1
|
Wei J, Luo J, Yang F, Dai W, Huang Z, Yan Y, Luo M. Comparative genomic and metabolomic analysis reveals the potential of a newly isolated Enterococcus faecium B6 involved in lipogenic effects. Gene 2024; 927:148668. [PMID: 38852695 DOI: 10.1016/j.gene.2024.148668] [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: 02/12/2024] [Revised: 06/01/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024]
Abstract
Evidence has indicated that Enterococcus plays a vital role in non-alcoholic fatty liver disease (NAFLD) development. However, the microbial genetic basis and metabolic potential in the disease are yet unknown. We previously isolated a bacteria Enterococcus faecium B6 (E. faecium B6) from children with NAFLD for the first time. Here, we aim to systematically investigate the potential of strain B6 in lipogenic effects. The lipogenic effects of strain B6 were explored in vitro and in vivo. The genomic and functional characterizations were investigated by whole-genome sequencing and comparative genomic analysis. Moreover, the metabolite profiles were unraveled by an untargeted metabolomic analysis. We demonstrated that strain B6 could effectively induce lipogenic effects in the liver of mice. Strain B6 contained a circular chromosome and two circular plasmids and posed various functions. Compared to the other two probiotic strains of E. faecium, strain B6 exhibited unique functions in pathways of ABC transporters, phosphotransferase system, and amino sugar and nucleotide sugar metabolism. Moreover, strain B6 produced several metabolites, mainly enriched in the protein digestion and absorption pathway. The unique potential of strain B6 in lipogenic effects was probably associated with glycolysis, fatty acid synthesis, and glutamine and choline transport. This study pioneeringly revealed the metabolic characteristics and specific detrimental traits of strain B6. The findings provided new insights into the underlying mechanisms of E. faecium in lipogenic effects, and laid essential foundations for further understanding of E. faecium-related disease.
Collapse
Affiliation(s)
- Jia Wei
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Jiayou Luo
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Fei Yang
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang 421001, Hunan, China
| | - Wen Dai
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Zhihang Huang
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Yulin Yan
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Miyang Luo
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China.
| |
Collapse
|
2
|
Graham LA, Hansen T, Yang Y, Sherik M, Ye Q, Soares BP, Kinrade B, Guo S, Davies PL. Adhesin domains responsible for binding bacteria to surfaces they colonize project outwards from companion split domains. Proteins 2024; 92:933-945. [PMID: 38591850 DOI: 10.1002/prot.26689] [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: 01/09/2024] [Revised: 03/07/2024] [Accepted: 03/26/2024] [Indexed: 04/10/2024]
Abstract
Bacterial adhesins attach their hosts to surfaces that the bacteria will colonize. This surface adhesion occurs through specific ligand-binding domains located towards the distal end of the long adhesin molecules. However, recognizing which of the many adhesin domains are structural and which are ligand binding has been difficult up to now. Here we have used the protein structure modeling program AlphaFold2 to predict structures for these giant 0.2- to 1.5-megadalton proteins. Crystal structures previously solved for several adhesin regions are in good agreement with the models. Whereas most adhesin domains are linked in a linear fashion through their N- and C-terminal ends, ligand-binding domains can be recognized by budding out from a companion core domain so that their ligand-binding sites are projected away from the axis of the adhesin for maximal exposure to their targets. These companion domains are "split" in their continuity by projecting the ligand-binding domain outwards. The "split domains" are mostly β-sandwich extender modules, but other domains like a β-solenoid can serve the same function. Bioinformatic analyses of Gram-negative bacterial sequences revealed wide variety ligand-binding domains are used in their Repeats-in-Toxin adhesins. The ligands for many of these domains have yet to be identified but known ligands include various cell-surface glycans, proteins, and even ice. Recognizing the ligands to which the adhesins bind could lead to ways of blocking colonization by bacterial pathogens. Engineering different ligand-binding domains into an adhesin has the potential to change the surfaces to which bacteria bind.
Collapse
Affiliation(s)
- Laurie A Graham
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Thomas Hansen
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Yanzhi Yang
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Mustafa Sherik
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Qilu Ye
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Blake P Soares
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Brett Kinrade
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Shuaiqi Guo
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| |
Collapse
|
3
|
Maccaro JJ, Figueroa LL, McFrederick QS. From pollen to putrid: Comparative metagenomics reveals how microbiomes support dietary specialization in vulture bees. Mol Ecol 2024; 33:e17421. [PMID: 38828760 DOI: 10.1111/mec.17421] [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: 01/21/2024] [Revised: 05/12/2024] [Accepted: 05/20/2024] [Indexed: 06/05/2024]
Abstract
For most animals, the microbiome is key for nutrition and pathogen defence, and is often shaped by diet. Corbiculate bees, including honey bees, bumble bees, and stingless bees, share a core microbiome that has been shaped, at least in part, by the challenges associated with pollen digestion. However, three species of stingless bees deviate from the general rule of bees obtaining their protein exclusively from pollen (obligate pollinivores) and instead consume carrion as their sole protein source (obligate necrophages) or consume both pollen and carrion (facultative necrophages). These three life histories can provide missing insights into microbiome evolution associated with extreme dietary transitions. Here, we investigate, via shotgun metagenomics, the functionality of the microbiome across three bee diet types: obligate pollinivory, obligate necrophagy, and facultative necrophagy. We find distinct differences in microbiome composition and gene functional profiles between the diet types. Obligate necrophages and pollinivores have more specialized microbes, whereas facultative necrophages have a diversity of environmental microbes associated with several dietary niches. Our study suggests that necrophagous bee microbiomes may have evolved to overcome cellular stress and microbial competition associated with carrion. We hypothesize that the microbiome evolved social phenotypes, such as biofilms, that protect the bees from opportunistic pathogens present on carcasses, allowing them to overcome novel nutritional challenges. Whether specific microbes enabled diet shifts or diet shifts occurred first and microbial evolution followed requires further research to disentangle. Nonetheless, we find that necrophagous microbiomes, vertebrate and invertebrate alike, have functional commonalities regardless of their taxonomy.
Collapse
Affiliation(s)
- Jessica J Maccaro
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Laura L Figueroa
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Quinn S McFrederick
- Department of Entomology, University of California Riverside, Riverside, California, USA
| |
Collapse
|
4
|
Kim Y, Kim D, Hieu NM, Byun H, Ahn JH. PySupercharge: a python algorithm for enabling ABC transporter bacterial secretion of all proteins through amino acid mutation. Microb Cell Fact 2024; 23:115. [PMID: 38643109 PMCID: PMC11031901 DOI: 10.1186/s12934-024-02342-z] [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: 11/26/2023] [Accepted: 02/19/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND The process of producing proteins in bacterial systems and secreting them through ATP-binding cassette (ABC) transporters is an area that has been actively researched and used due to its high protein production capacity and efficiency. However, some proteins are unable to pass through the ABC transporter after synthesis, a phenomenon we previously determined to be caused by an excessive positive charge in certain regions of their amino acid sequence. If such an excessive charge is removed, the secretion of any protein through ABC transporters becomes possible. RESULTS In this study, we introduce 'linear charge density' as the criteria for possibility of protein secretion through ABC transporters and confirm that this criterion can be applied to various non-secretable proteins, such as SARS-CoV-2 spike proteins, botulinum toxin light chain, and human growth factors. Additionally, we develop a new algorithm, PySupercharge, that enables the secretion of proteins containing regions with high linear charge density. It selectively converts positively charged amino acids into negatively charged or neutral amino acids after linear charge density analysis to enable protein secretion through ABC transporters. CONCLUSIONS PySupercharge, which also minimizes functional/structural stability loss of the pre-mutation proteins through the use of sequence conservation data, is currently being operated on an accessible web server. We verified the efficacy of PySupercharge-driven protein supercharging by secreting various previously non-secretable proteins commonly used in research, and so suggest this tool for use in future research requiring effective protein production.
Collapse
Affiliation(s)
- Yerin Kim
- Department of Chemistry and Biology, Korea Science Academy of Korea Advanced Institute of Science and Technology, Busan, South Korea
| | - Danny Kim
- Department of Chemistry and Biology, Korea Science Academy of Korea Advanced Institute of Science and Technology, Busan, South Korea
| | - Nguyen-Mihn Hieu
- Department of Chemistry and Biology, Korea Science Academy of Korea Advanced Institute of Science and Technology, Busan, South Korea
| | - Hyunjong Byun
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Jung Hoon Ahn
- Department of Chemistry and Biology, Korea Science Academy of Korea Advanced Institute of Science and Technology, Busan, South Korea.
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea.
| |
Collapse
|
5
|
Moradkasani S, Maurin M, Farrokhi AS, Esmaeili S. Development, Strategies, and Challenges for Tularemia Vaccine. Curr Microbiol 2024; 81:126. [PMID: 38564047 DOI: 10.1007/s00284-024-03658-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/01/2024] [Indexed: 04/04/2024]
Abstract
Francisella tularensis is a facultative intracellular bacterial pathogen that affects both humans and animals. It was developed into a biological warfare weapon as a result. In this article, the current status of tularemia vaccine development is presented. A live-attenuated vaccine that was designed over 50 years ago using the less virulent F. tularensis subspecies holarctica is the only prophylactic currently available, but it has not been approved for use in humans or animals. Other promising live, killed, and subunit vaccine candidates have recently been developed and tested in animal models. This study will investigate some possible vaccines and the challenges they face during development.
Collapse
Affiliation(s)
- Safoura Moradkasani
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, KabudarAhang, Hamadan, Iran
- Department of Epidemiology and Biostatics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Max Maurin
- CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Universite Grenoble Alpes, 38000, Grenoble, France
| | | | - Saber Esmaeili
- National Reference Laboratory for Plague, Tularemia and Q Fever, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Akanlu, KabudarAhang, Hamadan, Iran.
- Department of Epidemiology and Biostatics, Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
6
|
Abby SS, Denise R, Rocha EPC. Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder Version 2. Methods Mol Biol 2024; 2715:1-25. [PMID: 37930518 DOI: 10.1007/978-1-0716-3445-5_1] [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] [Indexed: 11/07/2023]
Abstract
Protein secretion systems are complex molecular machineries that translocate proteins through the outer membrane and sometimes through multiple other barriers. They have evolved by co-option of components from other envelope-associated cellular machineries, making them sometimes difficult to identify and discriminate. Here, we describe how to identify protein secretion systems in bacterial genomes using the MacSyFinder program. This flexible computational tool uses the knowledge gathered from experimental studies to identify homologous systems in genome data. It can be used with a set of predefined MacSyFinder models, "TXSScan," to identify all major secretion systems of diderm bacteria (i.e., with inner and LPS-containing outer membranes) as well as evolutionarily related cell appendages (pili and flagella). For this, it identifies and clusters co-localized genes encoding proteins of secretion systems using sequence similarity search with Hidden Markov Model (HMM) protein profiles. Finally, it checks if the clusters' genetic content and genomic organization satisfy the constraints of the model. TXSScan models can be altered in the command line or customized to search for variants of known secretion systems. Models can also be built from scratch to identify novel systems. In this chapter, we describe a complete pipeline of analysis, starting from (i) the integration of information from a reference set of experimentally studied systems, (ii) the identification of conserved proteins and the construction of their HMM protein profiles, (iii) the definition and optimization of "macsy-models," and (iv) their use and online distribution as tools to search genomic data for secretion systems of interest. MacSyFinder is available here: https://github.com/gem-pasteur/macsyfinder, and MacSyFinder models here: https://github.com/macsy-models .
Collapse
Affiliation(s)
- Sophie S Abby
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Grenoble, France.
| | - Rémi Denise
- APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| |
Collapse
|
7
|
Huh E, Choi JG, Choi Y, Ju IG, Kim B, Shin YJ, An JM, Park MG, Yim SV, Chung SJ, Seo SU, Kim D, Kim CH, Kim DH, Oh MS. P. mirabilis-derived pore-forming haemolysin, HpmA drives intestinal alpha-synuclein aggregation in a mouse model of neurodegeneration. EBioMedicine 2023; 98:104887. [PMID: 37995468 PMCID: PMC10709029 DOI: 10.1016/j.ebiom.2023.104887] [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: 05/30/2023] [Revised: 11/04/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Recent studies suggesting the importance of the gut-microbiome in intestinal aggregated alpha synuclein (α-syn) have led to the exploration of the possible role of the gut-brain axis in central nervous system degeneration. Proteus mirabilis (P. mirabilis), a gram-negative facultative anaerobic bacterium, has been linked to brain neurodegeneration in animal studies. We hypothesised that P. mirabilis-derived virulence factors aggregate intestinal α-synuclein and could prompt the pathogenesis of dopaminergic neurodegeneration in the brain. METHODS We used vagotomised- and antibiotic-treated male murine models to determine the pathogenesis of P. mirabilis during brain neurodegeneration. The neurodegenerative factor that is driven by P. mirabilis was determined using genetically mutated P. mirabilis. The pathological functions and interactions of the virulence factors were determined in vitro. FINDINGS The results showed that P. mirabilis-induced motor dysfunction and neurodegeneration are regulated by intestinal α-syn aggregation in vagotomised- or antibiotic-treated murine models. We deduced that the specific virulence factor, haemolysin A (HpmA), plays a role in the pathogenesis of P. mirabilis. HpmA is involved in α-synuclein oligomerisation and membrane pore formation, resulting in the activation of mTOR-mediated autophagy signalling in intestinal neuroendocrine cells. INTERPRETATION Taken together, the results of the present study suggest that HpmA can interact with α-syn and act as a possible indicator of brain neurodegenerative diseases that are induced by P. mirabilis. FUNDING This study was supported by a grant from the National Research Foundation of Korea.
