip-adhesin (UclD) identified high-affinity glycan receptor targets, with highest affinity for sialyllacto-N-fucopentose VI, a structure likely to be expressed on the gut epithelium. Comparison of the UclD adhesin to the homologous UcaD tip-adhesin from Proteus mirabilis revealed that although they possess a similar tertiary structure, apart from lacto-N-fucopentose VI that bound to both adhesins at low-micromolar affinity, they recognize different fucose- and glucose-containing oligosaccharides. Competitive surface plasmon resonance analysis together with co-structural investigation of UcaD in complex with monosaccharides revealed a broad-specificity glycan binding pocket shared between UcaD and UclD that could accommodate these interactions. Overall, our study describes a mechanism of adaptation that augments establishment of an ExPEC gut reservoir to seed disseminated infections, providing a pathway for the development of targeted anti-adhesion therapeutics. ExPEC infection of the urinary tract and bloodstream is frequently seeded from an intestinal reservoir, necessitating an understanding of the mechanisms that promote gut colonisation. Here we employed molecular and structural approaches to define the regulation and function of ExPEC Ucl fimbriae as a gut colonisation factor. We describe how mutations in the non-coding regulatory region of the ucl promoter cause increased Ucl fimbriae expression and promote enhanced gut colonisation via tuned induction by a global regulator that senses oxygen stress. We further define the glycan receptor targets of Ucl fimbriae and characterise the structural features of the Ucl adhesin that facilitate these interactions. These findings explain how ExPEC can adapt to survival in the gut to seed extra-intestinal infection.
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Affiliation(s)
- Steven J. Hancock
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Alvin W. Lo
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Thomas Ve
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Glycomics, Griffith University Gold Coast Campus, Gold Coast, Queensland, Australia
| | - Christopher J. Day
- Institute for Glycomics, Griffith University Gold Coast Campus, Gold Coast, Queensland, Australia
| | - Lendl Tan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Alejandra A. Mendez
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Minh-Duy Phan
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Nguyen Thi Khanh Nhu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Kate M. Peters
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Amanda C. Richards
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Brittany A. Fleming
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Chyden Chang
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Dalton H. Y. Ngu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Brian M. Forde
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Thomas Haselhorst
- Institute for Glycomics, Griffith University Gold Coast Campus, Gold Coast, Queensland, Australia
| | - Kelvin G. K. Goh
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Scott A. Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael P. Jennings
- Institute for Glycomics, Griffith University Gold Coast Campus, Gold Coast, Queensland, Australia
| | - Matthew A. Mulvey
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Mark A. Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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Tierrafría VH, Rioualen C, Salgado H, Lara P, Gama-Castro S, Lally P, Gómez-Romero L, Peña-Loredo P, López-Almazo AG, Alarcón-Carranza G, Betancourt-Figueroa F, Alquicira-Hernández S, Polanco-Morelos JE, García-Sotelo J, Gaytan-Nuñez E, Méndez-Cruz CF, Muñiz LJ, Bonavides-Martínez C, Moreno-Hagelsieb G, Galagan JE, Wade JT, Collado-Vides J. RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12. Microb Genom 2022; 8. [PMID: 35584008 PMCID: PMC9465075 DOI: 10.1099/mgen.0.000833] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Genomics has set the basis for a variety of methodologies that produce high-throughput datasets identifying the different players that define gene regulation, particularly regulation of transcription initiation and operon organization. These datasets are available in public repositories, such as the Gene Expression Omnibus, or ArrayExpress. However, accessing and navigating such a wealth of data is not straightforward. No resource currently exists that offers all available high and low-throughput data on transcriptional regulation in Escherichia coli K-12 to easily use both as whole datasets, or as individual interactions and regulatory elements. RegulonDB (https://regulondb.ccg.unam.mx) began gathering high-throughput dataset collections in 2009, starting with transcription start sites, then adding ChIP-seq and gSELEX in 2012, with up to 99 different experimental high-throughput datasets available in 2019. In this paper we present a radical upgrade to more than 2000 high-throughput datasets, processed to facilitate their comparison, introducing up-to-date collections of transcription termination sites, transcription units, as well as transcription factor binding interactions derived from ChIP-seq, ChIP-exo, gSELEX and DAP-seq experiments, besides expression profiles derived from RNA-seq experiments. For ChIP-seq experiments we offer both the data as presented by the authors, as well as data uniformly processed in-house, enhancing their comparability, as well as the traceability of the methods and reproducibility of the results. Furthermore, we have expanded the tools available for browsing and visualization across and within datasets. We include comparisons against previously existing knowledge in RegulonDB from classic experiments, a nucleotide-resolution genome viewer, and an interface that enables users to browse datasets by querying their metadata. A particular effort was made to automatically extract detailed experimental growth conditions by implementing an assisted curation strategy applying Natural language processing and machine learning. We provide summaries with the total number of interactions found in each experiment, as well as tools to identify common results among different experiments. This is a long-awaited resource to make use of such wealth of knowledge and advance our understanding of the biology of the model bacterium E. coli K-12.
