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Oktem-Okullu S, Karaman T, Akcelik-Deveci S, Timucin E, Sezerman OU, Mansur-Ozen N, Buyukcolak Y, Tiftikci A. Effect of the switch status of Helicobacter pylori outer inflammatory protein A on gastric diseases. AMB Express 2023; 13:109. [PMID: 37817013 PMCID: PMC10564699 DOI: 10.1186/s13568-023-01621-z] [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: 06/29/2023] [Accepted: 10/03/2023] [Indexed: 10/12/2023] Open
Abstract
Helicobacter pylori OipA (Outer Inflammatory Protein A) is an outer membrane protein that takes role in the adherence and colonization to the stomach. oipA gene expression is regulated by the slipped-strand mispairing mechanism through a hypermutable CT dinucleotide repeat motif in the 5΄ region. Alterations in the CT number repeats cause frame-shift mutations to result in phase variation of oipA expression. While a functional "On" status has been recognized as a risk factor for peptic ulcer diseases and gastric cancer in many studies, some controversial findings still exist. To this end, this study compiled the sequence data of oipA from 10 different studies between 2000-2019 and 50 oipA DNA sequences from our own research that examined the relationship between the phase On/Off status of oipA and gastric diseases based on CT repeat number. Overall, we have reached 536 oipA DNA sequences from patients. This large collection of oipA sequences first clarified the absolute conservation of the peptide-pentamer of FWLHA for phase ''On'' status, suggesting this pentamer as a superior marker for the determination of oipA status than counting the number of CT repeats. Combining the sequence and patient data, we have re-analyzed the association between the ''On'' status of oipA and gastric diseases. Our results showed a strong association between oipA ''On'' status and gastric cancer supporting previous findings. We also investigated the AlphaFold2 computed structure of OipA that adopts a beta-barrel fold closely resembling to the autotransporter family of H. pylori. Altogether, this study confirms a strong association between oipA ''On'' statuses and severe gastrointestinal diseases like cancer and provides useful insights into the FWLHA pentamer as an indicator of "On" status of oipA putative autotransporter function rather than CT repeats number.
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Affiliation(s)
- Sinem Oktem-Okullu
- Department of Medical Microbiology, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Atasehir, Istanbul, 34752, Turkey.
| | - Tayyip Karaman
- Department of Medical Biotechnology, Institute of Health and Science, Acibadem Mehmet Ali Aydinlar University, Atasehir, Istanbul, 34752, Turkey
| | - Sümeyye Akcelik-Deveci
- Department of Medical Biotechnology, Institute of Health and Science, Acibadem Mehmet Ali Aydinlar University, Atasehir, Istanbul, 34752, Turkey
| | - Emel Timucin
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Atasehir, Istanbul, 34752, Turkey
| | - Osman Ugur Sezerman
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Atasehir, Istanbul, 34752, Turkey
| | - Nesteren Mansur-Ozen
- Department of Medical Biotechnology, Institute of Health and Science, Acibadem Mehmet Ali Aydinlar University, Atasehir, Istanbul, 34752, Turkey
| | - Yaren Buyukcolak
- Department of Medical Biotechnology, Institute of Health and Science, Acibadem Mehmet Ali Aydinlar University, Atasehir, Istanbul, 34752, Turkey
| | - Arzu Tiftikci
- Department of Internal Medicine, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Atasehir, Istanbul, 34752, Turkey
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Tancos MA, McMahon MB, Garrett WM, Luster DG, Rogers EE. Comparative Secretome Analyses of Toxigenic and Atoxigenic Rathayibacter Species. PHYTOPATHOLOGY 2021; 111:1530-1540. [PMID: 33499664 DOI: 10.1094/phyto-11-20-0495-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phytopathogenic Rathayibacter species are unique bacterial plant pathogens because they are obligately vectored by plant parasitic anguinid nematodes to the developing seedheads of forage grasses and cereals. This understudied group of plant-associated Actinomycetes includes the neurotoxigenic plant pathogen R. toxicus, which causes annual ryegrass toxicity in grazing livestock. R. toxicus is currently endemic to Australia and is listed as a plant pathogen select agent by the U.S. Department of Agriculture-Animal and Plant Health Inspection Service. The complex Rathayibacter disease cycle requires intimate interactions with the nematode vector and plant hosts, which warrants an increased understanding of the secretory and surface-associated proteins that mediate these diverse eukaryotic interactions. Here we present the first comparative secretome analysis for this complex, nematode-vectored Rathayibacter genus that compares the three agronomically damaging toxigenic and atoxigenic Rathayibacter species, R. toxicus, R. iranicus, and R. tritici. The exoproteomic comparison identified 1,423 unique proteins between the three species via liquid chromatography-tandem mass spectrometry, leading to the identification of putative pathogenicity-related proteins and proteins that may mediate nematode attachment. Of the uniquely identified proteins, 94 homologous proteins were conserved between the three Rathayibacter exoproteomes and comprised between 43.4 and 58.6% of total protein abundance. Comparative analyses revealed both conserved and uniquely expressed extracellular proteins, which, interestingly, had more similarities to extracellular proteins commonly associated with bacterial animal pathogens than classic plant pathogens. This comparative exoproteome analysis will facilitate the characterization of proteins essential for vector attachment and host colonization and assist in the development of serological diagnostic assays.