Collapse
Affiliation(s)
- Eugene Huh
- Department of Oriental Pharmaceutical Science and Kyung Hee East-West Pharmaceutical Research Institute, College of Pharmacy, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea; Neurobiota Research Center, College of Pharmacy, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Jin Gyu Choi
- Department of Oriental Pharmaceutical Science and Kyung Hee East-West Pharmaceutical Research Institute, College of Pharmacy, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Yujin Choi
- Department of Biochemical and Pharmaceutical Sciences, Graduate School, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - In Gyoung Ju
- Department of Oriental Pharmaceutical Science and Kyung Hee East-West Pharmaceutical Research Institute, College of Pharmacy, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea; Neurobiota Research Center, College of Pharmacy, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Bora Kim
- Neurobiota Research Center, College of Pharmacy, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Yoon-Jung Shin
- Neurobiota Research Center, College of Pharmacy, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Jong Min An
- Department of Biomedical Science, Graduate School, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Myoung Gyu Park
- MetaCen Therapeutics Inc. R&D Center, 256 Changryongdae-ro, Yeongtong-gu, Suwon-si, Gyeonggi-Do, 16229, Republic of Korea
| | - Sung Vin Yim
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Su Jin Chung
- Department of Neurology, Myongji Hospital, Hanyang University College of Medicine, 155 Hwasu-ro, Deokyang-gu, Goyang-si, Gyeonggi-Do, 10475, Republic of Korea
| | - Sang-Uk Seo
- Department of Microbiology, College of Medicine, The Catholic University of Korea, 222 Banpodae-ro, Seocho-gu, Seoul, 06591, Republic of Korea
| | - Dokyoung Kim
- Department of Biomedical Science, Graduate School, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea; Department of Anatomy and Neurobiology, College of Medicine, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Chun Hyung Kim
- Paean Biotechnology, 17 Techno 4-ro, Yuseong-gu, Daejeon, 34013, Republic of Korea
| | - Dong Hyun Kim
- Neurobiota Research Center, College of Pharmacy, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea
| | - Myung Sook Oh
- Department of Oriental Pharmaceutical Science and Kyung Hee East-West Pharmaceutical Research Institute, College of Pharmacy, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea; Neurobiota Research Center, College of Pharmacy, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea; Department of Biochemical and Pharmaceutical Sciences, Graduate School, Kyung Hee University, 26, Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea; Department of Integrated Drug Development and Natural Products, Graduate School, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Republic of Korea.
| |
Collapse
|
8
|
Bui DC, Luo T, McBride JW. Type 1 secretion system and effectors in Rickettsiales. Front Cell Infect Microbiol 2023; 13:1175688. [PMID: 37256108 PMCID: PMC10225607 DOI: 10.3389/fcimb.2023.1175688] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/02/2023] [Indexed: 06/01/2023] Open
Abstract
Obligate intracellular bacteria in the order Rickettsiales are transmitted by arthropod vectors and cause life-threatening infections in humans and animals. While both type 1 and type 4 secretion systems (T1SS and T4SS) have been identified in this group, the most extensive studies of Rickettsiales T1SS and associated effectors have been performed in Ehrlichia. These studies have uncovered important roles for the T1SS effectors in pathobiology and immunity. To evade innate immune responses and promote intracellular survival, Ehrlichia and other related obligate pathogens secrete multiple T1SS effectors which interact with a diverse network of host targets associated with essential cellular processes. T1SS effectors have multiple functional activities during infection including acting as nucleomodulins and ligand mimetics that activate evolutionarily conserved cellular signaling pathways. In Ehrlichia, an array of newly defined major immunoreactive proteins have been identified that are predicted as T1SS substrates and have conformation-dependent antibody epitopes. These findings highlight the underappreciated and largely uncharacterized roles of T1SS effector proteins in pathobiology and immunity. This review summarizes current knowledge regarding roles of T1SS effectors in Rickettsiales members during infection and explores newly identified immunoreactive proteins as potential T1SS substrates and targets of a protective host immune response.
Collapse
Affiliation(s)
- Duc-Cuong Bui
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Tian Luo
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Jere W. McBride
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, United States
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, United States
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, United States
| |
Collapse
|
9
|
Wu J, Liu W, Zhu L, Li N, Luo G, Gu M, Peng M, Zeng S, Wu S, Zhang S, Chen Q, Cai M, Cao W, Jiang Y, Luo C, Tian D, Shi M, Shu Y, Chang G, Luo H. Dysbiosis of oropharyngeal microbiome and antibiotic resistance in hospitalized COVID-19 patients. J Med Virol 2023; 95:e28727. [PMID: 37185870 DOI: 10.1002/jmv.28727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is ongoing and multiple studies have elucidated its pathogenesis, however, the related- microbiome imbalance caused by SARS-CoV-2 is still not clear. In this study, we have comprehensively compared the microbiome composition and associated function alterations in the oropharyngeal swabs of healthy controls and coronavirus disease 2019 (COVID-19) patients with moderate or severe symptoms by metatranscriptomic sequencing. We did observe a reduced microbiome alpha-diversity but significant enrichment of opportunistic microorganisms in patients with COVID-19 compared with healthy controls, and the microbial homeostasis was rebuilt following the recovery of COVID-19 patients. Correspondingly, less functional genes in multiple biological processes and weakened metabolic pathways such as carbohydrate metabolism, energy metabolism were also observed in COVID-19 patients. We only found higher relative abundance of limited genera such as Lachnoanaerobaculum between severe patients and moderate patients while no worthy-noting microbiome diversity and function alteration were observed. Finally, we noticed that the co-occurrence of antibiotic resistance and virulence was closely related to the microbiome alteration caused by SRAS-CoV-2. Overall, our findings demonstrate that microbial dysbiosis may enhance the pathogenesis of SARS-CoV-2 and the antibiotics treatment should be critically considered.
Collapse
Affiliation(s)
- Jiani Wu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- Department of AIDS and STD Control and Prevention, Shaoxing Center for Disease Control and Prevention, Shaoxing, China
| | - Wei Liu
- Department of Immunology, Center for Disease Prevention and Control of PLA, Beijing, China
| | - Lin Zhu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Nina Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Gengyan Luo
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Ming Gu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Minwu Peng
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Shike Zeng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Shu Wu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Shengze Zhang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Qiqi Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Meiqi Cai
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Wei Cao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Ying Jiang
- Environment Health Department, Shenzhen Nanshan Center for Disease Control and Prevention, Shenzhen, China
| | - Chuming Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Dechao Tian
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Mang Shi
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Guohui Chang
- Department of Immunology, Center for Disease Prevention and Control of PLA, Beijing, China
| | - Huanle Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Shenzhen, China
| |
Collapse
|
10
|
Selim MS, Kassem AB, El-Bassiouny NA, Salahuddin A, Abu El-Ela RY, Hamza MS. Polymorphic renal transporters and cisplatin's toxicity in urinary bladder cancer patients: current perspectives and future directions. Med Oncol 2023; 40:80. [PMID: 36650399 PMCID: PMC9845168 DOI: 10.1007/s12032-022-01928-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/10/2022] [Indexed: 01/19/2023]
Abstract
Urinary bladder cancer (UBC) holds a potentially profound social burden and affects over 573,278 new cases annually. The disease's primary risk factors include occupational tobacco smoke exposure and inherited genetic susceptibility. Over the past 30 years, a number of treatment modalities have emerged, including cisplatin, a platinum molecule that has demonstrated effectiveness against UBC. Nevertheless, it has severe dose-limiting side effects, such as nephrotoxicity, among others. Since intracellular accumulation of platinum anticancer drugs is necessary for cytotoxicity, decreased uptake or enhanced efflux are the root causes of platinum resistance and response failure. Evidence suggests that genetic variations in any transporter involved in the entry or efflux of platinum drugs alter their kinetics and, to a significant extent, determine patients' responses to them. This review aims to consolidate and describe the major transporters and their polymorphic variants in relation to cisplatin-induced toxicities and resistance in UBC patients. We concluded that the efflux transporters ABCB1, ABCC2, SLC25A21, ATP7A, and the uptake transporter OCT2, as well as the organic anion uptake transporters OAT1 and OAT2, are linked to cisplatin accumulation, toxicity, and resistance in urinary bladder cancer patients. While suppressing the CTR1 gene's expression reduced cisplatin-induced nephrotoxicity and ototoxicity, inhibiting the expression of the MATE1 and MATE2-K genes has been shown to increase cisplatin's nephrotoxicity and resistance. The roles of ABCC5, ABCA8, ABCC10, ABCB10, ABCG1, ATP7B, ABCG2, and mitochondrial SLC25A10 in platinum-receiving urinary bladder cancer patients should be the subject of further investigation.
Collapse
Affiliation(s)
- Mohamed S Selim
- Clinical Pharmacy Practice Department, Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt.
| | - Amira B Kassem
- Clinical Pharmacy & Pharmacy Practice Department, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
| | - Noha A El-Bassiouny
- Clinical Pharmacy & Pharmacy Practice Department, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
| | - Ahmad Salahuddin
- Biochemistry Department, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
- Biochemistry Department, Scientific Research Center, Al-Ayen University, Thi-Qar, Iraq
| | - Raghda Y Abu El-Ela
- Medical Oncology Department, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Marwa Samir Hamza
- Clinical Pharmacy Practice Department, Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| |
Collapse
|
11
|
The inside scoop: Comparative genomics of two intranuclear bacteria, "Candidatus Berkiella cookevillensis" and "Candidatus Berkiella aquae". PLoS One 2022; 17:e0278206. [PMID: 36584052 PMCID: PMC9803151 DOI: 10.1371/journal.pone.0278206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/12/2022] [Indexed: 12/31/2022] Open
Abstract
"Candidatus Berkiella cookevillensis" (strain CC99) and "Candidatus Berkiella aquae" (strain HT99), belonging to the Coxiellaceae family, are gram-negative bacteria isolated from amoebae in biofilms present in human-constructed water systems. Both bacteria are obligately intracellular, requiring host cells for growth and replication. The intracellular bacteria-containing vacuoles of both bacteria closely associate with or enter the nuclei of their host cells. In this study, we analyzed the genome sequences of CC99 and HT99 to better understand their biology and intracellular lifestyles. The CC99 genome has a size of 2.9Mb (37.9% GC) and contains 2,651 protein-encoding genes (PEGs) while the HT99 genome has a size of 3.6Mb (39.4% GC) and contains 3,238 PEGs. Both bacteria encode high proportions of hypothetical proteins (CC99: 46.5%; HT99: 51.3%). The central metabolic pathways of both bacteria appear largely intact. Genes for enzymes involved in the glycolytic pathway, the non-oxidative branch of the phosphate pathway, the tricarboxylic acid pathway, and the respiratory chain were present. Both bacteria, however, are missing genes for the synthesis of several amino acids, suggesting reliance on their host for amino acids and intermediates. Genes for type I and type IV (dot/icm) secretion systems as well as type IV pili were identified in both bacteria. Moreover, both bacteria contain genes encoding large numbers of putative effector proteins, including several with eukaryotic-like domains such as, ankyrin repeats, tetratricopeptide repeats, and leucine-rich repeats, characteristic of other intracellular bacteria.