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Affiliation(s)
- Víctor H Tierrafría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico.,Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
| | - Claire Rioualen
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Heladia Salgado
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Paloma Lara
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Socorro Gama-Castro
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Patrick Lally
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
| | - Laura Gómez-Romero
- Instituto Nacional de Medicina Genómica, INMEGEN, Periférico Sur 4809, Arenal Tepepan, Tlalpan 14610, CDMX, Mexico
| | - Pablo Peña-Loredo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Andrés G López-Almazo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Gabriel Alarcón-Carranza
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Felipe Betancourt-Figueroa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Shirley Alquicira-Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - J Enrique Polanco-Morelos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Jair García-Sotelo
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro 76230, Querétaro, Mexico
| | - Estefani Gaytan-Nuñez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Carlos-Francisco Méndez-Cruz
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Luis J Muñiz
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - César Bonavides-Martínez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico
| | - Gabriel Moreno-Hagelsieb
- Department of Biology, Wilfrid Laurier University, 75 University Ave W, Waterloo, ON N2L 3C5, Canada
| | - James E Galagan
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, NY, USA.,Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY, USA
| | - Julio Collado-Vides
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, Mexico.,Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Universitat Pompeu Fabra(UPF), Barcelona, Spain
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36
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Biofilm and Gene Expression Characteristics of the Carbapenem-Resistant Enterobacterales, Escherichia coli IMP, and Klebsiella pneumoniae NDM-1 Associated with Common Bacterial Infections. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19084788. [PMID: 35457654 PMCID: PMC9024719 DOI: 10.3390/ijerph19084788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/12/2022] [Accepted: 04/12/2022] [Indexed: 01/16/2023]
Abstract
In light of the limited therapeutic options with Carbapenem-Resistant Enterobacterales (CRE) infections, understanding the bacterial risk factors, such as biofilm formation and related gene expression of CRE, is vital. This study investigates the biofilm formation and biofilm-related gene expression of two enteric Enterobacterales with major CR determinants Escherichia coli IMP and Klebsiella pneumoniae NDM-1, which were seen in high prevalence in most common bacterial infections over the past few years. To our knowledge, this is the first study that demonstrated the relationship between biofilm formation and the related gene expression, to understand the potential molecular mechanisms during the biofilm formation in CRE. Biofilms were quantified by tissue culture plate assay at the stages of the biofilm development: initial attachment (6 h), microcolony formation (12 h), maturation (24 h), and dispersion (48 h). In a dispersion, event bacteria detach without any mechanical means and colonise another area. To investigate the influence of different growth conditions on biofilm formation, biofilms were quantified under different growth conditions. In parallel, quantitative real-time PCR (qPCR) assessed the biofilm-related gene expression of a cluster of genes, including biofilm maturation, quorum sensing, stress survival, and antibiotic resistance. Structural changes during biofilm development were assessed via confocal laser scanning microscopy (CLSM). We observed that the biofilm formation of CRE is correlated with the biofilm development stages, with maximum biofilm observed at 24 h at the maturation stage. Our data also showed that biofilm growth, under the condition tested, is the major factor influencing the variability of biofilm gene expression quantification assays. qPCR analyses have demonstrated that the expression of biofilm-related genes is highly correlated with phenotypic biofilm development, and these findings can be further expanded to understand the variation in regulation of such genes in these significant CRE pathogens. Our study demonstrated that both CRE strains, E. coli IMP and K. pneumoniae NDM-1, are high biofilm formers, and genes involved in biofilm development are upregulated during biofilm growth. The characteristic of the increased biofilm formation with the upregulation of antibiotic-resistant and biofilm-related genes indicates the successful pathogenic role of biofilms of these selected CRE and is attributed to their multi-drug resistance ability and successful dissemination of CRE in common bacterial infections.
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37
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Roth M, Jaquet V, Lemeille S, Bonetti EJ, Cambet Y, François P, Krause KH. Transcriptomic Analysis of E. coli after Exposure to a Sublethal Concentration of Hydrogen Peroxide Revealed a Coordinated Up-Regulation of the Cysteine Biosynthesis Pathway. Antioxidants (Basel) 2022; 11:antiox11040655. [PMID: 35453340 PMCID: PMC9026346 DOI: 10.3390/antiox11040655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 12/13/2022] Open
Abstract
Hydrogen peroxide (H2O2) is a key defense component of host-microbe interaction. However, H2O2 concentrations generated by immune cells or epithelia are usually insufficient for bacterial killing and rather modulate bacterial responses. Here, we investigated the impact of sublethal H2O2 concentration on gene expression of E. coli BW25113 after 10 and 60 min of exposure. RNA-seq analysis revealed that approximately 12% of bacterial genes were strongly dysregulated 10 min following exposure to 2.5 mM H2O2. H2O2 exposure led to the activation of a specific antioxidant response and a general stress response. The latter was characterized by a transient down-regulation of genes involved in general metabolism, such as nucleic acid biosynthesis and translation, with a striking and coordinated down-regulation of genes involved in ribosome formation, and a sustained up-regulation of the SOS response. We confirmed the rapid transient and specific response mediated by the transcription factor OxyR leading to up-regulation of antioxidant systems, including the catalase-encoding gene (katG), that rapidly degrade extracellular H2O2 and promote bacterial survival. We documented a strong and transient up-regulation of genes involved in sulfur metabolism and cysteine biosynthesis, which are under the control of the transcription factor CysB. This strong specific transcriptional response to H2O2 exposure had no apparent impact on bacterial survival, but possibly replenishes the stores of oxidized cysteine and glutathione. In summary, our results demonstrate that different stress response mechanisms are activated by H2O2 exposure and highlight the cysteine synthesis as an antioxidant response in E. coli.
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Affiliation(s)
- Myriam Roth
- Department of Pathology and Immunology, Medical School, University of Geneva, 1211 Geneva, Switzerland; (V.J.); (S.L.); (K.-H.K.)
- Correspondence: ; Tel.: +41-223-794-257
| | - Vincent Jaquet
- Department of Pathology and Immunology, Medical School, University of Geneva, 1211 Geneva, Switzerland; (V.J.); (S.L.); (K.-H.K.)
