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Svetlova AO, Karaseva MA, Berdyshev IM, Chukhontseva KN, Pobeguts OV, Galyamina MA, Smirnov IP, Polyakov NB, Zavialova MG, Kostrov SV, Demidyuk IV. Protease S of entomopathogenic bacterium Photorhabdus laumondii: expression, purification and effect on greater wax moth Galleria mellonella. Mol Biol Rep 2024; 51:713. [PMID: 38824247 DOI: 10.1007/s11033-024-09654-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/20/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Protease S (PrtS) from Photorhabdus laumondii belongs to the group of protealysin-like proteases (PLPs), which are understudied factors thought to play a role in the interaction of bacteria with other organisms. Since P. laumondii is an insect pathogen and a nematode symbiont, the analysis of the biological functions of PLPs using the PrtS model provides novel data on diverse types of interactions between bacteria and hosts. METHODS AND RESULTS Recombinant PrtS was produced in Escherichia coli. Efficient inhibition of PrtS activity by photorin, a recently discovered emfourin-like protein inhibitor from P. laumondii, was demonstrated. The Galleria mellonella was utilized to examine the insect toxicity of PrtS and the impact of PrtS on hemolymph proteins in vitro. The insect toxicity of PrtS is reduced compared to protease homologues from non-pathogenic bacteria and is likely not essential for the infection process. However, using proteomic analysis, potential PrtS targets have been identified in the hemolymph. CONCLUSIONS The spectrum of identified proteins indicates that the function of PrtS is to modulate the insect immune response. Further studies of PLPs' biological role in the PrtS and P. laumondii model must clarify the details of PrtS interaction with the insect immune system during bacterial infection.
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Affiliation(s)
| | | | | | | | - Olga V Pobeguts
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Maria A Galyamina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Igor P Smirnov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Nikita B Polyakov
- Gamaleya National Research Center of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Maria G Zavialova
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - Ilya V Demidyuk
- National Research Centre "Kurchatov Institute", Moscow, Russia.
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2
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Yan T, Li M, Wang Q, Wang M, Liu L, Ma C, Xiang X, Zhou Q, Liu Z, Gong Z. Structures, functions, and regulatory networks of universal stress proteins in clinically relevant pathogenic Bacteria. Cell Signal 2024; 116:111032. [PMID: 38185228 DOI: 10.1016/j.cellsig.2023.111032] [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: 10/06/2023] [Revised: 12/14/2023] [Accepted: 12/30/2023] [Indexed: 01/09/2024]
Abstract
Universal stress proteins are a class of proteins widely present in bacteria, archaea, plants, and invertebrates, playing essential roles in bacterial adaptation to various environmental stresses. The functions of bacterial universal stress proteins are versatile, including resistance to oxidative stress, maintenance of cell wall integrity, DNA damage repair, regulation of cell division and growth, among others. When facing stresses such as temperature changes, pH shifts, fluctuations in oxygen concentration, and exposure to toxins, these proteins can bind to specific DNA sequences and rapidly adjust bacterial metabolic pathways and gene expression patterns to adapt to the new environment. In summary, bacterial universal stress proteins play a crucial role in bacterial adaptability and survival. A comprehensive understanding of bacterial stress response mechanisms and the development of new antibacterial strategies are of great significance. This review summarizes the research progress on the structure, function, and regulatory factors of universal stress proteins in clinically relevant bacteria, aiming to facilitate deeper investigations by clinicians and researchers into universal stress proteins.
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Affiliation(s)
- Tao Yan
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Min Li
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Qiuyan Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Meng Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lijuan Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Chengcheng Ma
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiaohong Xiang
- School of Pharmacy, Chongqing Medical and Pharmaceutical College, Chongqing, China
| | - Qiang Zhou
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhou Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.
| | - Zhen Gong
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.