Collapse
|
12
|
The hemolysin A secretion system is a multi-engine pump containing three ABC transporters. Cell 2022; 185:3329-3340.e13. [DOI: 10.1016/j.cell.2022.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/20/2022] [Accepted: 07/18/2022] [Indexed: 11/17/2022]
|
13
|
Tarsitano J, Ramis LY, Alonso LG, Russo DM, Zorreguieta A. RapD Is a Multimeric Calcium-Binding Protein That Interacts With the Rhizobium leguminosarum Biofilm Exopolysaccharide, Influencing the Polymer Lengths. Front Microbiol 2022; 13:895526. [PMID: 35875570 PMCID: PMC9298526 DOI: 10.3389/fmicb.2022.895526] [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: 03/14/2022] [Accepted: 05/12/2022] [Indexed: 11/15/2022] Open
Abstract
Rhizobium leguminosarum synthesizes an acidic polysaccharide mostly secreted to the extracellular medium, known as exopolysaccharide (EPS) and partially retained on the bacterial surface as a capsular polysaccharide (CPS). Rap proteins, extracellular protein substrates of the PrsDE type I secretion system (TISS), share at least one Ra/CHDL (cadherin-like) domain and are involved in biofilm matrix development either through cleaving the polysaccharide by Ply glycanases or by altering the bacterial adhesive properties. It was shown that the absence or excess of extracellular RapA2 (a monomeric CPS calcium-binding lectin) alters the biofilm matrix’s properties. Here, we show evidence of the role of a new Rap protein, RapD, which comprises an N-terminal Ra/CHDL domain and a C-terminal region of unknown function. RapD was completely released to the extracellular medium and co-secreted with the other Rap proteins in a PrsDE-dependent manner. Furthermore, high levels of RapD secretion were found in biofilms under conditions that favor EPS production. Interestingly, size exclusion chromatography of the EPS produced by the ΔrapA2ΔrapD double mutant showed a profile of EPS molecules of smaller sizes than those of the single mutants and the wild type strain, suggesting that both RapA2 and RapD proteins influence EPS processing on the cell surface. Biophysical studies showed that calcium triggers proper folding and multimerization of recombinant RapD. Besides, further conformational changes were observed in the presence of EPS. Enzyme-Linked ImmunoSorbent Assay (ELISA) and Binding Inhibition Assays (BIA) indicated that RapD specifically binds the EPS and that galactose residues would be involved in this interaction. Taken together, these observations indicate that RapD is a biofilm matrix-associated multimeric protein that influences the properties of the EPS, the main structural component of the rhizobial biofilm.
Collapse
Affiliation(s)
- Julián Tarsitano
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Lila Y. Ramis
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Leonardo G. Alonso
- Instituto de Nanobiotecnología (NANOBIOTEC), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daniela M. Russo
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- *Correspondence: Daniela M. Russo,
| | - Angeles Zorreguieta
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Angeles Zorreguieta,
| |
Collapse
|
14
|
Puhm M, Hendrikson J, Kivisaar M, Teras R. Pseudomonas putida Biofilm Depends on the vWFa-Domain of LapA in Peptides-Containing Growth Medium. Int J Mol Sci 2022; 23:ijms23115898. [PMID: 35682576 PMCID: PMC9180339 DOI: 10.3390/ijms23115898] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 01/27/2023] Open
Abstract
The biofilm of Pseudomonas putida is complexly regulated by several intercellular and extracellular factors. The cell surface adhesin LapA of this bacterium is a central factor for the biofilm and, consequently, the regulation of lapA expression, for example, by Fis. It has been recently shown that peptides in growth media enhance the formation of P. putida biofilm, but not as a source of carbon and nitrogen. Moreover, the peptide-dependent biofilm appeared especially clearly in the fis-overexpression strain, which also has increased LapA. Therefore, we investigate here whether there is a relationship between LapA and peptide-dependent biofilm. The P. putida strains with inducible lapA expression and LapA without the vWFa domain, which is described as a domain similar to von Willebrand factor domain A, were constructed. Thereafter, the biofilm of these strains was assessed in growth media containing extracellular peptides in the shape of tryptone and without it. We show that the vWFa domain in LapA is necessary for biofilm enhancement by the extracellular peptides in the growth medium. The importance of vWFa in LapA was particularly evident for the fis-overexpression strain F15. The absence of the vWFa domain diminished the positive effect of Fis on the F15 biofilm.
Collapse
|
15
|
Filipi K, Rahman WU, Osickova A, Osicka R. Kingella kingae RtxA Cytotoxin in the Context of Other RTX Toxins. Microorganisms 2022; 10:518. [PMID: 35336094 PMCID: PMC8953716 DOI: 10.3390/microorganisms10030518] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/04/2022] Open
Abstract
The Gram-negative bacterium Kingella kingae is part of the commensal oropharyngeal flora of young children. As detection methods have improved, K. kingae has been increasingly recognized as an emerging invasive pathogen that frequently causes skeletal system infections, bacteremia, and severe forms of infective endocarditis. K. kingae secretes an RtxA cytotoxin, which is involved in the development of clinical infection and belongs to an ever-growing family of cytolytic RTX (Repeats in ToXin) toxins secreted by Gram-negative pathogens. All RTX cytolysins share several characteristic structural features: (i) a hydrophobic pore-forming domain in the N-terminal part of the molecule; (ii) an acylated segment where the activation of the inactive protoxin to the toxin occurs by a co-expressed toxin-activating acyltransferase; (iii) a typical calcium-binding RTX domain in the C-terminal portion of the molecule with the characteristic glycine- and aspartate-rich nonapeptide repeats; and (iv) a C-proximal secretion signal recognized by the type I secretion system. RTX toxins, including RtxA from K. kingae, have been shown to act as highly efficient 'contact weapons' that penetrate and permeabilize host cell membranes and thus contribute to the pathogenesis of bacterial infections. RtxA was discovered relatively recently and the knowledge of its biological role remains limited. This review describes the structure and function of RtxA in the context of the most studied RTX toxins, the knowledge of which may contribute to a better understanding of the action of RtxA in the pathogenesis of K. kingae infections.
Collapse
Affiliation(s)
| | | | | | - Radim Osicka
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic; (K.F.); (W.U.R.); (A.O.)
| |
Collapse
|
16
|
Chen Z, Zhao Z, Hui X, Zhang J, Hu Y, Chen R, Cai X, Hu Y, Wang Y. T1SEstacker: A Tri-Layer Stacking Model Effectively Predicts Bacterial Type 1 Secreted Proteins Based on C-Terminal Non-repeats-in-Toxin-Motif Sequence Features. Front Microbiol 2022; 12:813094. [PMID: 35211101 PMCID: PMC8861453 DOI: 10.3389/fmicb.2021.813094] [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: 11/11/2021] [Accepted: 12/20/2021] [Indexed: 11/21/2022] Open
Abstract
Type 1 secretion systems play important roles in pathogenicity of Gram-negative bacteria. However, the substrate secretion mechanism remains largely unknown. In this research, we observed the sequence features of repeats-in-toxin (RTX) proteins, a major class of type 1 secreted effectors (T1SEs). We found striking non-RTX-motif amino acid composition patterns at the C termini, most typically exemplified by the enriched “[FLI][VAI]” at the most C-terminal two positions. Machine-learning models, including deep-learning ones, were trained using these sequence-based non-RTX-motif features and further combined into a tri-layer stacking model, T1SEstacker, which predicted the RTX proteins accurately, with a fivefold cross-validated sensitivity of ∼0.89 at the specificity of ∼0.94. Besides substrates with RTX motifs, T1SEstacker can also well distinguish non-RTX-motif T1SEs, further suggesting their potential existence of common secretion signals. T1SEstacker was applied to predict T1SEs from the genomes of representative Salmonella strains, and we found that both the number and composition of T1SEs varied among strains. The number of T1SEs is estimated to reach 100 or more in each strain, much larger than what we expected. In summary, we made comprehensive sequence analysis on the type 1 secreted RTX proteins, identified common sequence-based features at the C termini, and developed a stacking model that can predict type 1 secreted proteins accurately.
Collapse
Affiliation(s)
- Zewei Chen
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Health Science Center, Shenzhen, China
| | - Ziyi Zhao
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Health Science Center, Shenzhen, China
| | - Xinjie Hui
- Department of Respiratory Medicine, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Junya Zhang
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Health Science Center, Shenzhen, China
| | - Yixue Hu
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Health Science Center, Shenzhen, China
| | - Runhong Chen
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Health Science Center, Shenzhen, China
| | - Xuxia Cai
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Health Science Center, Shenzhen, China
| | - Yueming Hu
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Health Science Center, Shenzhen, China
| | - Yejun Wang
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Health Science Center, Shenzhen, China
| |
Collapse
|
17
|
Cytolysin A (ClyA): A Bacterial Virulence Factor with Potential Applications in Nanopore Technology, Vaccine Development, and Tumor Therapy. Toxins (Basel) 2022; 14:toxins14020078. [PMID: 35202106 PMCID: PMC8880466 DOI: 10.3390/toxins14020078] [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: 12/28/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 12/26/2022] Open
Abstract
Cytolysin A (ClyA) is a pore-forming toxin that is produced by some bacteria from the Enterobacteriaceae family. This review provides an overview of the current state of knowledge regarding ClyA, including the prevalence of the encoding gene and its transcriptional regulation, the secretion pathway used by the protein, and the mechanism of protein assembly, and highlights potential applications of ClyA in biotechnology. ClyA expression is regulated at the transcriptional level, primarily in response to environmental stressors, and ClyA can exist stably both as a soluble monomer and as an oligomeric membrane complex. At high concentrations, ClyA induces cytolysis, whereas at low concentrations ClyA can affect intracellular signaling. ClyA is secreted in outer membrane vesicles (OMVs), which has important implications for biotechnology applications. For example, the native pore-forming ability of ClyA suggests that it could be used as a component of nanopore-based technologies, such as sequencing platforms. ClyA has also been exploited in vaccine development owing to its ability to present antigens on the OMV surface and provoke a robust immune response. In addition, ClyA alone or OMVs carrying ClyA fusion proteins have been investigated for their potential use as anti-tumor agents.
Collapse
|
18
|
Mekasha S, Linke D. Secretion Systems in Gram-Negative Bacterial Fish Pathogens. Front Microbiol 2022; 12:782673. [PMID: 34975803 PMCID: PMC8714846 DOI: 10.3389/fmicb.2021.782673] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/24/2021] [Indexed: 12/17/2022] Open
Abstract
Bacterial fish pathogens are one of the key challenges in the aquaculture industry, one of the fast-growing industries worldwide. These pathogens rely on arsenal of virulence factors such as toxins, adhesins, effectors and enzymes to promote colonization and infection. Translocation of virulence factors across the membrane to either the extracellular environment or directly into the host cells is performed by single or multiple dedicated secretion systems. These secretion systems are often key to the infection process. They can range from simple single-protein systems to complex injection needles made from dozens of subunits. Here, we review the different types of secretion systems in Gram-negative bacterial fish pathogens and describe their putative roles in pathogenicity. We find that the available information is fragmented and often descriptive, and hope that our overview will help researchers to more systematically learn from the similarities and differences between the virulence factors and secretion systems of the fish-pathogenic species described here.
Collapse
Affiliation(s)
- Sophanit Mekasha
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| |
Collapse
|
19
|
Farihan Afnan Mohd Rozi M, Noor Zaliha Raja Abd Rahman R, Thean Chor Leow A, Shukuri Mohamad Ali M. Ancestral Sequence Reconstruction of Ancient Lipase from Family I.3 Bacterial Lipolytic Enzymes. Mol Phylogenet Evol 2021; 168:107381. [PMID: 34968679 DOI: 10.1016/j.ympev.2021.107381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/27/2021] [Accepted: 11/29/2021] [Indexed: 01/14/2023]
Abstract
Family I.3 lipase is distinguished from other families by the amino acid sequence and secretion mechanism. Little is known about the evolutionary process driving these differences. This study attempt to understand how the diverse temperature stabilities of bacterial lipases from family I.3 evolved. To achieve that, eighty-three protein sequences sharing a minimum 30% sequence identity with Antarctic Pseudomonas sp. AMS8 lipase were used to infer phylogenetic tree. Using ancestral sequence reconstruction (ASR) technique, the last universal common ancestor (LUCA) sequence of family I.3 was reconstructed. A gene encoding LUCA was synthesized, cloned and expressed as inclusion bodies in E. coli system. Insoluble form of LUCA was refolded using urea dilution method and then purified using affinity chromatography. The purified LUCA exhibited an optimum temperature and pH at 70℃ and 10 respectively. Various metal ions increased or retained the activity of LUCA. LUCA also demonstrated tolerance towards various organic solvents in 25% v/v concentration. The finding from this study could support the understanding on temperature and environment during ancient time. In overall, reconstructed ancestral enzymes have improved physicochemical properties that make them suitable for industrial applications and ASR technique can be employed as a general technique for enzyme engineering.
