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Article ; Online: Subdomains of the

Roberts, Jacquelyn R / Tran, Sirena C / Frick-Cheng, Arwen E / Bryant, Kaeli N / Okoye, Chiamaka D / McDonald, W Hayes / Cover, Timothy L / Ohi, Melanie D

Life science alliance

2024 Volume 7, Issue 6

Abstract: ... ...

Abstract	The
MeSH term(s)	Helicobacter pylori ; Type IV Secretion Systems/chemistry ; Periplasm
Chemical Substances	Type IV Secretion Systems
Language	English
Publishing date	2024-04-17
Publishing country	United States
Document type	Journal Article
ISSN	2575-1077
ISSN (online)	2575-1077
DOI	10.26508/lsa.202302560
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Article ; Online: Identification of an Essential LolD-Like Protein in Helicobacter pylori.

McClain, Mark S / Bryant, Kaeli N / McDonald, W Hayes / Algood, Holly M Scott / Cover, Timothy L

Journal of bacteriology

2023 Volume 205, Issue 4, Page(s) e0005223

Abstract: The localization of lipoprotein (Lol) system is used by Gram-negative bacteria to export lipoproteins to the outer membrane. Lol proteins and models of how Lol transfers lipoproteins from the inner to the outer membrane have been extensively ... ...

Abstract	The localization of lipoprotein (Lol) system is used by Gram-negative bacteria to export lipoproteins to the outer membrane. Lol proteins and models of how Lol transfers lipoproteins from the inner to the outer membrane have been extensively characterized in the model organism Escherichia coli, but in numerous bacterial species, lipoprotein synthesis and export pathways deviate from the E. coli paradigm. For example, in the human gastric bacterium Helicobacter pylori, a homolog of the E. coli outer membrane component LolB is not found, E. coli LolC and LolE correspond to a single inner membrane component (LolF), and a homolog of the E. coli cytoplasmic ATPase LolD has not been identified. In the present study, we sought to identify a LolD-like protein in H. pylori. We used affinity-purification mass spectrometry to identify interaction partners of the H. pylori ATP-binding cassette (ABC) family permease LolF and identified the ABC family ATP-binding protein HP0179 as its interaction partner. We engineered H. pylori to conditionally express HP0179 and showed that HP0179 and its conserved ATP binding and ATP hydrolysis motifs are essential for H. pylori growth. We then performed affinity purification-mass spectrometry using HP0179 as the bait and identified LolF as its interaction partner. These results indicate that H. pylori HP0179 is a LolD-like protein and provide a more complete understanding of lipoprotein localization processes in H. pylori, a bacterium in which the Lol system deviates from the E. coli paradigm.
MeSH term(s)	Humans ; Escherichia coli/metabolism ; Helicobacter pylori/genetics ; Helicobacter pylori/metabolism ; Escherichia coli Proteins/metabolism ; Protein Transport ; Lipoproteins/genetics ; Lipoproteins/metabolism ; Gram-Negative Bacteria/metabolism ; Adenosine Triphosphate/metabolism ; Bacterial Outer Membrane Proteins/metabolism
Chemical Substances	Escherichia coli Proteins ; Lipoproteins ; Adenosine Triphosphate (8L70Q75FXE) ; Bacterial Outer Membrane Proteins
Language	English
Publishing date	2023-03-27
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/jb.00052-23
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Article ; Online: Remodeling of the gastric environment in

Shuman, Jennifer H B / Lin, Aung Soe / Westland, Mandy D / Bryant, Kaeli N / Piazuelo, M Blanca / Reyzer, Michelle L / Judd, Audra M / McDonald, W Hayes / McClain, Mark S / Schey, Kevin L / Algood, Holly M S / Cover, Timothy L

mSystems

2023 Volume 9, Issue 1, Page(s) e0109823

Abstract: Helicobacter ... ...

Abstract	Helicobacter pylori
MeSH term(s)	Animals ; Humans ; Gastritis, Atrophic/chemically induced ; Helicobacter pylori ; Stomach Neoplasms/pathology ; Gerbillinae ; Gastric Mucosa/pathology ; Gastritis/pathology ; Atrophy/pathology ; Helicobacter Infections/complications ; Precancerous Conditions/pathology ; Carcinogenesis/pathology
Language	English
Publishing date	2023-12-07
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN (online)	2379-5077
DOI	10.1128/msystems.01098-23
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Article ; Online: An infection-induced oxidation site regulates legumain processing and tumor growth.