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3
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Roberts K, Osme A, De Salvo C, Zoli E, Herrada J, McCormick TS, Ghannoum M, Cominelli F, Di Martino L. Candida tropicalis Affects Candida albicans Virulence by Limiting Its Capacity to Adhere to the Host Intestinal Surface, Leading to Decreased Susceptibility to Colitis in Mice. J Fungi (Basel) 2024; 10:245. [PMID: 38667916 PMCID: PMC11051055 DOI: 10.3390/jof10040245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/15/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Candida (C.) infections represent a serious health risk for people affected by inflammatory bowel disease. An important fungal virulence factor is the capacity of the fungus to form biofilms on the colonized surface of the host. This research study aimed to determine the effect of a C. tropicalis and C. albicans co-infection on dextran sodium sulfate (DSS)-induced colitis in mice. The colitis severity was evaluated using histology and a colonoscopy. The mice were mono-inoculated with C. albicans or C. tropicalis or co-challenged with both species. The mice were administered 3% DSS to induce acute colitis. The biofilm activity was assessed using (2-methoxy-4-nitro-5-sulfophenyl)-5-[(phenylamino)carbonyl] 2H-tetrazoliumhydroxide (XTT) and dry-weight assays. The abundance of C. albicans in the colon tissues was assessed by immunohistochemistry. The co-challenged mice showed a decreased colitis severity compared to the mono-inoculated mice. The dry-weight assay demonstrated a marked decrease in C. albicans biofilm production in a C. albicans culture incubated with C. tropicalis supernatant. Immunohistochemical staining showed that C. albicans was more abundant in the mucosa of C. albicans mono-inoculated mice compared to the co-inoculated group. These data indicate an antagonistic microbial interaction between the two Candida species, where C. tropicalis may produce molecules capable of limiting the ability of C. albicans to adhere to the host intestinal surface, leading to a reduction in biofilm formation.
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Affiliation(s)
- Kyle Roberts
- Center for Medical Mycology and Integrated Microbiome Core, Department of Dermatology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH 44106, USA; (K.R.); (J.H.); (T.S.M.); (M.G.)
| | - Abdullah Osme
- Department of Anatomic Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Carlo De Salvo
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (C.D.S.); (F.C.)
| | - Eleonora Zoli
- Case Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA;
- Department of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Janet Herrada
- Center for Medical Mycology and Integrated Microbiome Core, Department of Dermatology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH 44106, USA; (K.R.); (J.H.); (T.S.M.); (M.G.)
| | - Thomas S. McCormick
- Center for Medical Mycology and Integrated Microbiome Core, Department of Dermatology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH 44106, USA; (K.R.); (J.H.); (T.S.M.); (M.G.)
| | - Mahmoud Ghannoum
- Center for Medical Mycology and Integrated Microbiome Core, Department of Dermatology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH 44106, USA; (K.R.); (J.H.); (T.S.M.); (M.G.)
| | - Fabio Cominelli
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (C.D.S.); (F.C.)
- Case Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA;
- Department of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Luca Di Martino
- Case Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA;
- Department of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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4
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Zangara MT, Darwish L, Coombes BK. Characterizing the Pathogenic Potential of Crohn's Disease-Associated Adherent-Invasive Escherichia coli. EcoSal Plus 2023; 11:eesp00182022. [PMID: 37220071 PMCID: PMC10729932 DOI: 10.1128/ecosalplus.esp-0018-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/04/2023] [Indexed: 01/28/2024]
Abstract
The microbiome of Crohn's disease (CD) patients is composed of a microbial community that is considered dysbiotic and proinflammatory in nature. The overrepresentation of Enterobacteriaceae species is a common feature of the CD microbiome, and much attention has been given to understanding the pathogenic role this feature plays in disease activity. Over 2 decades ago, a new Escherichia coli subtype called adherent-invasive E. coli (AIEC) was isolated and linked to ileal Crohn's disease. Since the isolation of the first AIEC strain, additional AIEC strains have been isolated from both inflammatory bowel disease (IBD) patients and non-IBD individuals using the original in vitro phenotypic characterization methods. Identification of a definitive molecular marker of the AIEC pathotype has been elusive; however, significant advancements have been made in understanding the genetic, metabolic, and virulence determinants of AIEC infection biology. Here, we review the current knowledge of AIEC pathogenesis to provide additional, objective measures that could be considered in defining AIEC and their pathogenic potential.