Collapse
Affiliation(s)
- Mohamad Farihan Afnan Mohd Rozi
- Enzyme and Microbial Technology Research Centre (EMTech), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre (EMTech), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Centre (EMTech), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre (EMTech), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| |
Collapse
|
20
|
González Bullón D, Uribe KB, Amuategi J, Martín C, Ostolaza H. Cholesterol stimulates the lytic activity of Adenylate Cyclase Toxin on lipid membranes by promoting toxin oligomerization and formation of pores with a greater effective size. FEBS J 2021; 288:6795-6814. [PMID: 34216517 PMCID: PMC9290974 DOI: 10.1111/febs.16107] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/27/2021] [Accepted: 07/02/2021] [Indexed: 11/28/2022]
Abstract
Several toxins acting on animal cells present different, but specific, interactions with cholesterol. Bordetella pertussis infects the human respiratory tract and causes whooping cough, a highly contagious and resurgent disease. Its virulence factor adenylate cyclase toxin (ACT) plays an important role in the course of infection. ACT is a pore‐forming cytolysin belonging to the Repeats in ToXin (RTX) family of leukotoxins/hemolysins and is capable of permeabilizing several cell types and lipid vesicles. Previously, we observed that in the presence of cholesterol ACT induces greater liposome permeabilization. Similarly, recent reports also implicate cholesterol in the cytotoxicity of an increasing number of pore‐forming RTX toxins. However, the mechanistic details by which this sterol promotes the lytic activity of ACT or of these other RTX toxins remain largely unexplored and poorly understood. Here, we have applied a combination of biophysical techniques to dissect the role of cholesterol in pore formation by ACT. Our results indicate that cholesterol enhances the lytic potency of ACT by promoting toxin oligomerization, a step which is indispensable for ACT to accomplish membrane permeabilization and cell lysis. Since our experimental design eliminates the possibility that this cholesterol effect derives from toxin accumulation due to lateral lipid phase segregation, we hypothesize that cholesterol facilitates lytic pore formation, by favoring a toxin conformation more prone to protein–protein interactions and oligomerization. Our data shed light on the complex relationship between lipid membranes and protein toxins acting on these membranes. Coupling cholesterol binding, increased oligomerization and increased lytic activity is likely pertinent for other RTX cytolysins.
Collapse
Affiliation(s)
- David González Bullón
- Department of Biochemistry and Molecular Biology, Biofisika Institute, (UPV/EHU, CSIC), University of Basque Country (UPV/EHU), Bilbao, Spain
| | - Kepa B Uribe
- Department of Biochemistry and Molecular Biology, Biofisika Institute, (UPV/EHU, CSIC), University of Basque Country (UPV/EHU), Bilbao, Spain
| | - Jone Amuategi
- Department of Biochemistry and Molecular Biology, Biofisika Institute, (UPV/EHU, CSIC), University of Basque Country (UPV/EHU), Bilbao, Spain
| | - César Martín
- Department of Biochemistry and Molecular Biology, Biofisika Institute, (UPV/EHU, CSIC), University of Basque Country (UPV/EHU), Bilbao, Spain
| | - Helena Ostolaza
- Department of Biochemistry and Molecular Biology, Biofisika Institute, (UPV/EHU, CSIC), University of Basque Country (UPV/EHU), Bilbao, Spain
| |
Collapse
|
21
|
Alav I, Kobylka J, Kuth MS, Pos KM, Picard M, Blair JMA, Bavro VN. Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria. Chem Rev 2021; 121:5479-5596. [PMID: 33909410 PMCID: PMC8277102 DOI: 10.1021/acs.chemrev.1c00055] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Tripartite efflux pumps and the related type 1 secretion systems (T1SSs) in Gram-negative organisms are diverse in function, energization, and structural organization. They form continuous conduits spanning both the inner and the outer membrane and are composed of three principal components-the energized inner membrane transporters (belonging to ABC, RND, and MFS families), the outer membrane factor channel-like proteins, and linking the two, the periplasmic adaptor proteins (PAPs), also known as the membrane fusion proteins (MFPs). In this review we summarize the recent advances in understanding of structural biology, function, and regulation of these systems, highlighting the previously undescribed role of PAPs in providing a common architectural scaffold across diverse families of transporters. Despite being built from a limited number of basic structural domains, these complexes present a staggering variety of architectures. While key insights have been derived from the RND transporter systems, a closer inspection of the operation and structural organization of different tripartite systems reveals unexpected analogies between them, including those formed around MFS- and ATP-driven transporters, suggesting that they operate around basic common principles. Based on that we are proposing a new integrated model of PAP-mediated communication within the conformational cycling of tripartite systems, which could be expanded to other types of assemblies.
Collapse
Affiliation(s)
- Ilyas Alav
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Jessica Kobylka
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Miriam S. Kuth
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Klaas M. Pos
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Martin Picard
- Laboratoire
de Biologie Physico-Chimique des Protéines Membranaires, CNRS
UMR 7099, Université de Paris, 75005 Paris, France
- Fondation
Edmond de Rothschild pour le développement de la recherche
Scientifique, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jessica M. A. Blair
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Vassiliy N. Bavro
- School
of Life Sciences, University of Essex, Colchester, CO4 3SQ United Kingdom
| |
Collapse
|
22
|
Patterson LL, Byerly CD, McBride JW. Anaplasmataceae: Dichotomous Autophagic Interplay for Infection. Front Immunol 2021; 12:642771. [PMID: 33912170 PMCID: PMC8075259 DOI: 10.3389/fimmu.2021.642771] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/15/2021] [Indexed: 12/19/2022] Open
Abstract
Autophagy is a vital conserved degradative process that maintains cellular homeostasis by recycling or eliminating dysfunctional cellular organelles and proteins. More recently, autophagy has become a well-recognized host defense mechanism against intracellular pathogens through a process known as xenophagy. On the host-microbe battlefield many intracellular bacterial pathogens have developed the ability to subvert xenophagy to establish infection. Obligately intracellular bacterial pathogens of the Anaplasmataceae family, including Ehrlichia chaffeensis, Anaplasma phaogocytophilium and Orientia tsutsugamushi have developed a dichotomous strategy to exploit the host autophagic pathway to obtain nutrients while escaping lysosomal destruction for intracellular survival within the host cell. In this review, the recent findings regarding how these master manipulators engage and inhibit autophagy for infection are explored. Future investigation to understand mechanisms used by Anaplasmataceae to exploit autophagy may advance novel antimicrobial therapies and provide new insights into how intracellular microbes exploit autophagy to survive.
Collapse
Affiliation(s)
- LaNisha L Patterson
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Caitlan D Byerly
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Jere W McBride
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States.,Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, United States.,Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, United States
| |
Collapse
|
23
|
Nahar N, Turni C, Tram G, Blackall PJ, Atack JM. Actinobacillus pleuropneumoniae: The molecular determinants of virulence and pathogenesis. Adv Microb Physiol 2021; 78:179-216. [PMID: 34147185 DOI: 10.1016/bs.ampbs.2020.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, is responsible for high economic losses in swine herds across the globe. Pleuropneumonia is characterized by severe respiratory distress and high mortality. The knowledge about the interaction between bacterium and host within the porcine respiratory tract has improved significantly in recent years. A. pleuropneumoniae expresses multiple virulence factors, which are required for colonization, immune clearance, and tissue damage. Although vaccines are used to protect swine herds against A. pleuropneumoniae infection, they do not offer complete coverage, and often only protect against the serovar, or serovars, used to prepare the vaccine. This review will summarize the role of individual A. pleuropneumoniae virulence factors that are required during key stages of pathogenesis and disease progression, and highlight progress made toward developing effective and broadly protective vaccines against an organism of great importance to global agriculture and food production.
Collapse
Affiliation(s)
- Nusrat Nahar
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Conny Turni
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Greg Tram
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Patrick J Blackall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia.
| | - John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia.
| |
Collapse
|
24
|
Bao H, Wang S, Zhao JH, Liu SL. Salmonella secretion systems: Differential roles in pathogen-host interactions. Microbiol Res 2020; 241:126591. [PMID: 32932132 DOI: 10.1016/j.micres.2020.126591] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/24/2020] [Accepted: 08/29/2020] [Indexed: 12/26/2022]
Abstract
The bacterial genus Salmonella includes a large group of food-borne pathogens that cause a variety of gastrointestinal or systemic diseases in hosts. Salmonella use several secretion devices to inject various effectors targeting eukaryotic hosts, or bacteria. In the past few years, considerable progress has been made towards understanding the structural features and molecular mechanisms of the secretion systems of Salmonella, particularly regarding their roles in host-pathogen interactions. In this review, we summarize the current advances about the main characteristics of the Salmonella secretion systems. Clarifying the roles of the secretion systems in the process of infecting various hosts will broaden our understanding of the importance of microbial interactions in maintaining human health and will provide information for developing novel therapeutic approaches.
Collapse
Affiliation(s)
- Hongxia Bao
- Genomics Research Center, College of Pharmacy, Harbin Medical University, Harbin, China; HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China; Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.
| | - Shuang Wang
- Department of Biopharmaceutical Sciences (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China
| | - Jian-Hua Zhao
- Genomics Research Center, College of Pharmacy, Harbin Medical University, Harbin, China; HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China; Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Shu-Lin Liu
- Genomics Research Center, College of Pharmacy, Harbin Medical University, Harbin, China; HMU-UCCSM Centre for Infection and Genomics, Harbin Medical University, Harbin, China; Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada.
| |
Collapse
|
25
|
Collins AJ, Smith TJ, Sondermann H, O'Toole GA. From Input to Output: The Lap/c-di-GMP Biofilm Regulatory Circuit. Annu Rev Microbiol 2020; 74:607-631. [PMID: 32689917 DOI: 10.1146/annurev-micro-011520-094214] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biofilms are the dominant bacterial lifestyle. The regulation of the formation and dispersal of bacterial biofilms has been the subject of study in many organisms. Over the last two decades, the mechanisms of Pseudomonas fluorescens biofilm formation and regulation have emerged as among the best understood of any bacterial biofilm system. Biofilm formation by P. fluorescens occurs through the localization of an adhesin, LapA, to the outer membrane via a variant of the classical type I secretion system. The decision between biofilm formation and dispersal is mediated by LapD, a c-di-GMP receptor, and LapG, a periplasmic protease, which together control whether LapA is retained or released from the cell surface. LapA localization is also controlled by a complex network of c-di-GMP-metabolizing enzymes. This review describes the current understanding of LapA-mediated biofilm formation by P. fluorescens and discusses several emerging models for the regulation and function of this adhesin.
Collapse
Affiliation(s)
- Alan J Collins
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA;
| | - T Jarrod Smith
- Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA; .,Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, USA
| | | | - George A O'Toole
- Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA;
| |
Collapse
|
26
|
Mustafa A, Ibrahim M, Rasheed MA, Kanwal S, Hussain A, Sami A, Ahmed R, Bo Z. Genome-wide Analysis of Four Enterobacter cloacae complex type strains: Insights into Virulence and Niche Adaptation. Sci Rep 2020; 10:8150. [PMID: 32424332 PMCID: PMC7235008 DOI: 10.1038/s41598-020-65001-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/23/2020] [Indexed: 02/04/2023] Open
Abstract
Enterobacter cloacae complex (Ecc) species are widely distributed opportunistic pathogens mainly associated with humans and plants. In this study, the genomes of clinical isolates including E. hormaechei, E. kobei, and E. ludwigii and non-clinical isolate including E. nimipressuralis were analysed in combination with the genome of E. asburiae by using the reference strain E. cloacae subsp. cloacae ATCC 13047; the Ecc strains were tested on artificial sputum media (ASM), which mimics the host, to evaluate T6SS genes as a case study. All five Ecc strains were sequenced in our lab. Comparative genome analysis of the Ecc strains revealed that genes associated with the survival of Ecc strains, including genes of metal-requiring proteins, defence-associated genes and genes associated with general physiology, were highly conserved in the genomes. However, the genes involved in virulence and drug resistance, specifically those involved in bacterial secretion, host determination and colonization of different strains, were present in different genomic regions. For example, T6SS accessory and core components, T4SS, and multidrug resistance genes/efflux system genes seemed vital for the survival of Ecc strains in various environmental niches, such as humans and plants. Moreover, the ASM host-mimicking growth medium revealed significantly high expression of T6SS genes, including PrpC, which is a regulatory gene of the T6SS, in all tested Ecc strains compared to the control medium. The variations in T6SS gene expression in ASM vs. control showed that the ASM system represents a simple, reproducible and economical alternative to animal models for studies such as those aimed at understanding the divergence of Ecc populations. In summary, genome sequencing of clinical and environmental Ecc genomes will assist in understanding the epidemiology of Ecc strains, including the isolation, virulence characteristics, prevention and treatment of infectious disease caused by these broad-host-range niche-associated species.