- REaders, Assay Development & Screening Unit (READS Unit), Faculty of Medecine, University of Geneva, 1211 Geneva, Switzerland;
| | - Sylvain Lemeille
- Department of Pathology and Immunology, Medical School, University of Geneva, 1211 Geneva, Switzerland; (V.J.); (S.L.); (K.-H.K.)
| | - Eve-Julie Bonetti
- Genomic Research Laboratory, Infectious Diseases Service, University Hospitals Geneva Medical Center, Michel-Servet 1, 1211 Geneva, Switzerland; (E.-J.B.); (P.F.)
| | - Yves Cambet
- REaders, Assay Development & Screening Unit (READS Unit), Faculty of Medecine, University of Geneva, 1211 Geneva, Switzerland;
| | - Patrice François
- Genomic Research Laboratory, Infectious Diseases Service, University Hospitals Geneva Medical Center, Michel-Servet 1, 1211 Geneva, Switzerland; (E.-J.B.); (P.F.)
| | - Karl-Heinz Krause
- Department of Pathology and Immunology, Medical School, University of Geneva, 1211 Geneva, Switzerland; (V.J.); (S.L.); (K.-H.K.)
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Involvement of E. coli 6S RNA in Oxidative Stress Response. Int J Mol Sci 2022; 23:ijms23073653. [PMID: 35409013 PMCID: PMC8998176 DOI: 10.3390/ijms23073653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 01/22/2023] Open
Abstract
6S RNA, a small non-coding RNA present in almost all bacteria, inhibits transcription via direct binding to RNA polymerase holoenzymes. The mechanism of 6S RNA action was investigated to a large extent in E. coli, however, lack of 6S RNA (ΔssrS) was demonstrated to be unfavorable but not essential for cell survival under various growth conditions. In the present study, we revealed, for the first time, a lethal phenotype of the ΔssrS strain in the presence of high concentrations of H2O2. This phenotype was rescued by complementation of the ssrS gene on a plasmid. We performed comparative qRT-PCR analyses on an enlarged set of mRNAs of genes associated with the oxidative stress response, allowing us to identify four genes known to be involved in this pathway (soxS, ahpC, sodA and tpx) that had decreased mRNA levels in the ΔssrS strain. Finally, we performed comparative proteomic analyses of the wild-type and ΔssrS strains, confirming that ΔssrS bacteria have reduced levels of the proteins AhpC and Tpx involved in H2O2 reduction. Our findings substantiate the crucial role of the riboregulator 6S RNA for bacterial coping with extreme stresses.
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A Fluorescent Probe to Detect Quick Disulfide Reductase Activity in Bacteria. Antioxidants (Basel) 2022; 11:antiox11020377. [PMID: 35204259 PMCID: PMC8868778 DOI: 10.3390/antiox11020377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/17/2022] Open
Abstract
The Trx and Grx systems, two disulfide reductase systems, play critical roles in various cell activities. There are great differences between the thiol redox systems in prokaryotes and mammals. Though fluorescent probes have been widely used to detect these systems in mammalian cells. Very few methods are available to detect rapid changes in the redox systems of prokaryotes. Here we investigated whether Fast-TRFS, a disulfide-containing fluorescent probe utilized in analysis of mammalian thioredoxin reductase, could be used to detect cellular disulfide reducibility in bacteria. Fast-TRFS exhibited good substrate qualities for both bacterial thioredoxin and GSH-glutaredoxin systems in vitro, with Trx system having higher reaction rate. Moreover, the Fast-TRFS was used to detect the disulfide reductase activity in various bacteria and redox-related gene null E. coli. Some glutaredoxin-deficient bacteria had stronger fast disulfide reducibility. The Trx system was shown to be the predominant disulfide reductase for fast disulfide reduction rather than the Grx system. These results demonstrated that Fast-TRFS is a viable probe to detect thiol-dependent disulfide reductases in bacteria. It also indicated that cellular disulfide reduction could be classified into fast and slow reaction, which are predominantly catalyzed by E. coli Trx and Grx system, respectively.
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40
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Derosa L, Routy B, Thomas AM, Iebba V, Zalcman G, Friard S, Mazieres J, Audigier-Valette C, Moro-Sibilot D, Goldwasser F, Silva CAC, Terrisse S, Bonvalet M, Scherpereel A, Pegliasco H, Richard C, Ghiringhelli F, Elkrief A, Desilets A, Blanc-Durand F, Cumbo F, Blanco A, Boidot R, Chevrier S, Daillère R, Kroemer G, Alla L, Pons N, Le Chatelier E, Galleron N, Roume H, Dubuisson A, Bouchard N, Messaoudene M, Drubay D, Deutsch E, Barlesi F, Planchard D, Segata N, Martinez S, Zitvogel L, Soria JC, Besse B. Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in patients with advanced non-small-cell lung cancer. Nat Med 2022; 28:315-324. [PMID: 35115705 DOI: 10.1038/s41591-021-01655-5] [Citation(s) in RCA: 228] [Impact Index Per Article: 114.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 12/06/2021] [Indexed: 12/13/2022]
Abstract
Aside from PD-L1 expression, biomarkers of response to immune checkpoint inhibitors (ICIs) in non-small-cell lung cancer (NSCLC) are needed. In a previous retrospective analysis, we documented that fecal Akkermansia muciniphila (Akk) was associated with clinical benefit of ICI in patients with NSCLC or kidney cancer. In the current study, we performed shotgun-metagenomics-based microbiome profiling in a large cohort of patients with advanced NSCLC (n = 338) treated with first- or second-line ICIs to prospectively validate the predictive value of fecal Akk. Baseline stool Akk was associated with increased objective response rates and overall survival in multivariate analyses, independent of PD-L1 expression, antibiotics, and performance status. Intestinal Akk was accompanied by a richer commensalism, including Eubacterium hallii and Bifidobacterium adolescentis, and a more inflamed tumor microenvironment in a subset of patients. However, antibiotic use (20% of cases) coincided with a relative dominance of Akk above 4.8% accompanied with the genus Clostridium, both associated with resistance to ICI. Our study shows significant differences in relative abundance of Akk that may represent potential biomarkers to refine patient stratification in future studies.