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Affiliation(s)
- Megan T. Zangara
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Lena Darwish
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Brian K. Coombes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, Hamilton, Ontario, Canada
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5
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Gevorgyan H, Abaghyan T, Mirumyan M, Yenkoyan K, Trchounian K. Propionic and valproic acids have an impact on bacteria viability, proton flux and ATPase activity. J Bioenerg Biomembr 2023; 55:397-408. [PMID: 37700074 DOI: 10.1007/s10863-023-09983-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 08/29/2023] [Indexed: 09/14/2023]
Abstract
Short-chain fatty acids like propionic (PPA) and valproic acids (VP) can alter gut microbiota, which is suggested to play a role in development of autism spectrum disorders (ASD). In this study we investigated the role of various concentrations of PPA and VP in gut enteric gram-negative Escherichia coli K12 and gram-positive Enterococcus hirae ATCC 9790 bacteria growth properties, ATPase activity and proton flux. The specific growth rate (µ) was 0.24 h-1 and 0.82 h-1 in E. coli and E. hirae, respectively. Different concentrations of PPA reduced the value of µ similarly in both strains. PPA affects membrane permeability only in E. hirae. PPA decreased DCCD-sensitive ATPase activity in the presence of K+ ions by 20% in E. coli and 40% in E. hirae suggesting the importance of the FOF1-K+ transport system in the regulation of PPA-disrupted homeostasis. Moreover, the H+ flux during PPA consumption could be the protective mechanism for enteric bacteria. VP has a selective effect on the µ depending on bacteria. The overwhelming effect of VP was detected on the K+-promoted ATPase activity in E. hirae. Taken together it can be suggested that PPA and VP have a disruptive effect on E. coli and E. hirae growth, viability, bioenergetic and biochemical properties, which are connected with the alteration of FOF1-ATPase activity and H+ flux rate or direction.
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Affiliation(s)
- Heghine Gevorgyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 A. Manoogian Str, Yerevan, 0025, Armenia
- Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, Yerevan, 0025, Armenia
- Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, Yerevan, 0025, Armenia
| | - Tamara Abaghyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 A. Manoogian Str, Yerevan, 0025, Armenia
- Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, Yerevan, 0025, Armenia
- Neuroscience Laboratory, Cobrain Center, Yerevan State Medical University named after M. Heratsi, Yerevan, 0025, Armenia
| | - Margarita Mirumyan
- Neuroscience Laboratory, Cobrain Center, Yerevan State Medical University named after M. Heratsi, Yerevan, 0025, Armenia
- Department of Biochemistry, Yerevan State Medical University named after M. Heratsi, Yerevan, 0025, Armenia
| | - Konstantin Yenkoyan
- Neuroscience Laboratory, Cobrain Center, Yerevan State Medical University named after M. Heratsi, Yerevan, 0025, Armenia.
- Department of Biochemistry, Yerevan State Medical University named after M. Heratsi, Yerevan, 0025, Armenia.
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 1 A. Manoogian Str, Yerevan, 0025, Armenia.
- Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, Yerevan, 0025, Armenia.
- Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, Yerevan, 0025, Armenia.
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6
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Abstract
The surge in inflammatory bowel diseases, like Crohn's disease (CD), is alarming. While the role of the gut microbiome in CD development is unresolved, the frequent isolation of adherent-invasive Escherichia coli (AIEC) strains from patient biopsies, together with their propensity to trigger gut inflammation, underpin the potential role of these bacteria as disease modifiers. In this review, we explore the spectrum of AIEC pathogenesis, including their metabolic versatility in the gut. We describe how AIEC strains hijack the host defense mechanisms to evade immune attrition and promote inflammation. Furthermore, we highlight the key traits that differentiate AIEC from commensal E. coli. Deciphering the main components of AIEC virulence is cardinal to the discovery of the next generation of antimicrobials that can selectively eradicate CD-associated bacteria.
