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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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Hashimoto M, Mao BH, Chiou CS, Huang WC, Nyoman Putra Dwija IB, Jeng SL, Wu JJ, Wang MC, Lin WH, Tseng CC, Teng CH. Association between Escherichia coli with NotI-restriction resistance and urinary tract infections. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:686-694. [PMID: 34963576 DOI: 10.1016/j.jmii.2021.11.010] [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: 03/03/2021] [Revised: 11/12/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Escherichia coli is the most common cause of urinary tract infections (UTIs). It is widely accepted that uropathogenic E. coli (UPEC) mainly emerge from the distal gut microbiota. Identification of bacterial characteristics that are able to differentiate UPEC from fecal commensal strains will facilitate the development of novel strategies to detect and monitor the spread of UPEC. METHODS Fifty fecal commensal, 83 UTI-associated and 40 biliary tract infection (BTI)-associated E. coli isolates were analyzed. The NotI restriction patterns of chromosomal DNA in the isolates were determined by pulse-field gel electrophoresis. The phylogenetic types and the presence of 9 known virulence genes of each isolate were determined by PCR analyses. Additionally, the susceptibilities of the isolates to antibiotics were revealed. Then the associations of NotI resistance with UTI-associated isolates, phylotypes, and antibiotic resistance were assessed. RESULTS NotI resistance was correlated with UTI-associated isolates, compared to the fecal isolates. Consistently, NotI-resistant isolates harbored a greater number of virulence factors and mainly belonged to phylotype B2. Additionally NotI resistance was correlated with chloramphenicol resistance among the bacteria. Among the fecal, UTI-associated and BTI-associated groups, the distribution of NotI-resistant group B2 isolates was correlated with UTI-associated bacteria. CONCLUSION NotI resistance alone is a potential marker for distinguishing fecal strains and UPEC, while the combination of NotI resistance and B2 phylogeny is a candidate marker to differentiate UPEC from fecal and other extraintestinal pathogenic E. coli. Additionally, NotI resistance may be valuable for assessing the potential of chloramphenicol resistance of E. coli.
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Affiliation(s)
- 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; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Bin-Hsu Mao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
| | - Chien-Shun Chiou
- The Central Region Laboratory, Center of Research and Diagnostics, Centers for Disease Control, Taichung City, Taiwan
| | - Wen-Chun Huang
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ida Bagus Nyoman Putra Dwija
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Microbiology Clinic Department, Faculty of Medicine, Udayana University, Denpasar, Bali, Indonesia
| | - Shuen-Lin Jeng
- Department of Statistics, Institute of Data Science, and Center for Innovative FinTech Business Models, National Cheng Kung University, Tainan, Taiwan
| | - Jiunn-Jong Wu
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Ming-Cheng Wang
- Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, Taiwan; Institute of Clinical Pharmacy and Pharmaceutical Sciences, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
| | - Wei-Hung Lin
- Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
| | - Chin-Chung Tseng
- Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, 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; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan.
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Qin L, Walk TC, Han P, Chen L, Zhang S, Li Y, Hu X, Xie L, Yang Y, Liu J, Lu X, Yu C, Tian J, Shaff JE, Kochian LV, Liao X, Liao H. Adaption of Roots to Nitrogen Deficiency Revealed by 3D Quantification and Proteomic Analysis. PLANT PHYSIOLOGY 2019; 179:329-347. [PMID: 30455286 PMCID: PMC6324228 DOI: 10.1104/pp.18.00716] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 11/02/2018] [Indexed: 05/16/2023]
Abstract
Rapeseed (Brassica napus) is an important oil crop worldwide. However, severe inhibition of rapeseed production often occurs in the field due to nitrogen (N) deficiency. The root system is the main organ to acquire N for plant growth, but little is known about the mechanisms underlying rapeseed root adaptions to N deficiency. Here, dynamic changes in root architectural traits of N-deficient rapeseed plants were evaluated by 3D in situ quantification. Root proteome responses to N deficiency were analyzed by the tandem mass tag-based proteomics method, and related proteins were characterized further. Under N deficiency, rapeseed roots become longer, with denser cells in the meristematic zone and larger cells in the elongation zone of root tips, and also become softer with reduced solidity. A total of 171 and 755 differentially expressed proteins were identified in short- and long-term N-deficient roots, respectively. The abundance of proteins involved in cell wall organization or biogenesis was highly enhanced, but most identified peroxidases were reduced in the N-deficient roots. Notably, peroxidase activities also were decreased, which might promote root elongation while lowering the solidity of N-deficient roots. These results were consistent with the cell wall components measured in the N-deficient roots. Further functional analysis using transgenic Arabidopsis (Arabidopsis thaliana) plants demonstrated that the two root-related differentially expressed proteins contribute to the enhanced root growth under N deficiency conditions. These results provide insights into the global changes of rapeseed root responses to N deficiency and may facilitate the development of rapeseed cultivars with high N use efficiency through root-based genetic improvements.