Collapse
Affiliation(s)
- Areeqa Mustafa
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai, 200240, China.,Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Muhammad Ibrahim
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai, 200240, China.,Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Muhammad Asif Rasheed
- Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Sumaira Kanwal
- Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Annam Hussain
- Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Asma Sami
- Genomics and Computational Biology Laboratory, Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Pakistan
| | - Raza Ahmed
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Pakistan
| | - Zhu Bo
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, Shanghai, 200240, China.
| |
Collapse
|
27
|
Ali SS, Sonbol FI, Sun J, Hussein MA, Hafez AEE, Abdelkarim EA, Kornaros M, Ali A, Azab M. Molecular characterization of virulence and drug resistance genes-producing Escherichia coli isolated from chicken meat: Metal oxide nanoparticles as novel antibacterial agents. Microb Pathog 2020; 143:104164. [PMID: 32198092 DOI: 10.1016/j.micpath.2020.104164] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/25/2020] [Accepted: 03/14/2020] [Indexed: 01/12/2023]
Abstract
Escherichia coli is a major global foodborne pathogen, infecting a wide range of animals and contaminating their meat products. E. coli, can lead to high morbidity and mortality with a huge economic loss especially if foodborne diseases are associated with multidrug resistant (MDR)- and multivirulent-producing pathogens. Due to the increased resistance to common antimicrobials used to treat livestock animals and human infections, the discovery of new and innovative nanomaterials are in high demand. Recently, metal oxides can be considered as effective inorganic agents with antimicrobial features. Hence, this study might be the first to evaluate the efficiency of metal oxide nanoparticles (MO-NPs) as novel antibacterial agents against MDR/multivirulent E. coli pathogens isolated from chicken meat. The occurrence of pathogenic E. coli was determined in fresh warm chicken meat parts (breast, thigh, liver and gizzard). Ninety-one of 132 (69%) chicken meat parts were Escherichia -positive with E. coli as the only species isolated. Out of identified 240 E. coli strains, 72.5% (174/240) were classified as MDR E. coli strains. Fifty-five profile patterns were obtained. From each pattern, one strain was randomly selected for further analysis of virulence and resistance genes. Extracted DNA was assessed for the presence of antibiotic resistance genes (blaIMP-7, blaIMP-25, blaTEM, blaSHV, blaOXA-2, tetA, aadA, and aac(3)-IV) and virulence genes (stx1, stx2, hlyA, eaeA, aggR, eltB, estIb, papA, afa and hlyD). Clustering analyses revealed that 10 E. coli harboring the highest number of virulence and resistance genes were shifted together into one cluster designated as cluster X. The average activities of zinc peroxide nanoparticles (ZnO2-NPs) were higher than that of zinc oxide nanoparticles (ZnO-NPs) and titanium dioxide nanoparticles (TiO2-NPs) by 20% and 29%, respectively. The anti-inflammatory activity of ZnO2-NPs in comparison with aspirin was assessed using membrane stabilization, albumin denaturation, and proteinase inhibition methods. Significant anti-inflammatory activity of ZnO2-NPs was achieved at concentration levels of 500-1000 μg/ml. It seems that MO-NPs are effective alternative agents, since they exhibited a competitive antibacterial capability against MDR/multivirulent-producing E. coli pathogens isolated from chicken meat. Hence, ZnO2-NPs are a promising nanoparticles-based material for controlling foodborne pathogens, thereby valued for food safety applications.
Collapse
Affiliation(s)
- Sameh S Ali
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China; Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
| | - Fatma I Sonbol
- Department of Microbiology, Faculty of Pharmacy Tanta University, Tanta, 31527, Egypt
| | - Jianzhong Sun
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China.
| | - Mohamed A Hussein
- Food Control Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, 44519, Egypt
| | - Abd-Elsalam E Hafez
- Food Control Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, 44519, Egypt
| | - Esraa A Abdelkarim
- Food Control Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, 44519, Egypt
| | - Michael Kornaros
- Laboratory of Biochemical Engineering & Environmental Technology (LBEET), Department of Chemical Engineering, University of Patras, 1 Karatheodori Str., University Campus, 26504, Patras, Greece
| | - Asmaa Ali
- Abbasia Chest Hospital, Ministry of Health, 11765, Cairo, Egypt
| | - Maha Azab
- Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| |
Collapse
|
28
|
Whole genome sequence analysis reveals the broad distribution of the RtxA type 1 secretion system and four novel putative type 1 secretion systems throughout the Legionella genus. PLoS One 2020; 15:e0223033. [PMID: 31935215 PMCID: PMC6959600 DOI: 10.1371/journal.pone.0223033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/17/2019] [Indexed: 01/18/2023] Open
Abstract
Type 1 secretion systems (T1SSs) are broadly distributed among bacteria and translocate effectors with diverse function across the bacterial cell membrane. Legionella pneumophila, the species most commonly associated with Legionellosis, encodes a T1SS at the lssXYZABD locus which is responsible for the secretion of the virulence factor RtxA. Many investigations have failed to detect lssD, the gene encoding the membrane fusion protein of the RtxA T1SS, in non-pneumophila Legionella, which has led to the assumption that this system is a virulence factor exclusively possessed by L. pneumophila. Here we discovered RtxA and its associated T1SS in a novel Legionella taurinensis strain, leading us to question whether this system may be more widespread than previously thought. Through a bioinformatic analysis of publicly available data, we classified and determined the distribution of four T1SSs including the RtxA T1SS and four novel T1SSs among diverse Legionella spp. The ABC transporter of the novel Legionella T1SS Legionella repeat protein secretion system shares structural similarity to those of diverse T1SS families, including the alkaline protease T1SS in Pseudomonas aeruginosa. The Legionella bacteriocin (1-3) secretion systems T1SSs are novel putative bacteriocin transporting T1SSs as their ABC transporters include C-39 peptidase domains in their N-terminal regions, with LB2SS and LB3SS likely constituting a nitrile hydratase leader peptide transport T1SSs. The LB1SS is more closely related to the colicin V T1SS in Escherichia coli. Of 45 Legionella spp. whole genomes examined, 19 (42%) were determined to possess lssB and lssD homologs. Of these 19, only 7 (37%) are known pathogens. There was no difference in the proportions of disease associated and non-disease associated species that possessed the RtxA T1SS (p = 0.4), contrary to the current consensus regarding the RtxA T1SS. These results draw into question the nature of RtxA and its T1SS as a singular virulence factor. Future studies should investigate mechanistic explanations for the association of RtxA with virulence.
Collapse
|
29
|
Ihling N, Uhde A, Scholz R, Schwarz C, Schmitt L, Büchs J. Scale-up of a Type I secretion system in E. coli using a defined mineral medium. Biotechnol Prog 2019; 36:e2911. [PMID: 31513739 DOI: 10.1002/btpr.2911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 08/02/2019] [Accepted: 09/09/2019] [Indexed: 12/17/2022]
Abstract
Secretion of heterologous proteins into the culture supernatant in laboratory strains of Escherichia coli is possible by utilizing a Type I secretion system (T1SS). One prominent example for a T1SS is based on the hemolysin A toxin. With this system, heterologous protein secretion has already been achieved. However, no cultivations in a defined mineral medium and in stirred tank bioreactors have been described in literature up to now, hampering the broad applicability of the system. In this study, a mineral medium was developed for cultivation under defined conditions. With this medium, the full potential and advantage of a secretion system in E. coli (low secretion of host proteins, no contamination with proteins from complex media compounds) can now be exploited. Additionally, quantification of the protein amount in the supernatant was demonstrated by application of the Bradford assay. In this work, host cell behavior was described in small scale by online monitoring of the oxygen transfer rate. Scalability was demonstrated by stirred tank fermentation yielding 540 mg/L HlyA1 in the supernatant. This work enhances the applicability of a protein secretion system in E. coli and paves the way for an industrial application.
Collapse
Affiliation(s)
- Nina Ihling
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany.,Bioeconomy Science Center (BioSC), Jülich, Germany
| | | | - Romy Scholz
- Bioeconomy Science Center (BioSC), Jülich, Germany.,Institute of Biochemistry, Heinrich-Heine University, Düsseldorf, Germany
| | | | - Lutz Schmitt
- Bioeconomy Science Center (BioSC), Jülich, Germany.,Institute of Biochemistry, Heinrich-Heine University, Düsseldorf, Germany
| | - Jochen Büchs
- AVT - Biochemical Engineering, RWTH Aachen University, Aachen, Germany.,Bioeconomy Science Center (BioSC), Jülich, Germany
| |
Collapse
|
30
|
Benz R, Piselli C, Potter AA. Channel Formation by LktA of Mannheimia (Pasteurella) haemolytica in Lipid Bilayer Membranes and Comparison of Channel Properties with Other RTX-Cytolysins. Toxins (Basel) 2019; 11:toxins11100604. [PMID: 31627319 PMCID: PMC6833087 DOI: 10.3390/toxins11100604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/22/2019] [Accepted: 10/10/2019] [Indexed: 12/17/2022] Open
Abstract
Cytolysin LktA is one of the major pathogenicity factors of Mannheimia haemolytica (formerly Pasteurella haemolytica) that is the cause of pasteurellosis, also known as shipping fever pneumonia, causing substantial loss of sheep and cattle during transport. LktA belongs to the family of RTX-toxins (Repeats in ToXins) that are produced as pathogenicity factors by a variety of Gram-negative bacteria. Sublytic concentrations of LktA cause inflammatory responses of ovine leukocytes. Higher concentrations result in formation of transmembrane channels in target cells that may cause cell lysis and apoptosis. In this study we investigated channel formation by LktA in artificial lipid bilayer membranes made of different lipids. LktA purified from culture supernatants by polyethylene glycol 4000 precipitation and lyophilization had to be activated to frequently form channels by solution in 6 M urea. The LktA channels had a single-channel conductance of about 60 pS in 0.1 M KCl, which is about one tenth of the conductance of most RTX-toxins with the exception of adenylate cyclase toxin of Bordetella pertussis. The LktA channels are highly cation-selective caused by negative net charges. The theoretical treatment of the conductance of LktA as a function of the bulk aqueous concentration allowed a rough estimate of the channel diameter, which is around 1.5 nm. The size of the LktA channel is discussed with respect to channels formed by other RTX-toxins. We present here the first investigation of LktA in a reconstituted system.
Collapse
Affiliation(s)
- Roland Benz
- Department of Life Sciences and Chemistry, Jacobs-University Bremen gGmbH Campusring, 1; 28759 Bremen, Germany.
| | - Claudio Piselli
- Department of Life Sciences and Chemistry, Jacobs-University Bremen gGmbH Campusring, 1; 28759 Bremen, Germany.
| | - Andrew A Potter
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, 120 Veterinary Road, Saskatoon, SK S7N5E3, Canada.
| |
Collapse
|
31
|
Wang X, Deng Z, Liu T. Marker‐Free System Using Ribosomal Promoters Enhanced Xylose/Glucose Isomerase Production inStreptomyces rubiginosus. Biotechnol J 2019; 14:e1900114. [DOI: 10.1002/biot.201900114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/05/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Xiaojie Wang
- State Key Laboratory of Microbial Metabolism, School of Life Science and BiotechnologyShanghai Jiao Tong UniversityShanghai 200030 P. R. China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Science and BiotechnologyShanghai Jiao Tong UniversityShanghai 200030 P. R. China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan 430071 P. R. China
- Hubei Engineering Laboratory for Synthetic MicrobiologyWuhan Institute of BiotechnologyWuhan 430075 P. R. China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan 430071 P. R. China
- Hubei Engineering Laboratory for Synthetic MicrobiologyWuhan Institute of BiotechnologyWuhan 430075 P. R. China
| |
Collapse
|
32
|
Li Y, Cao S, Zhang L, Yuan J, Zhao Q, Wen Y, Wu R, Huang X, Yan Q, Huang Y, Ma X, Han X, Miao C, Wen X. A requirement of TolC1 for effective survival, colonization and pathogenicity of Actinobacillus pleuropneumoniae. Microb Pathog 2019; 134:103596. [PMID: 31212036 DOI: 10.1016/j.micpath.2019.103596] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 06/11/2019] [Accepted: 06/11/2019] [Indexed: 01/18/2023]
Abstract
To establish infection in the host, pathogens have evolved sophisticated systems to cope with environmental conditions and to protect cells against host immunity. TolC is the outer membrane channel component of type 1 secretion systems and multidrug efflux pumps that plays critical roles during the infection process in many pathogens. However, little is known about the exact roles of TolC1 in the pathogenicity of A. pleuropneumoniae, an etiological agent of the porcine contagious pleuropneumoniae that causes severe respiratory disease. In this study, deletion of tolC1 causes apparent ultrastructural defects in A. pleuropneumoniae cell examined by transmission electron microscopy. The tolC1 mutant is hypersensitivity to oxidative, osmotic and acid challenges by in vitro stress assays. Analysis on secreted proteins shows that the excretion of ApxIIA and an ApxIVA-like protein, ApxIVA-S, is abolished in the absence of TolC1. This result confirms the essential role of TolC1 in the secretion of Apx toxins and this is the first identification of an ApxIVA-like protein in in vitro culture of A. pleuropneumoniae. Besides, disruption of TolC1 leads to a significant attenuation of virulence in mice by an intraperitoneal route of A. pleuropneumoniae. The basis for the attenuation is further investigated using a mouse intranasal infection model, which reveals an impaired ability to colonize and induce lesions in the lungs for the loss of TolC1 of A. pleuropneumoniae. In conclusion, our findings demonstrate significant roles of TolC1 in facilitating bacterial survival in hostile conditions, maximum colonization as well as pathogenicity during the infection of A. pleuropneumoniae.