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Affiliation(s)
- Sarah Mansour
- Department of Medical Microbiology & Immunology, Faculty of Medicine & Dentistry, University of Alberta, Canada
| | - Tahreem Asrar
- Department of Medical Microbiology & Immunology, Faculty of Medicine & Dentistry, University of Alberta, Canada
| | - Wael Elhenawy
- Department of Medical Microbiology & Immunology, Faculty of Medicine & Dentistry, University of Alberta, Canada,Division of Gastroenterology, Department of Medicine, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada,Li Ka Shing Institute of Virology, Canada,Women and Children’s Health Research Institute, Edmonton, Alberta, Canada,Antimicrobial Resistance, One Health Consortium - Edmonton, AB, Canada,CONTACT Wael Elhenawy Department of Medical Microbiology & Immunology, Faculty of Medicine & Dentistry, University of Alberta
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7
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Zhan Z, Tang H, Zhang Y, Huang X, Xu M. Potential of gut-derived short-chain fatty acids to control enteric pathogens. Front Microbiol 2022; 13:976406. [PMID: 36204607 PMCID: PMC9530198 DOI: 10.3389/fmicb.2022.976406] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/05/2022] [Indexed: 11/19/2022] Open
Abstract
Short-chain fatty acids (SCFAs) are a very important group of metabolites located in the gut that play a crucial role in the regulation of gut function and pathogen resistance. Since many enteric pathogens respond differently to various SCFAs, substantial efforts have been made to understand the regulatory effects of SCFA types on enteric pathogens. The application of protein post-translational modifications (PTMs) in bacterial research provides a new perspective for studying the regulation of enteric pathogens by different SCFAs. Existing evidence suggests that the SCFAs acetate, propionate, and butyrate influence bacterial processes by extensively promoting the acylation of key bacterial proteins. SCFAs can also prevent the invasion of pathogenic bacteria by regulating the barrier function and immune status of the host gut. In this review, we describe the mechanisms by which different SCFAs modulate the pathogenicity of enteric pathogens from multiple perspectives. We also explore some recent findings on how enteric pathogens counteract SCFA inhibition. Lastly, we discuss the prospects and limitations of applying SCFAs to control enteric pathogens.
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Affiliation(s)
- Ziyang Zhan
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Hao Tang
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xinxiang Huang
- Department of Biochemistry and Molecular Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
- *Correspondence: Xinxiang Huang,
| | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Institute of Digestive Diseases, Jiangsu University, Zhenjiang, Jiangsu, China
- Min Xu,
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8
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Galyamina MA, Zubov AI, Ladygina VG, Li AV, Matyushkina DS, Pobeguts OV, Fisunov GY. Comparative Proteomic Analysis of the Mycoplasma gallisepticum Nucleoid Fraction before and after Infection. Bull Exp Biol Med 2022; 172:336-340. [PMID: 35001316 DOI: 10.1007/s10517-022-05388-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Indexed: 11/26/2022]
Abstract
Mycoplasma gallisepticum belongs to the class Mollicutes and induces severe chronic respiratory disease in chickens. It lacks the cell wall and contains a very small genome and, accordingly, a reduced set of regulatory proteins. It is assumed that one of the regulatory mechanisms in mycoplasmas may be the dynamics of the spatial organization of the chromosome. M. gallisepticum has only two known nucleoid-associated (NAP) histone-like proteins (Hup_1 and Hup_2). To search for new potential NAP that may play a role in the infection process, we isolated nucleoid fractions from M. gallisepticum cells before and after infection of HD3 chicken erythroblast cell line and performed a comparative proteomic analysis of these fractions. We identified several potential NAP that included the components of the terminal organelle and adhesion, VlhA antigen, NADH oxidase, and PykF pyruvate kinase.