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Affiliation(s)
- Lu Qin
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture, Wuhan 430062, China
| | | | - Peipei Han
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture, Wuhan 430062, China
| | - Liyu Chen
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sheng Zhang
- Institute of Biotechnology, Cornell University, Ithaca, New York 14853-2703
| | - Yinshui Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture, Wuhan 430062, China
| | - Xiaojia Hu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture, Wuhan 430062, China
| | - Lihua Xie
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture, Wuhan 430062, China
| | - Yong Yang
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Cornell University, Ithaca, New York 14853
| | - Jiping Liu
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Cornell University, Ithaca, New York 14853
| | - Xing Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Root Biology Center, South China Agricultural University, Guangzhou 510642, China
| | - Changbing Yu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture, Wuhan 430062, China
| | - Jiang Tian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Root Biology Center, South China Agricultural University, Guangzhou 510642, China
| | - Jon E Shaff
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Cornell University, Ithaca, New York 14853
| | - Leon V Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon S7N 4J8, Canada
| | - Xing Liao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetics Improvement of Oil Crops of the Ministry of Agriculture, Wuhan 430062, China
| | - Hong Liao
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Parent E, Burns P, Desrochers A, Boulianne M. A Ligated Intestinal Loop Model in Anesthetized Specific Pathogen Free Chickens to Study Clostridium Perfringens Virulence. J Vis Exp 2018. [PMID: 30371671 DOI: 10.3791/57523] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Necrotic enteritis was studied in chickens using various in vivo infection models. Most of these use a combination of predisposing factors, such as coccidiosis and diet, with gavage or administration via the feed using Clostridium perfringens. In these models, the comparison of multiple C. perfringens strains for virulence studies requires a large number of hosts to obtain significant results. Mortality during the course of the study can be high depending on the experimental model, hence raising ethical concerns regarding animal welfare in research. The development of new infection models requiring fewer animals to study pathogenesis, yet providing statistically significant and valid results, is important in reducing animal use in research. Intestinal ligated loop models have been used to study clostridial infections in various species such as mice, rabbits and calves. Following surgical procedures to create ligated loop segments, C. perfringens strains are injected directly into the loops to establish a close contact between the bacteria and the intestinal mucosa. Samples of the small intestine and luminal contents are taken at the termination of the procedures after a few hours. Multiple bacterial strains can be inoculated in each animal, hence reducing the number of required subjects in the experiments. Also, procedures are performed under general anesthesia to reduce animal pain. In chickens, this model would be more appropriate than oral administration to compare C. perfringens strain pathogenicity because fewer animals are needed, no predisposing factors are required to induce the disease, and pain is controlled by analgesics. The intestinal ligated loop model is poorly described in chickens and standardization is essential for its optimal use. This manuscript provides all the necessary steps to create numerous intestinal ligated loops in chickens and brings information on the critical points to obtain valid results.