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Affiliation(s)
- Matthew A Tancos
- Foreign Disease-Weed Science Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Frederick, MD
| | - Michael B McMahon
- Foreign Disease-Weed Science Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Frederick, MD
| | - Wesley M Garrett
- Animal Biosciences and Biotechnology Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD
| | - Douglas G Luster
- Foreign Disease-Weed Science Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Frederick, MD
| | - Elizabeth E Rogers
- Foreign Disease-Weed Science Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Frederick, MD
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Yu J, Lu L. BamA is a pivotal protein in cell envelope synthesis and cell division in Deinococcus radiodurans. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:1365-1374. [PMID: 31103441 DOI: 10.1016/j.bbamem.2019.05.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 05/11/2019] [Accepted: 05/13/2019] [Indexed: 12/29/2022]
Abstract
The beta-barrel assembly machinery (BAM) is an indispensable complex for protein transportation located at the outer membrane of bacteria. BAM is composed of five subunits (BamA-E) in the model bacterium Escherichia coli. DR_0379 is a BamA homolog in Deinococcus radiodurans, but the other subunits have not been detected in this species. In the present study, deletion of bamA resulted in decreased growth rate and altered morphology of D. radiodurans. ΔbamA cells underwent abnormal cell division, leading to aggregated bacteria of diverse size and shape, and the cell envelope was detached from the cell surface, resulting in reduced resistance to high ionic strength. Oxidative stress resistance was significantly enhanced in the mutant, which may be attributed to increased manganese ion concentration and Mn/Fe ratio. Numerous proteins were released into the medium from ΔbamA cells, including surface layer (S-layer) proteins and various transporters located in the periplasm and outer membrane. These results indicate that BamA affects the synthesis and assembly of the outer membrane and S-layer, and thereby influences material transport and cell division. The findings highlight the special functions of BamA in D. radiodurans, and promote our understanding of the multi-layer structure of the D. radiodurans cell envelope.
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Affiliation(s)
- Jiangliu Yu
- College of Life Science, Anhui Agricultural University, 130 Changjiangxilu, Hefei 230036, PR China.
| | - Luchun Lu
- College of Life Science, Anhui Agricultural University, 130 Changjiangxilu, Hefei 230036, PR China
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Coppens F, Castaldo G, Debraekeleer A, Subedi S, Moonens K, Lo A, Remaut H. Hop‐familyHelicobacterouter membrane adhesins form a novel class of Type 5‐like secretion proteins with an interrupted β‐barrel domain. Mol Microbiol 2018; 110:33-46. [DOI: 10.1111/mmi.14075] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2018] [Indexed: 01/10/2023]
Affiliation(s)
- Fanny Coppens
- Structural and Molecular Microbiology VIB‐VUB Center for Structural Biology, VIB Brussels Belgium
- Structural Biology Brussels Vrije Universiteit Brussel Brussels Belgium
| | - Gaetano Castaldo
- Structural and Molecular Microbiology VIB‐VUB Center for Structural Biology, VIB Brussels Belgium
- Structural Biology Brussels Vrije Universiteit Brussel Brussels Belgium
| | - Ayla Debraekeleer
- Structural and Molecular Microbiology VIB‐VUB Center for Structural Biology, VIB Brussels Belgium
- Structural Biology Brussels Vrije Universiteit Brussel Brussels Belgium
| | - Suresh Subedi
- Structural and Molecular Microbiology VIB‐VUB Center for Structural Biology, VIB Brussels Belgium
- Structural Biology Brussels Vrije Universiteit Brussel Brussels Belgium
| | - Kristof Moonens
- Structural and Molecular Microbiology VIB‐VUB Center for Structural Biology, VIB Brussels Belgium
- Structural Biology Brussels Vrije Universiteit Brussel Brussels Belgium
| | - Alvin Lo
- Structural and Molecular Microbiology VIB‐VUB Center for Structural Biology, VIB Brussels Belgium
- Structural Biology Brussels Vrije Universiteit Brussel Brussels Belgium
| | - Han Remaut
- Structural and Molecular Microbiology VIB‐VUB Center for Structural Biology, VIB Brussels Belgium
- Structural Biology Brussels Vrije Universiteit Brussel Brussels Belgium
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Ranava D, Caumont-Sarcos A, Albenne C, Ieva R. Bacterial machineries for the assembly of membrane-embedded β-barrel proteins. FEMS Microbiol Lett 2018; 365:4961134. [DOI: 10.1093/femsle/fny087] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/03/2018] [Indexed: 12/11/2022] Open
Affiliation(s)
- David Ranava
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Anne Caumont-Sarcos
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Cécile Albenne
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Raffaele Ieva
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
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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.
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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
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