Collapse
Affiliation(s)
- Ying Li
- Department of Immunology, School of Basic Medical Science, Southwest Medical University, No. 319 Zhongshan Road, Luzhou, Sichuan, China; Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, Sichuan, China
| | - Sanjie Cao
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, Sichuan, China.
| | - Luhua Zhang
- Department of Pathogenic Biology, School of Basic Medical Science, Southwest Medical University, No. 319 Zhongshan Road, Luzhou, Sichuan, China
| | - Jianlin Yuan
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, Sichuan, China
| | - Qin Zhao
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, Sichuan, China
| | - Yiping Wen
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, Sichuan, China
| | - Rui Wu
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, Sichuan, China
| | - Xiaobo Huang
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, Sichuan, China
| | - Qigui Yan
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, Sichuan, China
| | - Yong Huang
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, Sichuan, China
| | - Xiaoping Ma
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, Sichuan, China
| | - Xinfeng Han
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, Sichuan, China
| | - Chang Miao
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, Sichuan, China
| | - Xintian Wen
- Research Center of Swine Diseases, College of Veterinary Medicine, Sichuan Agricultural University, No. 211 Huimin Road, Chengdu, Sichuan, China.
| |
Collapse
|
33
|
|
34
|
Ruano-Gallego D, Fraile S, Gutierrez C, Fernández LÁ. Screening and purification of nanobodies from E. coli culture supernatants using the hemolysin secretion system. Microb Cell Fact 2019; 18:47. [PMID: 30857538 PMCID: PMC6410518 DOI: 10.1186/s12934-019-1094-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 02/25/2019] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND The hemolysin (Hly) secretion system of E. coli allows the one-step translocation of hemolysin A (HlyA) from the bacterial cytoplasm to the extracellular medium, without a periplasmic intermediate. In this work, we investigate whether the Hly secretion system of E. coli is competent to secrete a repertoire of functional single-domain VHH antibodies (nanobodies, Nbs), facilitating direct screening of VHH libraries and the purification of selected Nb from the extracellular medium. RESULTS We employed a phagemid library of VHHs obtained by immunization of a dromedary with three protein antigens from enterohemorrhagic E. coli (EHEC), namely, the extracellular secreted protein A (EspA), the extracellular C-terminal region of Intimin (Int280), and the translocated intimin receptor middle domain (TirM). VHH clones binding each antigen were enriched and amplified by biopanning, and subsequently fused to the C-terminal secretion signal of HlyA to be expressed and secreted in a E. coli strain carrying the Hly export machinery (HlyB, HlyD and TolC). Individual E. coli clones were grown and induced in 96-well microtiter plates, and the supernatants of the producing cultures directly used in ELISA for detection of Nbs binding EspA, Int280 and TirM. A set of Nb sequences specifically binding each of these antigens were identified, indicating that the Hly system is able to secrete a diversity of functional Nbs. We performed thiol alkylation assays demonstrating that Nbs are correctly oxidized upon secretion, forming disulphide bonds between cysteine pairs despite the absence of a periplasmic intermediate. In addition, we show that the secreted Nb-HlyA fusions can be directly purified from the supernatant of E. coli cultures, avoiding cell lysis and in a single affinity chromatography step. CONCLUSIONS Our data demonstrate the Hly secretion system of E. coli can be used as an expression platform for screening and purification of Nb binders from VHH repertories.
Collapse
Affiliation(s)
- David Ruano-Gallego
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM-Cantoblanco, 28049 Madrid, Spain
| | - Sofía Fraile
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM-Cantoblanco, 28049 Madrid, Spain
| | - Carlos Gutierrez
- Research Institute of Biomedical and Health Sciences, Veterinary Faculty, Universidad de Las Palmas de Gran Canaria (UPGC), 35413 Arucas, Las Palmas, Canary Islands Spain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus UAM-Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
35
|
Caffalette CA, Corey RA, Sansom MSP, Stansfeld PJ, Zimmer J. A lipid gating mechanism for the channel-forming O antigen ABC transporter. Nat Commun 2019; 10:824. [PMID: 30778065 PMCID: PMC6379404 DOI: 10.1038/s41467-019-08646-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/23/2019] [Indexed: 12/15/2022] Open
Abstract
Extracellular glycan biosynthesis is a widespread microbial protection mechanism. In Gram-negative bacteria, the O antigen polysaccharide represents the variable region of outer membrane lipopolysaccharides. Fully assembled lipid-linked O antigens are translocated across the inner membrane by the WzmWzt ABC transporter for ligation to the lipopolysaccharide core, with the transporter forming a continuous transmembrane channel in a nucleotide-free state. Here, we report its structure in an ATP-bound conformation. Large structural changes within the nucleotide-binding and transmembrane regions push conserved hydrophobic residues at the substrate entry site towards the periplasm and provide a model for polysaccharide translocation. With ATP bound, the transporter forms a large transmembrane channel with openings toward the membrane and periplasm. The channel's periplasmic exit is sealed by detergent molecules that block solvent permeation. Molecular dynamics simulation data suggest that, in a biological membrane, lipid molecules occupy this periplasmic exit and prevent water flux in the transporter's resting state.
Collapse
Affiliation(s)
- Christopher A Caffalette
- Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | | | - Jochen Zimmer
- Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
| |
Collapse
|
36
|
Zhang S, Jain M, Fleites LA, Rayside PA, Gabriel DW. Identification and Characterization of Menadione and Benzethonium Chloride as Potential Treatments of Pierce's Disease of Grapevines. PHYTOPATHOLOGY 2019; 109:233-239. [PMID: 30407880 DOI: 10.1094/phyto-07-18-0244-fi] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Xylella fastidiosa infects a wide range of plant hosts and causes Pierce's disease (PD) of grapevines. The type 1 multidrug resistance (MDR) efflux system is essential for pathogenicity and survival of bacterial pathogens in planta. X. fastidiosa, with a single MDR system, is significantly more vulnerable to inhibition by small-molecule treatments than most bacterial pathogens that typically carry redundant MDR systems. A high-throughput cell viability assay using a green fluorescent protein-marked strain of X. fastidiosa Temecula 1 was developed to screen two Prestwick combinatorial small-molecule libraries of drugs and phytochemicals (1,600 chemicals in total) approved by the Food and Drug Administration and European Medicines Agency for cell growth inhibition. The screens revealed 215 chemicals that inhibited bacterial growth by >50% at 50 µM concentrations. Seven chemicals proved to lyse X. fastidiosa cells at 25 µM, including four phytochemicals. Menadione (2-methyl-1,4-naphthoquinone, vitamin K) from the phytochemical library and benzethonium chloride (a topical disinfectant) from the chemical library both showed significant bactericidal activity against X. fastidiosa. Both menadione and benzethonium chloride foliar spray (15 and 5 mM, respectively) and soil drench (5 and 25 mM, respectively) treatments were equally effective in reducing PD symptoms by 54 to 59% and revealed that the effects of both chemical treatments became systemic. However, menadione was phytotoxic when applied as a foliar spray at effective concentrations, causing significant loss of photosynthetic capacity.
Collapse
Affiliation(s)
- S Zhang
- Department of Plant Pathology, University of Florida, Gainesville 32611
| | - M Jain
- Department of Plant Pathology, University of Florida, Gainesville 32611
| | - L A Fleites
- Department of Plant Pathology, University of Florida, Gainesville 32611
| | - P A Rayside
- Department of Plant Pathology, University of Florida, Gainesville 32611
| | - D W Gabriel
- Department of Plant Pathology, University of Florida, Gainesville 32611
| |
Collapse
|
37
|
Transcriptome and Comparative Genomics Analyses Reveal New Functional Insights on Key Determinants of Pathogenesis and Interbacterial Competition in Pectobacterium and Dickeya spp. Appl Environ Microbiol 2019; 85:AEM.02050-18. [PMID: 30413477 DOI: 10.1128/aem.02050-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/29/2018] [Indexed: 02/07/2023] Open
Abstract
Soft-rot Enterobacteriaceae (SRE), typified by Pectobacterium and Dickeya genera, are phytopathogenic bacteria inflicting soft-rot disease in crops worldwide. By combining genomic information from 100 SRE with whole-transcriptome data sets, we identified novel genomic and transcriptional associations among key pathogenicity themes in this group. Comparative genomics revealed solid linkage between the type I secretion system (T1SS) and the carotovoricin bacteriophage (Ctv) conserved in 96.7% of Pectobacterium genomes. Moreover, their coactivation during infection indicates a novel functional association involving T1SS and Ctv. Another bacteriophage-borne genomic region, mostly confined to less than 10% of Pectobacterium strains, was found, presumably comprising a novel lineage-specific prophage in the genus. We also detected the transcriptional coregulation of a previously predicted toxin/immunity pair (WHH and SMI1_KNR4 families), along with the type VI secretion system (T6SS), which includes hcp and/or vgrG genes, suggesting a role in disease development as T6SS-dependent effectors. Further, we showed that another predicted T6SS-dependent endonuclease (AHH family) exhibited toxicity in ectopic expression assays, indicating antibacterial activity. Additionally, we report the striking conservation of the group 4 capsule (GFC) cluster in 100 SRE strains which consistently features adjacently conserved serotype-specific gene arrays comprising a previously unknown organization in GFC clusters. Also, extensive sequence variations found in gfcA orthologs suggest a serotype-specific role in the GfcABCD machinery.IMPORTANCE Despite the considerable loss inflicted on important crops yearly by Pectobacterium and Dickeya diseases, investigations on key virulence and interbacterial competition assets relying on extensive comparative genomics are still surprisingly lacking for these genera. Such approaches become more powerful over time, underpinned by the growing amount of genomic information in public databases. In particular, our findings point to new functional associations among well-known genomic themes enabling alternative means of neutralizing SRE diseases through disruption of pivotal virulence programs. By elucidating novel transcriptional and genomic associations, this study adds valuable information on virulence candidates that could be decisive in molecular applications in the near future. The utilization of 100 genomes of Pectobacterium and Dickeya strains in this study is unprecedented for comparative analyses in these taxa, and it provides novel insights on the biology of economically important plant pathogens.
Collapse
|
38
|
Substrate polyspecificity and conformational relevance in ABC transporters: new insights from structural studies. Biochem Soc Trans 2018; 46:1475-1484. [PMID: 30514765 DOI: 10.1042/bst20180146] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/09/2018] [Accepted: 10/30/2018] [Indexed: 12/17/2022]
Abstract
Transport of molecules and ions across biological membranes is an essential process in all organisms. It is carried out by a range of evolutionarily conserved primary and secondary transporters. A significant portion of the primary transporters belong to the ATP-binding cassette (ABC) superfamily, which utilise the free-energy from ATP hydrolysis to shuttle many different substrates across various biological membranes, and consequently, are involved in both normal and abnormal physiology. In humans, ABC transporter-associated pathologies are perhaps best exemplified by multidrug-resistance transporters that efflux many xenobiotic compounds due to their remarkable substrate polyspecificity. Accordingly, understanding the transport mechanism(s) is of great significance, and indeed, much progress has been made in recent years, particularly from structural studies on ABC exporters. Consequently, the general mechanism of 'alternate access' has been modified to describe individual transporter nuances, though some aspects of the transport process remain unclear. Moreover, as new information has emerged, the physiological relevance of the 'open-apo' conformation of MsbA (a bacterial exporter) has been questioned and, by extension, its contribution to mechanistic models. We present here a comprehensive overview of the most recently solved structures of ABC exporters, focusing on new insights regarding the nature of substrate polyspecificity and the physiological relevance of the 'open-apo' conformation. This review evaluates the claim that the latter may be an artefact of detergent solubilisation, and we hypothesise that the biophysical properties of the membrane play a key role in the function of ABC exporters allowing them to behave like a 'spring-hinge' during their transport cycle.
Collapse
|
39
|
Schultz LG, Tasic L, Fattori J. Chaperone-Assisted Secretion in Bacteria: Protein and DNA Transport via Cell Membranes. CURR PROTEOMICS 2018. [DOI: 10.2174/1570164615666180820154821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Bacteria use an impressive arsenal of secretion systems (1-7) to infect their host cells by exporting
proteins, DNA and DNA-protein complexes via cell membranes. They use chaperone-usher
pathways for host colonization as well. To be targeted for transportation across one (Gram-positive) or
two membranes (Gram-negative), clients must be selected, guided and unfolded to pass through type 3
(T3SS) or type 4 (T4SS) secretion systems. For these processes, bacteria count on secretory chaperones
that guide macromolecular transport via membranes. Moreover, if we know how these processes
occur, we might be able to stop them and avoid bacterial infections. Thus, structural and functional
characterizations of secretory chaperones become interesting, as these proteins are the perfect targets
for blocking bacteria action. Therefore, this review focuses on a story of known mechanisms of chaperone-
secretion assisted transport with special attention on virulence proteins and DNA transport in
bacteria.