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Affiliation(s)
- Eric Parent
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal
| | | | - André Desrochers
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal
| | - Martine Boulianne
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal;
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Insights into drug resistance mechanisms in Clostridium difficile. Essays Biochem 2017; 61:81-88. [PMID: 28258232 DOI: 10.1042/ebc20160062] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 01/03/2017] [Accepted: 01/05/2017] [Indexed: 01/05/2023]
Abstract
The incidence of Clostridium difficile infection has been elevated and becoming common in hospitals worldwide. Although antibiotics usually serve as the primary treatment for bacterial infection including C. difficile infection, limitations and failures have been evident due to drug resistance. Antibiotic resistance in C. difficile has been recognized as one of the most important factors to promote the infection and increase the level of severity and the recurrence rate. Several outbreaks in many countries have been linked to the emergence of hypervirulent drug-resistant strains. This pathogen harbours various mechanisms against the actions of antibiotics. The present study highlights three main drug-resistant strategies in C. difficile including drug inactivation, target modification and efflux pump. Other mechanisms that potentially contribute to drug-resistant traits in this organism are also discussed.
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Fields FR, Lee SW, McConnell MJ. Using bacterial genomes and essential genes for the development of new antibiotics. Biochem Pharmacol 2016; 134:74-86. [PMID: 27940263 DOI: 10.1016/j.bcp.2016.12.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/05/2016] [Indexed: 10/20/2022]
Abstract
The shrinking antibiotic development pipeline together with the global increase in antibiotic resistant infections requires that new molecules with antimicrobial activity are developed. Traditional empirical screening approaches of natural and non-natural compounds have identified the majority of antibiotics that are currently available, however this approach has produced relatively few new antibiotics over the last few decades. The vast amount of bacterial genome sequence information that has become available since the sequencing of the first bacterial genome more than 20years ago holds potential for contributing to the discovery of novel antimicrobial compounds. Comparative genomic approaches can identify genes that are highly conserved within and between bacterial species, and thus may represent genes that participate in key bacterial processes. Whole genome mutagenesis studies can also identify genes necessary for bacterial growth and survival under different environmental conditions, making them attractive targets for the development of novel inhibitory compounds. In addition, transcriptomic and proteomic approaches can be used to characterize RNA and protein levels on a cellular scale, providing information on bacterial physiology that can be applied to antibiotic target identification. Finally, bacterial genomes can be mined to identify biosynthetic pathways that produce many intrinsic antimicrobial compounds and peptides. In this review, we provide an overview of past and current efforts aimed at using bacterial genomic data in the discovery and development of novel antibiotics.
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Affiliation(s)
- Francisco R Fields
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Shaun W Lee
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Michael J McConnell
- Biomedical Institute of Seville, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain.
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Ceciliani F, Restelli L, Lecchi C. Proteomics in farm animals models of human diseases. Proteomics Clin Appl 2014; 8:677-88. [PMID: 24595991 DOI: 10.1002/prca.201300080] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 11/18/2013] [Accepted: 01/14/2014] [Indexed: 12/21/2022]
Abstract
The need to provide in vivo complex environments to understand human diseases strongly relies on the use of animal models, which traditionally include small rodents and rabbits. It is becoming increasingly evident that the few species utilised to date cannot be regarded as universal. There is a great need for new animal species that are naturally endowed with specific features relevant to human diseases. Farm animals, including pigs, cows, sheep and horses, represent a valid alternative to commonly utilised rodent models. There is an ample scope for the application of proteomic techniques in farm animals, and the establishment of several proteomic maps of plasma and tissue has clearly demonstrated that farm animals provide a disease environment that closely resembles that of human diseases. The present review offers a snapshot of how proteomic techniques have been applied to farm animals to improve their use as biomedical models. Focus will be on specific topics of biomedical research in which farm animal models have been characterised through the application of proteomic techniques.