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Affiliation(s)
- Lisa Derosa
- Gustave Roussy Cancer Campus, Villejuif, France.,Cancer Medicine Department, Gustave Roussy, Villejuif, France.,Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée, Ligue Nationale contre le Cancer, Villejuif, France.,Université Paris-Saclay, Ile-de-France, France
| | - Bertrand Routy
- Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Hematology-Oncology Division, Montréal, Quebec, Canada.,Centre de Recherche du CHUM (CRCHUM), Montréal, Quebec, Canada
| | - Andrew Maltez Thomas
- Department CIBIO, University of Trento, Trento, Italy.,European Institute of Oncology (IEO) IRCCS, Milan, Italy
| | - Valerio Iebba
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Gerard Zalcman
- Thoracic Oncology Department-CIC1425/CLIP2 Paris-Nord, Hospital Bichat-Claude Bernard, AP-HP, Université Paris-Diderot, Paris, France
| | - Sylvie Friard
- Pneumology Department, Foch Hospital, Suresnes, France
| | - Julien Mazieres
- Department of Pneumology, Toulouse University Hospital, Toulouse, France
| | | | - Denis Moro-Sibilot
- Department of Thoracic Oncology, Centre Hospitalier Universitaire, Grenoble, France
| | - François Goldwasser
- UPR 4466, Paris Descartes University, Sorbonne Paris Cité, Paris, France.,Department of Medical Oncology, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France.,Immunomodulatory Therapies Multidisciplinary Study Group (CERTIM), Paris, France
| | - Carolina Alves Costa Silva
- Gustave Roussy Cancer Campus, Villejuif, France.,Cancer Medicine Department, Gustave Roussy, Villejuif, France
| | | | | | - Arnaud Scherpereel
- Department of Pulmonary and Thoracic Oncology, University of Lille, University Hospital (CHU), Lille, France
| | | | - Corentin Richard
- Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Hematology-Oncology Division, Montréal, Quebec, Canada.,Centre de Recherche du CHUM (CRCHUM), Montréal, Quebec, Canada
| | - François Ghiringhelli
- Cancer Biology Transfer Platform, Centre Georges-François Leclerc, Dijon, France.,Centre de Recherche INSERM LNC-UMR1231, Dijon, France.,Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France
| | - Arielle Elkrief
- Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Hematology-Oncology Division, Montréal, Quebec, Canada.,Centre de Recherche du CHUM (CRCHUM), Montréal, Quebec, Canada
| | - Antoine Desilets
- Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Hematology-Oncology Division, Montréal, Quebec, Canada.,Centre de Recherche du CHUM (CRCHUM), Montréal, Quebec, Canada
| | | | - Fabio Cumbo
- Department CIBIO, University of Trento, Trento, Italy
| | - Aitor Blanco
- Department CIBIO, University of Trento, Trento, Italy
| | - Romain Boidot
- Unit of Molecular Biology, Department of Biology and Pathology of Tumors, Georges-François Leclerc Cancer Center, UNICANCER, Dijon, France
| | - Sandy Chevrier
- Unit of Molecular Biology, Department of Biology and Pathology of Tumors, Georges-François Leclerc Cancer Center, UNICANCER, Dijon, France
| | | | - Guido Kroemer
- Gustave Roussy Cancer Campus, Villejuif, France.,UPR 4466, Paris Descartes University, Sorbonne Paris Cité, Paris, France.,Centre de Recherche des Cordeliers, INSERM U1138, Equipe labellisée-Ligue contre le cancer, Université de Paris, Institut Universitaire de France, Paris, France.,Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Laurie Alla
- Université Paris-Saclay, INRAE, MGP, Jouy en Josas, France
| | - Nicolas Pons
- Université Paris-Saclay, INRAE, MGP, Jouy en Josas, France
| | | | | | - Hugo Roume
- Université Paris-Saclay, INRAE, MGP, Jouy en Josas, France
| | | | - Nicole Bouchard
- Centre Hospitalier de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Meriem Messaoudene
- Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Hematology-Oncology Division, Montréal, Quebec, Canada.,Centre de Recherche du CHUM (CRCHUM), Montréal, Quebec, Canada
| | | | - Eric Deutsch
- Gustave Roussy Cancer Campus, Villejuif, France.,Université Paris-Saclay, Ile-de-France, France.,Department of Radiation Oncology, Gustave Roussy, Villejuif, France.,INSERM U1030, Radiothérapie Moléculaire et Innovation Thérapeutique, Villejuif, France
| | - Fabrice Barlesi
- Gustave Roussy Cancer Campus, Villejuif, France.,Cancer Medicine Department, Gustave Roussy, Villejuif, France
| | - David Planchard
- Gustave Roussy Cancer Campus, Villejuif, France.,Cancer Medicine Department, Gustave Roussy, Villejuif, France
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy.,European Institute of Oncology (IEO) IRCCS, Milan, Italy
| | - Stéphanie Martinez
- Service des Maladies Respiratoires, Centre Hospitalier d'Aix-en-Provence, Aix-en-Provence, France
| | - Laurence Zitvogel
- Gustave Roussy Cancer Campus, Villejuif, France. .,Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée, Ligue Nationale contre le Cancer, Villejuif, France. .,Université Paris-Saclay, Ile-de-France, France. .,Center of Clinical Investigations in Biotherapies of Cancer (BIOTHERIS) 1428, Villejuif, France.