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Affiliation(s)
- M A Galyamina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical-Biological Agency of Russia, Moscow, Russia.
| | - A I Zubov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical-Biological Agency of Russia, Moscow, Russia
| | - V G Ladygina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical-Biological Agency of Russia, Moscow, Russia
| | - A V Li
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical-Biological Agency of Russia, Moscow, Russia
| | - D S Matyushkina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical-Biological Agency of Russia, Moscow, Russia
| | - O V Pobeguts
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical-Biological Agency of Russia, Moscow, Russia
| | - G Yu Fisunov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical-Biological Agency of Russia, Moscow, Russia
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9
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Mirzaei R, Dehkhodaie E, Bouzari B, Rahimi M, Gholestani A, Hosseini-Fard SR, Keyvani H, Teimoori A, Karampoor S. Dual role of microbiota-derived short-chain fatty acids on host and pathogen. Biomed Pharmacother 2021; 145:112352. [PMID: 34840032 DOI: 10.1016/j.biopha.2021.112352] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 12/12/2022] Open
Abstract
A growing body of documents shows microbiota produce metabolites such as short-chain fatty acids (SCFAs) as crucial executors of diet-based microbial influence the host and bacterial pathogens. The production of SCFAs depends on the metabolic activity of intestinal microflora and is also affected by dietary changes. SCFAs play important roles in maintaining colonic health as an energy source, as a regulator of gene expression and cell differentiation, and as an anti-inflammatory agent. Additionally, the regulated expression of virulence genes is critical for successful infection by an intestinal pathogen. Bacteria rely on sensing environmental signals to find preferable niches and reach the infectious state. This review will present data supporting the diverse functional roles of microbiota-derived butyrate, propionate, and acetate on host cellular activities such as immune modulation, energy metabolism, nervous system, inflammation, cellular differentiation, and anti-tumor effects, among others. On the other hand, we will discuss and summarize data about the role of these SCFAs on the virulence factor of bacterial pathogens. In this regard, receptors and signaling routes for SCFAs metabolites in host and pathogens will be introduced.
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Affiliation(s)
- Rasoul Mirzaei
- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran; Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Elahe Dehkhodaie
- Department of Biology, Science and Research Branch, Islamic Azad University Tehran, Iran
| | - Behnaz Bouzari
- Department of Pathology, Firouzgar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Mandana Rahimi
- Department of Pathology, School of Medicine, Hasheminejad Kidney Center, Iran University of Medical Sciences, Tehran, Iran
| | - Abolfazl Gholestani
- Department of Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Reza Hosseini-Fard
- Department of Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Keyvani
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Ali Teimoori
- Department of Virology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran; Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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10
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Isolation of Nucleoid Fraction from Mycoplasma gallisepticum Cells with Synchronized Cell Division. Bull Exp Biol Med 2021; 171:760-763. [PMID: 34705179 DOI: 10.1007/s10517-021-05311-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Indexed: 10/20/2022]
Abstract
It is assumed that unknown mechanisms can be involved in adaptation Mycoplasma gallisepticum to unfavorable factors, one of these can be local rearrangements of the structure and spatial organization of the chromosome. To study these mechanisms, we obtained a culture of M. gallisepticum with synchronized division and isolated the nucleoid fraction from this culture by the method of mild cell lysis and centrifugation in a sucrose gradient. Liquid chromatography-mass spectrometry analysis of the proteome showed that in comparison with the cell lysate, the nucleoid fraction was enriched with DNA-binding proteins. This analysis will help to find new nucleoid-associated proteins and to study their dynamics, distribution, and their role during infection and under stress conditions.