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Affiliation(s)
- Fabrizio Ceciliani
- Department of Veterinary Sciences and Public Health, Università di Milano, Milan, Italy; Interdepartmental Centre for Studies on Mammary Gland, Università di Milano, Milan, Italy
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Chilton CH, Gharbia SE, Fang M, Misra R, Poxton IR, Borriello SP, Shah HN. Comparative proteomic analysis of Clostridium difficile isolates of varying virulence. J Med Microbiol 2014; 63:489-503. [DOI: 10.1099/jmm.0.070409-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The soluble proteome of three Clostridium difficile strains of varying pathogenic potential, designated B-1, Tra 5/5 and 027 SM, were compared using differential in-gel electrophoresis in which the proteins of each strain were labelled with CyDyes. This enabled visual inspection of the 2D profiles of strains and identification of differentially expressed proteins using image analysis software. Unlabelled protein reference maps of the predominant proteins were then generated for each strain using 2D gel electrophoresis followed by protein sequencing of each spot using a Reflectron matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometer. Increased coverage of the proteome was achieved using 1D gel electrophoresis in a bottom-up approach using LC-MS/MS of 1 cm gel slices. A total of 888 different proteins were detected by comparative analysis of isolates grown in parallel for 64 h on blood agar plates. Of these, only 38 % were shared between all isolates. One hundred and ten proteins were identified as showing ≥2-fold difference in expression between strains. Differential expression was shown in a number of potential virulence and colonization factors. Toxin B was detected in the more virulent strains B-1 and 027 SM, but not in the lower virulent strain Tra 5/5, despite all strains possessing an intact pathogenicity locus. The S-layer protein (Cwp2) was identified in strains 027 SM and Tra 5/5 but not strain B-1, and differences in the post-translational modification of SlpA were noted for strain B-1. The variant S-layer profile of strain B-1 was confirmed by genomic comparison, which showed a 58 kb insertion in the S-layer operon of strain B-1. Differential post-translation modification events were also noted in flagellar proteins, thought to be due to differential glycosylation. This study highlights genomic and proteomic variation of different Clostridium difficile strains and suggests a number of factors may play a role in mediating the varying virulence of these different strains.
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Affiliation(s)
- C. H. Chilton
- Leeds Institute for Biomedical and Clinical Sciences, University of Leeds, Leeds LS1 3EX, UK
| | - S. E. Gharbia
- Public Health England, Centre for Infections, London NW9 5EQ, UK
| | - M. Fang
- Public Health England, Centre for Infections, London NW9 5EQ, UK
| | - R. Misra
- Public Health England, Centre for Infections, London NW9 5EQ, UK
| | - I. R. Poxton
- College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh EH16 4SB, UK
| | - S. P. Borriello
- Veterinary Medicines Directorate, Addlestone, Surrey KT15 3NB, UK
| | - H. N. Shah
- Public Health England, Centre for Infections, London NW9 5EQ, UK
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Wu X, Hurdle JG. The Clostridium difficile proline racemase is not essential for early logarithmic growth and infection. Can J Microbiol 2014; 60:251-4. [PMID: 24693984 PMCID: PMC4076780 DOI: 10.1139/cjm-2013-0903] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Proline racemase (PrdF), which is important for energy metabolism via the Stickland pathway and is unique to certain clostridia, was investigated as a potential anti-Clostridium difficile target by examining its effects on the growth and virulence of C. difficile. Inactivation of PrdF by insertional mutagenesis did not affect early logarithmic growth but only attenuated growth in the mid- and late logarithmic phases. There was no effect on virulence in vivo, suggesting that PrdF is also not required for C. difficile infection. These findings indicate that PrdF as well as other enzymes encoded by the proline reductase operon are all nonessential and are unsuitable targets for anti-C. difficile drug discovery.