| | | | - Benjamin Besse
- Gustave Roussy Cancer Campus, Villejuif, France.,Cancer Medicine Department, Gustave Roussy, Villejuif, France.,Université Paris-Saclay, Ile-de-France, France
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41
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Mahilkar A, Venkataraman P, Mall A, Saini S. Experimental Evolution of Anticipatory Regulation in Escherichia coli. Front Microbiol 2022; 12:796228. [PMID: 35087497 PMCID: PMC8787300 DOI: 10.3389/fmicb.2021.796228] [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: 10/16/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Environmental cues in an ecological niche are often temporal in nature. For instance, in temperate climates, temperature is higher in daytime compared to during night. In response to these temporal cues, bacteria have been known to exhibit anticipatory regulation, whereby triggering response to a yet to appear cue. Such an anticipatory response in known to enhance Darwinian fitness, and hence, is likely an important feature of regulatory networks in microorganisms. However, the conditions under which an anticipatory response evolves as an adaptive response are not known. In this work, we develop a quantitative model to study response of a population to two temporal environmental cues, and predict variables which are likely important for evolution of anticipatory regulatory response. We follow this with experimental evolution of Escherichia coli in alternating environments of rhamnose and paraquat for ∼850 generations. We demonstrate that growth in this cyclical environment leads to evolution of anticipatory regulation. As a result, pre-exposure to rhamnose leads to a greater fitness in paraquat environment. Genome sequencing reveals that this anticipatory regulation is encoded via mutations in global regulators. Overall, our study contributes to understanding of how environment shapes the topology of regulatory networks in an organism.
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Affiliation(s)
- Anjali Mahilkar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Pavithra Venkataraman
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Akshat Mall
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Supreet Saini
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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42
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Pareek V, Gupta R, Devineau S, Sivasankaran SK, Bhargava A, Khan MA, Srikumar S, Fanning S, Panwar J. Does Silver in Different Forms Affect Bacterial Susceptibility and Resistance? A Mechanistic Perspective. ACS APPLIED BIO MATERIALS 2022; 5:801-817. [PMID: 35073697 DOI: 10.1021/acsabm.1c01179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The exceptional increase in antibiotic resistance in past decades motivated the scientific community to use silver as a potential antibacterial agent. However, due to its unknown antibacterial mechanism and the pattern of bacterial resistance to silver species, it has not been revolutionized in the health sector. This study deciphers mechanistic aspects of silver species, i.e., ions and lysozyme-coated silver nanoparticles (L-Ag NPs), against E. coli K12 through RNA sequencing analysis. The obtained results support the reservoir nature of nanoparticles for the controlled release of silver ions into bacteria. This study differentiates between the antibacterial mechanism of silver species by discussing the pathway of their entry in bacteria, sequence of events inside cells, and response of bacteria to overcome silver stress. Controlled release of ions from L-Ag NPs not only reduces bacterial growth but also reduces the likelihood of resistance development. Conversely, direct exposure of silver ions, leads to rapid activation of the bacterial defense system leading to development of resistance against silver ions, like the well-known antibiotic resistance problem. These findings provide valuable insight on the mechanism of silver resistance and antibacterial strategies deployed by E. coli K12, which could be a potential target for the generation of aim-based and effective nanoantibiotics.
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Affiliation(s)
- Vikram Pareek
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani 333031, India.,School of Public Health, Physiotherapy and Sports Science, Centre for Food Safety, Science Centre South, University College Dublin, Dublin 4, Ireland
| | - Rinki Gupta
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani 333031, India
| | | | | | - Arpit Bhargava
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani 333031, India
| | - Mohd Azeem Khan
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani 333031, India
| | - Shabrinath Srikumar
- Department of Food, Nutrition and Health, College of Food and Agriculture, UAE University, Al Ain 15551, UAE
| | - Séamus Fanning
- School of Public Health, Physiotherapy and Sports Science, Centre for Food Safety, Science Centre South, University College Dublin, Dublin 4, Ireland.,Institute for Global Food Security, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
| | - Jitendra Panwar
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani 333031, India
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43
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Decker KT, Gao Y, Rychel K, Al Bulushi T, Chauhan S, Kim D, Cho BK, Palsson B. proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms. Nucleic Acids Res 2022; 50:D1077-D1084. [PMID: 34791440 PMCID: PMC8728212 DOI: 10.1093/nar/gkab1043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/05/2021] [Accepted: 10/14/2021] [Indexed: 12/03/2022] Open
Abstract
The transcriptional regulatory network in prokaryotes controls global gene expression mostly through transcription factors (TFs), which are DNA-binding proteins. Chromatin immunoprecipitation (ChIP) with DNA sequencing methods can identify TF binding sites across the genome, providing a bottom-up, mechanistic understanding of how gene expression is regulated. ChIP provides indispensable evidence toward the goal of acquiring a comprehensive understanding of cellular adaptation and regulation, including condition-specificity. ChIP-derived data's importance and labor-intensiveness motivate its broad dissemination and reuse, which is currently an unmet need in the prokaryotic domain. To fill this gap, we present proChIPdb (prochipdb.org), an information-rich, interactive web database. This website collects public ChIP-seq/-exo data across several prokaryotes and presents them in dashboards that include curated binding sites, nucleotide-resolution genome viewers, and summary plots such as motif enrichment sequence logos. Users can search for TFs of interest or their target genes, download all data, dashboards, and visuals, and follow external links to understand regulons through biological databases and the literature. This initial release of proChIPdb covers diverse organisms, including most major TFs of Escherichia coli, and can be expanded to support regulon discovery across the prokaryotic domain.