Collapse
Affiliation(s)
- Lilian Goulart Schultz
- Chemical Biology Laboratory, Organic Chemistry Department, Institute of Chemistry, University of Campinas, P.O. Box 6154, Campinas, 13083-970, SP, Brazil
| | - Ljubica Tasic
- Chemical Biology Laboratory, Organic Chemistry Department, Institute of Chemistry, University of Campinas, P.O. Box 6154, Campinas, 13083-970, SP, Brazil
| | - Juliana Fattori
- Chemical Biology Laboratory, Organic Chemistry Department, Institute of Chemistry, University of Campinas, P.O. Box 6154, Campinas, 13083-970, SP, Brazil
| |
Collapse
|
40
|
Brown AC, Boesze-Battaglia K, Balashova NV, Mas Gómez N, Speicher K, Tang HY, Duszyk ME, Lally ET. Membrane localization of the Repeats-in-Toxin (RTX) Leukotoxin (LtxA) produced by Aggregatibacter actinomycetemcomitans. PLoS One 2018; 13:e0205871. [PMID: 30335797 PMCID: PMC6193665 DOI: 10.1371/journal.pone.0205871] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/02/2018] [Indexed: 12/31/2022] Open
Abstract
The oral bacterium, Aggregatibacter actinomycetemcomitans, which is associated with localized aggressive periodontitis, as well as systemic infections including endocarditis, produces numerous virulence factors, including a repeats-in-toxin (RTX) protein called leukotoxin (LtxA), which kills human immune cells. The strains of A. actinomycetemcomitans most closely associated with disease have been shown to produce the most LtxA, suggesting that LtxA plays a significant role in the virulence of this organism. LtxA, like many of the RTX toxins, can be divided into four functional domains: an N-terminal hydrophobic domain, which contains a significant fraction of hydrophobic residues and has been proposed to play a role in the membrane interaction of the toxin; the central domain, which contains two lysine residues that are the sites of post-translational acylation; the repeat domain that is characteristic of the RTX toxins, and a C-terminal domain thought to be involved in secretion. In its initial interaction with the host cell, LtxA must bind to both cholesterol and an integrin receptor, lymphocyte function-associated antigen-1 (LFA-1). While both interactions are essential for toxicity, the domains of LtxA involved remain unknown. We therefore undertook a series of experiments, including tryptophan quenching and trypsin digestion, to characterize the structure of LtxA upon interaction with membranes of various lipid compositions. Our results demonstrate that LtxA adopts a U-shaped conformation in the membrane, with the N- and C-terminal domains residing outside of the membrane.
Collapse
Affiliation(s)
- Angela C. Brown
- Department of Pathology, University of Pennsylvania, School of Dental Medicine, Philadelphia, PA, United States of America
| | - Kathleen Boesze-Battaglia
- Department of Biochemistry, University of Pennsylvania, School of Dental Medicine, Philadelphia, PA, United States of America
| | - Nataliya V. Balashova
- Department of Pathology, University of Pennsylvania, School of Dental Medicine, Philadelphia, PA, United States of America
| | - Nestor Mas Gómez
- Department of Pathology, University of Pennsylvania, School of Dental Medicine, Philadelphia, PA, United States of America
| | - Kaye Speicher
- Wistar Institute, Philadelphia, PA, United States of America
| | - Hsin-Yao Tang
- Wistar Institute, Philadelphia, PA, United States of America
| | - Margaret E. Duszyk
- Department of Pathology, University of Pennsylvania, School of Dental Medicine, Philadelphia, PA, United States of America
| | - Edward T. Lally
- Department of Pathology, University of Pennsylvania, School of Dental Medicine, Philadelphia, PA, United States of America
- * E-mail:
| |
Collapse
|
41
|
Zhou Y, Ojeda-May P, Nagaraju M, Kim B, Pu J. Mapping Free Energy Pathways for ATP Hydrolysis in the E. coli ABC Transporter HlyB by the String Method. Molecules 2018; 23:molecules23102652. [PMID: 30332773 PMCID: PMC6222333 DOI: 10.3390/molecules23102652] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 11/16/2022] Open
Abstract
HlyB functions as an adenosine triphosphate (ATP)-binding cassette (ABC) transporter that enables bacteria to secrete toxins at the expense of ATP hydrolysis. Our previous work, based on potential energy profiles from combined quantum mechanical and molecular mechanical (QM/MM) calculations, has suggested that the highly conserved H-loop His residue H662 in the nucleotide binding domain (NBD) of E. coli HlyB may catalyze the hydrolysis of ATP through proton relay. To further test this hypothesis when entropic contributions are taken into account, we obtained QM/MM minimum free energy paths (MFEPs) for the HlyB reaction, making use of the string method in collective variables. The free energy profiles along the MFEPs confirm the direct participation of H662 in catalysis. The MFEP simulations of HlyB also reveal an intimate coupling between the chemical steps and a local protein conformational change involving the signature-loop residue S607, which may serve a catalytic role similar to an Arg-finger motif in many ATPases and GTPases in stabilizing the phosphoryl-transfer transition state.
Collapse
Affiliation(s)
- Yan Zhou
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Pedro Ojeda-May
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Mulpuri Nagaraju
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Bryant Kim
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| |
Collapse
|
42
|
Kleiner-Grote GRM, Risse JM, Friehs K. Secretion of recombinant proteins from E. coli. Eng Life Sci 2018; 18:532-550. [PMID: 32624934 DOI: 10.1002/elsc.201700200] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/07/2018] [Accepted: 03/13/2018] [Indexed: 11/10/2022] Open
Abstract
The microorganism Escherichia coli is commonly used for recombinant protein production. Despite several advantageous characteristics like fast growth and high protein yields, its inability to easily secrete recombinant proteins into the extracellular medium remains a drawback for industrial production processes. To overcome this limitation, a multitude of approaches to enhance the extracellular yield and the secretion efficiency of recombinant proteins have been developed in recent years. Here, a comprehensive overview of secretion mechanisms for recombinant proteins from E. coli is given and divided into three main sections. First, the structure of the E. coli cell envelope and the known natural secretion systems are described. Second, the use and optimization of different one- or two-step secretion systems for recombinant protein production, as well as further permeabilization methods are discussed. Finally, the often-overlooked role of cell lysis in secretion studies and its analysis are addressed. So far, effective approaches for increasing the extracellular protein concentration to more than 10 g/L and almost 100% secretion efficiency exist, however, the large range of optimization methods and their combinations suggests that the potential for secretory protein production from E. coli has not yet been fully realized.
Collapse
Affiliation(s)
| | - Joe M Risse
- Fermentation Engineering Bielefeld University Bielefeld Germany.,Center for Biotechnology Bielefeld University Bielefeld Germany
| | - Karl Friehs
- Fermentation Engineering Bielefeld University Bielefeld Germany.,Center for Biotechnology Bielefeld University Bielefeld Germany
| |
Collapse
|
43
|
Rapicavoli J, Ingel B, Blanco‐Ulate B, Cantu D, Roper C. Xylella fastidiosa: an examination of a re-emerging plant pathogen. MOLECULAR PLANT PATHOLOGY 2018; 19:786-800. [PMID: 28742234 PMCID: PMC6637975 DOI: 10.1111/mpp.12585] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 07/13/2017] [Accepted: 07/19/2017] [Indexed: 05/10/2023]
Abstract
UNLABELLED Xylella fastidiosa is a Gram-negative bacterial plant pathogen with an extremely wide host range. This species has recently been resolved into subspecies that correlate with host specificity. This review focuses on the status of X. fastidiosa pathogenic associations in plant hosts in which the bacterium is either endemic or has been recently introduced. Plant diseases associated with X. fastidiosa have been documented for over a century, and much about what is known in the context of host-pathogen interactions is based on these hosts, such as grape and citrus, in which this pathogen has been well described. Recent attention has focused on newly emerging X. fastidiosa diseases, such as in olives. TAXONOMY Bacteria; Gammaproteobacteria; family Xanthomonadaceae; genus Xylella; species fastidiosa. MICROBIOLOGICAL PROPERTIES Gram-negative rod (0.25-0.35 × 0.9-3.5 μm), non-flagellate, motile via Type IV pili-mediated twitching, fastidious. HOST RANGE Xylella fastidiosa has a broad host range that includes ornamental, ecological and agricultural plants belonging to over 300 different species in 63 different families. To date, X. fastidiosa has been found to be pathogenic in over 100 plant species. In addition, it can establish non-symptomatic associations with many plants as a commensal endophyte. Here, we list the four distinct subspecies of X. fastidiosa and some of the agriculturally relevant diseases caused by them: X. fastidiosa ssp. fastidiosa causes Pierce's disease (PD) of grapevine (Vitis vinifera); X. fastidiosa ssp. multiplex causes almond leaf scorch (ALS) and diseases on other nut and shade tree crops; X. fastidiosa ssp. pauca causes citrus variegated chlorosis (CVC) (Citrus spp.), coffee leaf scorch and olive quick decline syndrome (OQDS) (Olea europaea); X. fastidiosa ssp. sandyi causes oleander leaf scorch (OLS) (Nerium oleander). Significant host specificity seemingly exists for some of the subspecies, although this could be a result of technical biases based on the limited number of plants tested, whereas some subspecies are not as stringent in their host range and can infect several plant hosts. DISEASE SYMPTOMS Most X. fastidiosa-related diseases appear as marginal leaf necrosis and scorching of the leaves. In the case of PD, X. fastidiosa can also cause desiccation of berries (termed 'raisining'), irregular periderm development and abnormal abscission of petioles. In olive trees affected with OQDS, leaves exhibit marginal necrosis and defoliation, and overall tree decline occurs. Plants with ALS and OLS also exhibit the characteristic leaf scorch symptoms. Not all X. fastidiosa-related diseases exhibit the typical leaf scorch symptoms. These include CVC and Phony Peach disease, amongst others. In the case of CVC, symptoms include foliar wilt and interveinal chlorosis on the upper surfaces of the leaves (similar to zinc deficiency), which correspond to necrotic, gum-like regions on the undersides of the leaves. Additional symptoms of CVC include defoliation, dieback and hardening of fruits. Plants infected with Phony Peach disease exhibit a denser, more compact canopy (as a result of shortened internodes, darker green leaves and delayed leaf senescence), premature bloom and reduced fruit size. Some occlusions occur in the xylem vessels, but there are no foliar wilting, chlorosis or necrosis symptoms . USEFUL WEBSITES: http://www.piercesdisease.org/; https://pubmlst.org/xfastidiosa/; http://www.xylella.lncc.br/; https://nature.berkeley.edu/xylella/; https://ec.europa.eu/food/plant/plant_health_biosecurity/legislation/emergency_measures/xylella-fastidiosa_en.
Collapse
Affiliation(s)
- Jeannette Rapicavoli
- Department of Plant Pathology and MicrobiologyUniversity of CaliforniaRiversideCA 92521USA
| | - Brian Ingel
- Department of Plant Pathology and MicrobiologyUniversity of CaliforniaRiversideCA 92521USA
| | | | - Dario Cantu
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCA 95616USA
| | - Caroline Roper
- Department of Plant Pathology and MicrobiologyUniversity of CaliforniaRiversideCA 92521USA
| |
Collapse
|
44
|
Jun D, Minic Z, Bhat SV, Vanderlinde EM, Yost CK, Babu M, Dahms TES. Metabolic Adaptation of a C-Terminal Protease A-Deficient Rhizobium leguminosarum in Response to Loss of Nutrient Transport. Front Microbiol 2018; 8:2617. [PMID: 29354107 PMCID: PMC5758756 DOI: 10.3389/fmicb.2017.02617] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/15/2017] [Indexed: 11/13/2022] Open
Abstract
Post-translational modification expands the functionality of the proteome beyond genetic encoding, impacting many cellular processes. Cleavage of the carboxyl terminus is one of the many different ways proteins can be modified for functionality. Gel-electrophoresis and mass spectrometric-based techniques were used to identify proteins impacted by deficiency of a C-terminal protease, CtpA, in Rhizobium leguminosarum bv. viciae 3841. Predicted CtpA substrates from 2D silver stained gels were predominantly outer membrane and transport proteins. Proteins with altered abundance in the wild type and ctpA (RL4692) mutant, separated by 2D difference gel electrophoresis, were selected for analysis by mass spectrometry. Of those identified, 9 were the periplasmic solute-binding components of ABC transporters, 5 were amino acid metabolic enzymes, 2 were proteins involved in sulfur metabolism, and 1 each was related to carbon metabolism, protein folding and signal transduction. Alterations to ABC-binding-cassette transporters, nutrient uptake efficiency and to amino acid metabolism indicated an impact on amino acid metabolism and transport for the ctpA mutant, which was validated by measured amino acid levels.