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11
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Influenza Virus Infection Impairs the Gut's Barrier Properties and Favors Secondary Enteric Bacterial Infection through Reduced Production of Short-Chain Fatty Acids. Infect Immun 2021; 89:e0073420. [PMID: 33820816 DOI: 10.1128/iai.00734-20] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Along with respiratory tract disease per se, viral respiratory infections can also cause extrapulmonary complications with a potentially critical impact on health. In the present study, we used an experimental model of influenza A virus (IAV) infection to investigate the nature and outcome of the associated gut disorders. In IAV-infected mice, the signs of intestinal injury and inflammation, altered gene expression, and compromised intestinal barrier functions peaked on day 7 postinfection. As a likely result of bacterial component translocation, gene expression of inflammatory markers was upregulated in the liver. These changes occurred concomitantly with an alteration of the composition of the gut microbiota and with a decreased production of the fermentative, gut microbiota-derived products short-chain fatty acids (SCFAs). Gut inflammation and barrier dysfunction during influenza were not attributed to reduced food consumption, which caused in part gut dysbiosis. Treatment of IAV-infected mice with SCFAs was associated with an enhancement of intestinal barrier properties, as assessed by a reduction in the translocation of dextran and a decrease in inflammatory gene expression in the liver. Lastly, SCFA supplementation during influenza tended to reduce the translocation of the enteric pathogen Salmonella enterica serovar Typhimurium and to enhance the survival of doubly infected animals. Collectively, influenza virus infection can remotely impair the gut's barrier properties and trigger secondary enteric infections. The latter phenomenon can be partially countered by SCFA supplementation.
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12
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Iablokov SN, Klimenko NS, Efimova DA, Shashkova T, Novichkov PS, Rodionov DA, Tyakht AV. Metabolic Phenotypes as Potential Biomarkers for Linking Gut Microbiome With Inflammatory Bowel Diseases. Front Mol Biosci 2021; 7:603740. [PMID: 33537340 PMCID: PMC7848230 DOI: 10.3389/fmolb.2020.603740] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022] Open
Abstract
The gut microbiome is of utmost importance to human health. While a healthy microbiome can be represented by a variety of structures, its functional capacity appears to be more important. Gene content of the community can be assessed by “shotgun” metagenomics, but this approach is still too expensive. High-throughput amplicon-based surveys are a method of choice for large-scale surveys of links between microbiome, diseases, and diet, but the algorithms for predicting functional composition need to be improved to achieve good precision. Here we show how feature engineering based on microbial phenotypes, an advanced method for functional prediction from 16S rRNA sequencing data, improves identification of alterations of the gut microbiome linked to the disease. We processed a large collection of published gut microbial datasets of inflammatory bowel disease (IBD) patients to derive their community phenotype indices (CPI)—high-precision semiquantitative profiles aggregating metabolic potential of the community members based on genome-wide metabolic reconstructions. The list of selected metabolic functions included metabolism of short-chain fatty acids, vitamins, and carbohydrates. The machine-learning approach based on microbial phenotypes allows us to distinguish the microbiome profiles of healthy controls from patients with Crohn's disease and from ones with ulcerative colitis. The classifiers were comparable in quality to conventional taxonomy-based classifiers but provided new findings giving insights into possible mechanisms of pathogenesis. Feature-wise partial dependence plot (PDP) analysis of contribution to the classification result revealed a diversity of patterns. These observations suggest a constructive basis for defining functional homeostasis of the healthy human gut microbiome. The developed features are promising interpretable candidate biomarkers for assessing microbiome contribution to disease risk for the purposes of personalized medicine and clinical trials.
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Affiliation(s)
- Stanislav N Iablokov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,P.G. Demidov Yaroslavl State University, Yaroslavl, Russia
| | - Natalia S Klimenko
- Atlas Biomed Group-Knomics LLC, London, United Kingdom.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - Tatiana Shashkova
- Atlas Biomed Group-Knomics LLC, London, United Kingdom.,Moscow Institute of Physics and Technology, Moscow, Russia
| | - Pavel S Novichkov
- PhenoBiome Inc., San Francisco, CA, United States.,Lawrence Berkeley National Lab, Berkeley, CA, United States
| | - Dmitry A Rodionov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Alexander V Tyakht
- Atlas Biomed Group-Knomics LLC, London, United Kingdom.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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