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Affiliation(s)
- Katherine T Decker
- Department of Bioengineering, University of California, San Diego, La Jolla, CA92093, USA
| | - Ye Gao
- Department of Bioengineering, University of California, San Diego, La Jolla, CA92093, USA
| | - Kevin Rychel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA92093, USA
| | - Tahani Al Bulushi
- Department of Bioengineering, University of California, San Diego, La Jolla, CA92093, USA
| | - Siddharth M Chauhan
- Department of Bioengineering, University of California, San Diego, La Jolla, CA92093, USA
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon34141, Republic of Korea
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA92093, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
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44
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Gupta A, Imlay JA. Escherichia coli induces DNA repair enzymes to protect itself from low-grade hydrogen peroxide stress. Mol Microbiol 2021; 117:754-769. [PMID: 34942039 DOI: 10.1111/mmi.14870] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/18/2021] [Accepted: 12/18/2021] [Indexed: 11/30/2022]
Abstract
E. coli responds to hydrogen peroxide (H2 O2 ) by inducing defenses that protect H2 O2 -sensitive enzymes. DNA is believed to be another important target of oxidation, and E. coli contains enzymes that can repair oxidative lesions in vitro. However, those enzymes are not known to be induced by H2 O2 , and experiments have indicated that they are not necessary for the cell to withstand natural (low-micromolar) concentrations. In this study we used H2 O2 -scavenging mutants to impose controlled doses of H2 O2 for extended time. Transcriptomic analysis revealed that in the presence of 1 µM cytoplasmic H2 O2 , the OxyR transcription factor induced xthA, encoding exonuclease III. The xthA mutants survived a conventional 15-minute exposure to even 100 times this level of H2 O2 . However, when these mutants were exposed to 1 µM H2 O2 for hours, they accumulated DNA lesions, failed to propagate, and eventually died. Although endonuclease III (nth) was not induced, nth mutants struggled to grow. Low-grade H2 O2 stress also activated the SOS regulon, and when this induction was blocked, cell replication stopped. Collectively, these data indicate that physiological levels of H2 O2 are a real threat to DNA, and the engagement of the base-excision-repair and SOS systems is necessary to enable propagation during protracted stress.
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Affiliation(s)
- Anshika Gupta
- Department of Microbiology, University of Illinois, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - James A Imlay
- Department of Microbiology, University of Illinois, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
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45
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Hill PWS, Moldoveanu AL, Sargen M, Ronneau S, Glegola-Madejska I, Beetham C, Fisher RA, Helaine S. The vulnerable versatility of Salmonella antibiotic persisters during infection. Cell Host Microbe 2021; 29:1757-1773.e10. [PMID: 34731646 DOI: 10.1016/j.chom.2021.10.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/23/2021] [Accepted: 10/08/2021] [Indexed: 11/30/2022]
Abstract
Tolerance and persistence are superficially similar phenomena by which bacteria survive bactericidal antibiotics. It is assumed that the same physiology underlies survival of individual tolerant and persistent bacteria. However, by comparing tolerance and persistence during Salmonella Typhimurium infection, we reveal that these two phenomena are underpinned by different bacterial physiologies. Multidrug-tolerant mutant Salmonella enter a near-dormant state protected from immune-mediated genotoxic damages. However, the numerous tolerant cells, optimized for survival, lack the capabilities necessary to initiate infection relapse following antibiotic withdrawal. In contrast, persisters retain an active state. This leaves them vulnerable to accumulation of macrophage-induced dsDNA breaks but concurrently confers the versatility to initiate infection relapse if protected by RecA-mediated DNA repair. Accordingly, recurrent, invasive, non-typhoidal Salmonella clinical isolates display hallmarks of persistence rather than tolerance during antibiotic treatment. Our study highlights the complex trade-off that antibiotic-recalcitrant Salmonella balance to act as a reservoir for infection relapse.
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Affiliation(s)
- Peter W S Hill
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK.
| | - Ana Laura Moldoveanu
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Molly Sargen
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Séverin Ronneau
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Izabela Glegola-Madejska
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Catrin Beetham
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Robert A Fisher
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Sophie Helaine
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK; Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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46
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Joudeh N, Saragliadis A, Schulz C, Voigt A, Almaas E, Linke D. Transcriptomic Response Analysis of Escherichia coli to Palladium Stress. Front Microbiol 2021; 12:741836. [PMID: 34690987 PMCID: PMC8533678 DOI: 10.3389/fmicb.2021.741836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/03/2021] [Indexed: 12/13/2022] Open
Abstract
Palladium (Pd), due to its unique catalytic properties, is an industrially important heavy metal especially in the form of nanoparticles. It has a wide range of applications from automobile catalytic converters to the pharmaceutical production of morphine. Bacteria have been used to biologically produce Pd nanoparticles as a new environmentally friendly alternative to the currently used energy-intensive and toxic physicochemical methods. Heavy metals, including Pd, are toxic to bacterial cells and cause general and oxidative stress that hinders the use of bacteria to produce Pd nanoparticles efficiently. In this study, we show in detail the Pd stress-related effects on E. coli. Pd stress effects were measured as changes in the transcriptome through RNA-Seq after 10 min of exposure to 100 μM sodium tetrachloropalladate (II). We found that 709 out of 3,898 genes were differentially expressed, with 58% of them being up-regulated and 42% of them being down-regulated. Pd was found to induce several common heavy metal stress-related effects but interestingly, Pd causes unique effects too. Our data suggests that Pd disrupts the homeostasis of Fe, Zn, and Cu cellular pools. In addition, the expression of inorganic ion transporters in E. coli was found to be massively modulated due to Pd intoxication, with 17 out of 31 systems being affected. Moreover, the expression of several carbohydrate, amino acid, and nucleotide transport and metabolism genes was vastly changed. These results bring us one step closer to the generation of genetically engineered E. coli strains with enhanced capabilities for Pd nanoparticles synthesis.