Collapse
Affiliation(s)
- Dong Jun
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Zoran Minic
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Supriya V. Bhat
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Elizabeth M. Vanderlinde
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
- Department of Biology, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Chris K. Yost
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Tanya E. S. Dahms
- Department of Chemistry and Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| |
Collapse
|
45
|
An A/U-Rich Enhancer Region Is Required for High-Level Protein Secretion through the HlyA Type I Secretion System. Appl Environ Microbiol 2017; 84:AEM.01163-17. [PMID: 29030442 DOI: 10.1128/aem.01163-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 10/06/2017] [Indexed: 11/20/2022] Open
Abstract
Efficient protein secretion is often a valuable alternative to classic cellular expression to obtain homogenous protein samples. Early on, bacterial type I secretion systems (T1SS) were employed to allow heterologous secretion of fusion proteins. However, this approach was not fully exploited, as many proteins could not be secreted at all or only at low levels. Here, we present an engineered microbial secretion system which allows the effective production of proteins up to a molecular mass of 88 kDa. This system is based on the hemolysin A (HlyA) T1SS of the Gram-negative bacterium Escherichia coli, which exports polypeptides when fused to a hemolysin secretion signal. We identified an A/U-rich enhancer region upstream of hlyA required for effective expression and secretion of selected heterologous proteins irrespective of their prokaryotic, viral, or eukaryotic origin. We further demonstrate that the ribosomal protein S1 binds to the hlyA A/U-rich enhancer region and that this region is involved in the high yields of secretion of functional proteins, like maltose-binding protein or human interferon alpha-2.IMPORTANCE A 5' untranslated region of the mRNA of substrates of type I secretion systems (T1SS) drastically enhanced the secretion efficiency of the endogenously secreted protein. The identification of ribosomal protein S1 as the interaction partner of this 5' untranslated region provides a rationale for the enhancement. This strategy furthermore can be transferred to fusion proteins allowing a broader, and eventually a more general, application of this system for secreting heterologous fusion proteins.
Collapse
|
46
|
Murata D, Okano H, Angkawidjaja C, Akutsu M, Tanaka SI, Kitahara K, Yoshizawa T, Matsumura H, Kado Y, Mizohata E, Inoue T, Sano S, Koga Y, Kanaya S, Takano K. Structural Basis for the Serratia marcescens Lipase Secretion System: Crystal Structures of the Membrane Fusion Protein and Nucleotide-Binding Domain. Biochemistry 2017; 56:6281-6291. [PMID: 29094929 DOI: 10.1021/acs.biochem.7b00985] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Serratia marcescens secretes a lipase, LipA, through a type I secretion system (T1SS). The T1SS for LipA, the Lip system, is composed of an inner membrane ABC transporter with its nucleotide-binding domains (NBD), LipB, a membrane fusion protein, LipC, and an outer membrane channel protein, LipD. Passenger protein secreted by this system has been functionally and structurally characterized well, but relatively little information about the transporter complex is available. Here, we report the crystallographic studies of LipC without the membrane anchor region, LipC-, and the NBD of LipB (LipB-NBD). LipC- crystallographic analysis has led to the determination of the structure of the long α-helical and lipoyl domains, but not the area where it interacts with LipB, suggesting that the region is flexible without LipB. The long α-helical domain has three α-helices, which interacts with LipD in the periplasm. LipB-NBD has the common overall architecture and ATP hydrolysis activity of ABC transporter NBDs. Using the predicted models of full-length LipB and LipD, the overall structural insight into the Lip system is discussed.
Collapse
Affiliation(s)
- Daichi Murata
- Department of Biomolecular Chemistry, Kyoto Prefectural University , Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Hiroyuki Okano
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Clement Angkawidjaja
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Masato Akutsu
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt , Max-von-Laue-Straße, 60438 Frankfurt am Main, Germany
| | - Shun-Ichi Tanaka
- College of Life Sciences, Ritsumeikan University , Noji-Higashi, Kusatsu 525-8577, Japan
| | - Kenyu Kitahara
- Department of Biomolecular Chemistry, Kyoto Prefectural University , Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Takuya Yoshizawa
- College of Life Sciences, Ritsumeikan University , Noji-Higashi, Kusatsu 525-8577, Japan
| | - Hiroyoshi Matsumura
- College of Life Sciences, Ritsumeikan University , Noji-Higashi, Kusatsu 525-8577, Japan
| | - Yuji Kado
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Eiichi Mizohata
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Tsuyoshi Inoue
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Satoshi Sano
- Department of Biomolecular Chemistry, Kyoto Prefectural University , Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Yuichi Koga
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Shigenori Kanaya
- Graduate School of Engineering, Osaka University , Yamadaoka, Suita 565-0871, Japan
| | - Kazufumi Takano
- Department of Biomolecular Chemistry, Kyoto Prefectural University , Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| |
Collapse
|
47
|
Type I Protein Secretion-Deceptively Simple yet with a Wide Range of Mechanistic Variability across the Family. EcoSal Plus 2017; 7. [PMID: 28084193 DOI: 10.1128/ecosalplus.esp-0019-2015] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A very large type I polypeptide begins to reel out from a ribosome; minutes later, the still unidentifiable polypeptide, largely lacking secondary structure, is now in some cases a thousand or more residues longer. Synthesis of the final hundred C-terminal residues commences. This includes the identity code, the secretion signal within the last 50 amino acids, designed to dock with a waiting ATP binding cassette (ABC) transporter. What happens next is the subject of this review, with the main, but not the only focus on hemolysin HlyA, an RTX protein toxin secreted by the type I system. Transport substrates range from small peptides to giant proteins produced by many pathogens. These molecules, without detectable cellular chaperones, overcome enormous barriers, crossing two membranes before final folding on the cell surface, involving a unique autocatalytic process.Unfolded HlyA is extruded posttranslationally, C-terminal first. The transenvelope "tunnel" is formed by HlyB (ABC transporter), HlyD (membrane fusion protein) straddling the inner membrane and periplasm and TolC (outer membrane). We present a new evaluation of the C-terminal secretion code, and the structure function of HlyD and HlyB at the heart of this nanomachine. Surprisingly, key details of the secretion mechanism are remarkably variable in the many type I secretion system subtypes. These include alternative folding processes, an apparently distinctive secretion code for each type I subfamily, and alternative forms of the ABC transporter; most remarkably, the ABC protein probably transports peptides or polypeptides by quite different mechanisms. Finally, we suggest a putative structure for the Hly-translocon, HlyB, the multijointed HlyD, and the TolC exit.
Collapse
|
48
|
Webb CT, Chandrapala D, Oslan SN, Bamert RS, Grinter RD, Dunstan RA, Gorrell RJ, Song J, Strugnell RA, Lithgow T, Kwok T. Reductive evolution in outer membrane protein biogenesis has not compromised cell surface complexity in Helicobacter pylori. Microbiologyopen 2017; 6. [PMID: 29055967 PMCID: PMC5727368 DOI: 10.1002/mbo3.513] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/19/2017] [Accepted: 05/25/2017] [Indexed: 12/18/2022] Open
Abstract
Helicobacter pylori is a gram‐negative bacterial pathogen that chronically inhabits the human stomach. To survive and maintain advantage, it has evolved unique host–pathogen interactions mediated by Helicobacter‐specific proteins in the bacterial outer membrane. These outer membrane proteins (OMPs) are anchored to the cell surface via a C‐terminal β‐barrel domain, which requires their assembly by the β‐barrel assembly machinery (BAM). Here we have assessed the complexity of the OMP C‐terminal β‐barrel domains employed by H. pylori, and characterized the H. pyloriBAM complex. Around 50 Helicobacter‐specific OMPs were assessed with predictive structural algorithms. The data suggest that H. pylori utilizes a unique β‐barrel architecture that might constitute H. pylori‐specific Type V secretions system. The structural and functional diversity in these proteins is encompassed by their extramembrane domains. Bioinformatic and biochemical characterization suggests that the low β‐barrel‐complexity requires only minimalist assembly machinery. The H. pylori proteins BamA and BamD associate to form a BAM complex, with features of BamA enabling an oligomerization that might represent a mechanism by which a minimalist BAM complex forms a larger, sophisticated machinery capable of servicing the outer membrane proteome of H. pylori.
Collapse
Affiliation(s)
- Chaille T. Webb
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
| | - Dilini Chandrapala
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
| | - Siti Nurbaya Oslan
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
- Department of BiochemistryFaculty of Biotechnology and Biomolecular SciencesUniversiti Putra MalaysiaSerdangSelangorMalaysia
- Enzyme and Microbial Technology Research CenterUniversiti Putra MalaysiaSerdangSelangorMalaysia
| | - Rebecca S. Bamert
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
| | - Rhys D. Grinter
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
| | - Rhys A. Dunstan
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
| | - Rebecca J. Gorrell
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
| | - Jiangning Song
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
- Monash Centre for Data ScienceFaculty of Information TechnologyMonash UniversityMelbourneAustralia
| | - Richard A. Strugnell
- Department of Microbiology & ImmunologyUniversity of MelbourneParkvilleAustralia
| | - Trevor Lithgow
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
| | - Terry Kwok
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of MicrobiologyMonash UniversityClaytonAustralia
- Infection & Immunity ProgramBiomedicine Discovery Institute and Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
| |
Collapse
|
49
|
Locher KP. Mechanistic diversity in ATP-binding cassette (ABC) transporters. Nat Struct Mol Biol 2017; 23:487-93. [PMID: 27273632 DOI: 10.1038/nsmb.3216] [Citation(s) in RCA: 518] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 03/30/2016] [Indexed: 12/18/2022]
Abstract
ABC transporters catalyze transport reactions, such as the high-affinity uptake of micronutrients into bacteria and the export of cytotoxic compounds from mammalian cells. Crystal structures of ABC domains and full transporters have provided a framework for formulating reaction mechanisms of ATP-driven substrate transport, but recent studies have suggested remarkable mechanistic diversity within this protein family. This review evaluates the differing mechanistic proposals and outlines future directions for the exploration of ABC-transporter-catalyzed reactions.
Collapse
Affiliation(s)
- Kaspar P Locher
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
50
|
Cannella SE, Ntsogo Enguéné VY, Davi M, Malosse C, Sotomayor Pérez AC, Chamot-Rooke J, Vachette P, Durand D, Ladant D, Chenal A. Stability, structural and functional properties of a monomeric, calcium-loaded adenylate cyclase toxin, CyaA, from Bordetella pertussis. Sci Rep 2017; 7:42065. [PMID: 28186111 PMCID: PMC5301233 DOI: 10.1038/srep42065] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 01/04/2017] [Indexed: 12/21/2022] Open
Abstract
Bordetella pertussis, the causative agent of whooping cough, secretes an adenylate cyclase toxin, CyaA, which invades eukaryotic cells and alters their physiology by cAMP overproduction. Calcium is an essential cofactor of CyaA, as it is the case for most members of the Repeat-in-ToXins (RTX) family. We show that the calcium-bound, monomeric form of CyaA, hCyaAm, conserves its permeabilization and haemolytic activities, even in a fully calcium-free environment. In contrast, hCyaAm requires sub-millimolar calcium in solution for cell invasion, indicating that free calcium in solution is involved in the CyaA toxin translocation process. We further report the first in solution structural characterization of hCyaAm, as deduced from SAXS, mass spectrometry and hydrodynamic studies. We show that hCyaAm adopts a compact and stable state that can transiently conserve its conformation even in a fully calcium-free environment. Our results therefore suggest that in hCyaAm, the C-terminal RTX-domain is stabilized in a high-affinity calcium-binding state by the N-terminal domains while, conversely, calcium binding to the C-terminal RTX-domain strongly stabilizes the N-terminal regions. Hence, the different regions of hCyaAm appear tightly connected, leading to stabilization effects between domains. The hysteretic behaviour of CyaA in response to calcium is likely shared by other RTX cytolysins.
Collapse
Affiliation(s)
- Sara E. Cannella
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, 75724 PARIS cedex 15, France
| | | | - Marilyne Davi
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, 75724 PARIS cedex 15, France
| | - Christian Malosse
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, 75724 PARIS cedex 15, France
| | | | - Julia Chamot-Rooke
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, 75724 PARIS cedex 15, France
| | - Patrice Vachette
- Institut de Biologie Intégrative de la Cellule, UMR 9198, Université Paris-Sud, F-91405 ORSAY Cedex, France
| | - Dominique Durand
- Institut de Biologie Intégrative de la Cellule, UMR 9198, Université Paris-Sud, F-91405 ORSAY Cedex, France
| | - Daniel Ladant
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, 75724 PARIS cedex 15, France
| | - Alexandre Chenal
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, 75724 PARIS cedex 15, France
| |
Collapse
|