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Affiliation(s)
- Xiaoqian Wu
- Department of Biology, University of Texas at Arlington, Arlington Texas, 76019, USA
| | - Julian G. Hurdle
- Department of Biology, University of Texas at Arlington, Arlington Texas, 76019, USA
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Ternan NG, Jain S, Graham RLJ, McMullan G. Semiquantitative analysis of clinical heat stress in Clostridium difficile strain 630 using a GeLC/MS workflow with emPAI quantitation. PLoS One 2014; 9:e88960. [PMID: 24586458 PMCID: PMC3933415 DOI: 10.1371/journal.pone.0088960] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 01/16/2014] [Indexed: 12/11/2022] Open
Abstract
Clostridium difficile is considered to be the most frequent cause of infectious bacterial diarrhoea in hospitals worldwide yet its adaptive ability remains relatively uncharacterised. Here, we used GeLC/MS and the exponentially modified protein abundance index (emPAI) calculation to determine proteomic changes in response to a clinically relevant heat stress. Reproducibility between both biological and technical replicates was good, and a 37°C proteome of 224 proteins was complemented by a 41°C proteome of 202 proteins at a 1% false discovery rate. Overall, 236 C. difficile proteins were identified and functionally categorised, of which 178 were available for comparative purposes. A total of 65 proteins (37%) were modulated by 1.5-fold or more at 41°C compared to 37°C and we noted changes in the majority of proteins associated with amino acid metabolism, including upregulation of the reductive branch of the leucine fermentation pathway. Motility was reduced at 41°C as evidenced by a 2.7 fold decrease in the flagellar filament protein, FliC, and a global increase in proteins associated with detoxification and adaptation to atypical conditions was observed, concomitant with decreases in proteins mediating transcriptional elongation and the initiation of protein synthesis. Trigger factor was down regulated by almost 5-fold. We propose that under heat stress, titration of the GroESL and dnaJK/grpE chaperones by misfolded proteins will, in the absence of trigger factor, prevent nascent chains from emerging efficiently from the ribosome causing translational stalling and also an increase in secretion. The current work has thus allowed development of a heat stress model for the key cellular processes of protein folding and export.
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Affiliation(s)
- Nigel G. Ternan
- Northern Ireland Centre for Food and Health (NICHE), School of Biomedical Sciences, University of Ulster, Coleraine, Co. Londonderry, Northern Ireland, United Kingdom
- * E-mail:
| | - Shailesh Jain
- Northern Ireland Centre for Food and Health (NICHE), School of Biomedical Sciences, University of Ulster, Coleraine, Co. Londonderry, Northern Ireland, United Kingdom
| | - Robert L. J. Graham
- School of Medicine, University of Manchester, Manchester, Greater Manchester, United Kingdom
| | - Geoff McMullan
- Northern Ireland Centre for Food and Health (NICHE), School of Biomedical Sciences, University of Ulster, Coleraine, Co. Londonderry, Northern Ireland, United Kingdom
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Chen JW, Scaria J, Mao C, Sobral B, Zhang S, Lawley T, Chang YF. Proteomic comparison of historic and recently emerged hypervirulent Clostridium difficile strains. J Proteome Res 2013; 12:1151-61. [PMID: 23298230 DOI: 10.1021/pr3007528] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Clostridium difficile in recent years has undergone rapid evolution and has emerged as a serious human pathogen. Proteomic approaches can improve the understanding of the diversity of this important pathogen, especially in comparing the adaptive ability of different C. difficile strains. In this study, TMT labeling and nanoLC-MS/MS driven proteomics were used to investigate the responses of four C. difficile strains to nutrient shift and osmotic shock. We detected 126 and 67 differentially expressed proteins in at least one strain under nutrition shift and osmotic shock, respectively. During nutrient shift, several components of the phosphotransferase system (PTS) were found to be differentially expressed, which indicated that the carbon catabolite repression (CCR) was relieved to allow the expression of enzymes and transporters responsible for the utilization of alternate carbon sources. Some classical osmotic shock associated proteins, such as GroEL, RecA, CspG, and CspF, and other stress proteins such as PurG and SerA were detected during osmotic shock. Furthermore, the recently emerged strains were found to contain a more robust gene network in response to both stress conditions. This work represents the first comparative proteomic analysis of historic and recently emerged hypervirulent C. difficile strains, complementing the previously published proteomics studies utilizing only one reference strain.
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Affiliation(s)
- Jenn-Wei Chen
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853, United States
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