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Affiliation(s)
- Nadeem Joudeh
- Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Christian Schulz
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - André Voigt
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Eivind Almaas
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Dirk Linke
- Department of Biosciences, University of Oslo, Oslo, Norway
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47
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Gu H, Cai X, Zhang X, Luo J, Zhang X, Hu X, Cai W, Li G. A previously uncharacterized two-component signaling system in uropathogenic Escherichia coli coordinates protection against host-derived oxidative stress with activation of hemolysin-mediated host cell pyroptosis. PLoS Pathog 2021; 17:e1010005. [PMID: 34653218 PMCID: PMC8550376 DOI: 10.1371/journal.ppat.1010005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 10/27/2021] [Accepted: 10/04/2021] [Indexed: 12/22/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) deploy an array of virulence factors to successfully establish urinary tract infections. Hemolysin is a pore-forming toxin, and its expression correlates with the severity of UPEC infection. Two-component signaling systems (TCSs) are a major mechanism by which bacteria sense environmental cues and respond by initiating adaptive responses. Here, we began this study by characterizing a novel TCS (C3564/C3565, herein renamed orhK/orhR for oxidative resistance and hemolysis kinase/regulator) that is encoded on a UPEC pathogenicity island, using bioinformatic and biochemical approaches. A prevalence analysis indicates that orhK/orhR is highly associated with the UPEC pathotype, and it rarely occurs in other E. coli pathotypes tested. We then demonstrated that OrhK/OrhR directly activates the expression of a putative methionine sulfoxide reductase system (C3566/C3567) and hemolysin (HlyA) in response to host-derived hydrogen peroxide (H2O2) exposure. OrhK/OrhR increases UPEC resistance to H2O2in vitro and survival in macrophages in cell culture via C3566/C3567. Additionally, OrhK/OrhR mediates hemolysin-induced renal epithelial cell and macrophage death via a pyroptosis pathway. Reducing intracellular H2O2 production by a chemical inhibitor impaired OrhK/OrhR-mediated activation of c3566-c3567 and hlyA. We also uncovered that UPEC links the two key virulence traits by cotranscribing the c3566-c3567 and hlyCABD operons. Taken together, our data suggest a paradigm in which a signal transduction system coordinates both bacterial pathogen defensive and offensive traits in the presence of host-derived signals; and this exquisite mechanism likely contributes to hemolysin-induced severe pathological outcomes. Uropathogenic Escherichia coli (UPEC) is the primary cause of urinary tract infections, and approximately half of UPEC isolates produce a pore-forming toxin, hemolysin. Clinically, hemolysin carriage is associated with severe pathology and symptoms during UPEC infections. However, overexpression of hemolysin can be detrimental to UPEC colonization. Therefore, fine-tuning of hemolysin expression in response to in vivo-relevant signals is critical for optimal UPEC fitness in the urinary tract. In this study, we describe a virulence strategy employed by UPEC, i.e., the bacteria use a two-component signaling (TCS) system to coordinate oxidative stress resistance and hemolysin-mediated pyroptosis of host cells in response to host-derived oxidative signals. The TCS achieves this coordination by cotranscribing genes encoding the oxidative stress resistance and the hemolysin. As a result, UPEC is able to link defense to offense, and this exquisite virulence mechanism likely contributes to UPEC fitness in vivo and hemolysin-induced severe pathological outcomes.
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Affiliation(s)
- Hongwei Gu
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
- Central Laboratory, Nanjing Integrated Traditional Chinese and Western Medicine Hospital Affiliated with Nanjing University of Chinese Medicine, Nanjing, China
| | - Xuwang Cai
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xinyang Zhang
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jie Luo
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Xiaoyang Zhang
- Central Laboratory, Nanjing Integrated Traditional Chinese and Western Medicine Hospital Affiliated with Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiao Hu
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Wentong Cai
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- * E-mail: (WC); (GL)
| | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- * E-mail: (WC); (GL)
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48
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Kuncharoen N, Yuki M, Kudo T, Okuma M, Booncharoen A, Mhuantong W, Tanasupawat S. Comparative genomics and proposal of Streptomyces radicis sp. nov., an endophytic actinomycete from roots of plants in Thailand. Microbiol Res 2021; 254:126889. [PMID: 34689101 DOI: 10.1016/j.micres.2021.126889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 08/29/2021] [Accepted: 09/30/2021] [Indexed: 10/20/2022]
Abstract
Strains DS1-2T and AZ1-7, which were isolated from roots of plants, were taxonomically characterized based on polyphasic taxonomic and taxogenomic approaches. Both strains were Gram-stain-positive and filamentous bacteria which contained LL-diaminopimelic acid in cell-wall peptidoglycan and glucose and ribose in whole-cell hydrolysates. MK-9(H6), MK-10(H6), MK-9(H8), MK-10(H8) and MK-10(H4) were major menaquinones; iso-C16:0 and iso-C16:1G were predominant cellular fatty acids; diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol mannoside presented as major phospholipids; and the DNA G+C contents of 73.2 mol%. Strains DS1-2T and AZ1-7 showed 97.6-98.0 % 16S rRNA gene sequence similarity, 81.0-82.0 % ANIb, 84.8-85.3 % ANIm and 22.0-23.1 % digital DDH to their related type strains: S. specialis GW41-1564T and S. hoynatensis S1412T. Comparative genomics results of these strains and their related type strains also revealed the differences and distributions of key genes associated with stress responses, environmental variables, plant interactions and bioactive metabolites. Based on the phenotypic, chemotaxonomic and genomic data, strains DS1-2T and AZ1-7 could be assigned to the novel species within the genus Streptomyces for which the name Streptomyces radicis sp. nov. is proposed. The type strain is DS1-2T (=JCM 32152T =KCTC 39738T =TISTR 2403T).
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Affiliation(s)
- Nattakorn Kuncharoen
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand; Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok 10900, Thailand
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Okuma
- Japan Collection of Microorganisms, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Auttaporn Booncharoen
- Food Biotechnology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Wuttichai Mhuantong
- Enzyme Technology Research Team, Biorefinery and Bioproducts Technology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand.
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49
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Li F, Xiong XS, Yang YY, Wang JJ, Wang MM, Tang JW, Liu QH, Wang L, Gu B. Effects of NaCl Concentrations on Growth Patterns, Phenotypes Associated With Virulence, and Energy Metabolism in Escherichia coli BW25113. Front Microbiol 2021; 12:705326. [PMID: 34484145 PMCID: PMC8415458 DOI: 10.3389/fmicb.2021.705326] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/21/2021] [Indexed: 12/02/2022] Open
Abstract
According to the sit-and-wait hypothesis, long-term environmental survival is positively correlated with increased bacterial pathogenicity because high durability reduces the dependence of transmission on host mobility. Many indirectly transmitted bacterial pathogens, such as Mycobacterium tuberculosis and Burkhoderia pseudomallei, have high durability in the external environment and are highly virulent. It is possible that abiotic stresses may activate certain pathways or the expressions of certain genes, which might contribute to bacterial durability and virulence, synergistically. Therefore, exploring how bacterial phenotypes change in response to environmental stresses is important for understanding their potentials in host infections. In this study, we investigated the effects of different concentrations of salt (sodium chloride, NaCl), on survival ability, phenotypes associated with virulence, and energy metabolism of the lab strain Escherichia coli BW25113. In particular, we investigated how NaCl concentrations influenced growth patterns, biofilm formation, oxidative stress resistance, and motile ability. In terms of energy metabolism that is central to bacterial survival, glucose consumption, glycogen accumulation, and trehalose content were measured in order to understand their roles in dealing with the fluctuation of osmolarity. According to the results, trehalose is preferred than glycogen at high NaCl concentration. In order to dissect the molecular mechanisms of NaCl effects on trehalose metabolism, we further checked how the impairment of trehalose synthesis pathway (otsBA operon) via single-gene mutants influenced E. coli durability and virulence under salt stress. After that, we compared the transcriptomes of E. coli cultured at different NaCl concentrations, through which differentially expressed genes (DEGs) and differential pathways with statistical significance were identified, which provided molecular insights into E. coli responses to NaCl concentrations. In sum, this study explored the in vitro effects of NaCl concentrations on E. coli from a variety of aspects and aimed to facilitate our understanding of bacterial physiological changes under salt stress, which might help clarify the linkages between bacterial durability and virulence outside hosts under environmental stresses.
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Affiliation(s)
- Fen Li
- Medical Technology School of Xuzhou Medical University, Xuzhou, China
| | - Xue-Song Xiong
- Medical Technology School of Xuzhou Medical University, Xuzhou, China
| | - Ying-Ying Yang
- School of Life Sciences, Xuzhou Medical University, Xuzhou, China
| | - Jun-Jiao Wang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Meng-Meng Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Jia-Wei Tang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Qing-Hua Liu
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Taipa, China
| | - Liang Wang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China.,Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Bing Gu
- Medical Technology School of Xuzhou Medical University, Xuzhou, China.,Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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50
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Qiu X, Gao T, Yang J, Wang E, Liu L, Yuan H. Water-Soluble Humic Materials Modulating Metabolism and Triggering Stress Defense in Sinorhizobium fredii. Microbiol Spectr 2021; 9:e0029321. [PMID: 34479412 PMCID: PMC8552645 DOI: 10.1128/spectrum.00293-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 07/29/2021] [Indexed: 11/23/2022] Open
Abstract
Bacteria have evolved a series of mechanisms to maintain their survival and reproduction in changeable and stressful environments. In-depth understanding of these mechanisms can allow for better developing and utilizing of bacteria with various biological functions. In this study, we found that water-soluble humic materials (WSHM), a well-known environment-friendly plant growth biostimulant, significantly promoted the free-living growth and survival of Sinorhizobium fredii CCBAU45436 in a bell-shaped, dose-dependent manner, along with more-efficient carbon source consumption and relief of medium acidification. By using RNA-Seq analysis, a total of 1,136 genes significantly up-/downregulated by external addition of WSHM were identified under test conditions. These differentially expressed genes (DEGs) were enriched in functional categories related to carbon/nitrogen metabolism, cellular stress response, and genetic information processing. Further protein-protein interaction (PPI) network analysis and reverse genetic engineering indicated that WSHM might reprogram the transcriptome through inhibiting the expression of key hub gene rsh, which encodes a bifunctional enzyme catalyzing synthesis and hydrolysis of the "magic spot" (p)ppGpp. In addition, the root colonization and viability in soil of S. fredii CCBAU45436 were increased by WSHM. These findings provide us with new insights into how WSHM benefit bacterial adaptations and demonstrate great application value to be a unique inoculant additive. IMPORTANCE Sinorhizobium fredii CCBAU45436 is a highly effective, fast-growing rhizobium that can establish symbiosis with multiple soybean cultivars. However, it is difficult to maintain the high-density effective viable cells in the rhizobial inoculant for the stressful conditions during production, storage, transport, and application. Here, we showed that WSHM greatly increased the viable cells of S. fredii CCBAU45436 in culture, modulating metabolism and triggering stress defense. The root colonization and viability in soil of S. fredii CCBAU45436 were also increased by WSHM. Our results shed new insights into the effects of WSHM on bacteria and the importance of metabolism and stress defense during the bacteria's whole life. In addition, the functional mechanism of WSHM may provide candidate genes for improving environmental adaptability and application potential of bacteria through genetic engineering.
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Affiliation(s)
- Xiaoqian Qiu
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Tongguo Gao
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Jinshui Yang
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Entao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Liang Liu
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Hongli Yuan
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
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