Kovalyova, Yekaterina / Bak, Daniel W / Gordon, Elizabeth M / Fung, Connie / Shuman, Jennifer H B / Cover, Timothy L / Amieva, Manuel R / Weerapana, Eranthie / Hatzios, Stavroula K

Nature chemical biology

2022 Volume 18, Issue 7, Page(s) 698–705

Abstract: Oxidative stress is a defining feature of most cancers, including those that stem from carcinogenic infections. Reactive oxygen species can drive tumor formation, yet the molecular oxidation events that contribute to tumorigenesis are largely unknown. ... ...

Abstract	Oxidative stress is a defining feature of most cancers, including those that stem from carcinogenic infections. Reactive oxygen species can drive tumor formation, yet the molecular oxidation events that contribute to tumorigenesis are largely unknown. Here we show that inactivation of a single, redox-sensitive cysteine in the host protease legumain, which is oxidized during infection with the gastric cancer-causing bacterium Helicobacter pylori, accelerates tumor growth. By using chemical proteomics to map cysteine reactivity in human gastric cells, we determined that H. pylori infection induces oxidation of legumain at Cys219. Legumain oxidation dysregulates intracellular legumain processing and decreases the activity of the enzyme in H. pylori-infected cells. We further show that the site-specific loss of Cys219 reactivity increases tumor growth and mortality in a xenograft model. Our findings establish a link between an infection-induced oxidation site and tumorigenesis while underscoring the importance of cysteine reactivity in tumor growth.
MeSH term(s)	Cell Transformation, Neoplastic/metabolism ; Cysteine/metabolism ; Cysteine Endopeptidases/metabolism ; Helicobacter Infections ; Helicobacter pylori ; Humans ; Oxidation-Reduction ; Stomach Neoplasms/metabolism ; Stomach Neoplasms/microbiology ; Stomach Neoplasms/pathology
Chemical Substances	Cysteine Endopeptidases (EC 3.4.22.-) ; asparaginylendopeptidase (EC 3.4.22.34) ; Cysteine (K848JZ4886)
Language	English
Publishing date	2022-03-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2202962-X
ISSN	1552-4469 ; 1552-4450
ISSN (online)	1552-4469
ISSN	1552-4450
DOI	10.1038/s41589-022-00992-x
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Article ; Online: Computational methods for corpus callosum segmentation on MRI: A systematic literature review.

Cover, G S / Herrera, W G / Bento, M P / Appenzeller, S / Rittner, L

Computer methods and programs in biomedicine

2018 Volume 154, Page(s) 25–35

Abstract: Background and objective: The corpus callosum (CC) is the largest white matter structure in the brain and has a significant role in central nervous system diseases. Its volume correlates with the severity and/or extent of neurodegenerative disease. Even ...

Abstract	Background and objective: The corpus callosum (CC) is the largest white matter structure in the brain and has a significant role in central nervous system diseases. Its volume correlates with the severity and/or extent of neurodegenerative disease. Even though the CC's role has been extensively studied over the last decades, and different algorithms and methods have been published regarding CC segmentation and parcellation, no reviews or surveys covering such developments have been reported so far. To bridge this gap, this paper presents a systematic literature review of computational methods focusing on CC segmentation and parcellation acquired on magnetic resonance imaging. Methods: IEEExplore, PubMed, EBSCO Host, and Scopus database were searched with the following search terms: ((Segmentation OR Parcellation) AND (Corpus Callosum) AND (DTI OR MRI OR Diffusion Tensor Imag* OR Diffusion Tractography OR Magnetic Resonance Imag)), resulting in 802 publications. Two reviewers independently evaluated all articles and 36 studies were selected through the systematic literature review process. Results:* This work reviewed four main segmentation methods groups: model-based, region-based, thresholding, and machine learning; 32 different validity metrics were reported. Even though model-based techniques are the most recurrently used for the segmentation task (13 articles), machine learning approaches achieved better outcomes of 95% when analyzing mean values for segmentation and classification metrics results. Moreover, CC segmentation is better established in T Conclusions: The analyzed computational methods used to perform CC segmentation on magnetic resonance imaging have not yet overcome all presented challenges owing to metrics variability and lack of traceable materials.
MeSH term(s)	Central Nervous System Diseases/diagnostic imaging ; Computer Simulation ; Corpus Callosum/diagnostic imaging ; Diffusion Tensor Imaging/methods ; Humans ; Image Processing, Computer-Assisted/methods ; Machine Learning ; Magnetic Resonance Imaging/methods ; Neurodegenerative Diseases/diagnostic imaging ; Reproducibility of Results
Keywords	covid19
Language	English
Publishing date	2018-02
Publishing country	Ireland
Document type	Journal Article ; Review
ZDB-ID	632564-6
ISSN	1872-7565 ; 0169-2607
ISSN (online)	1872-7565
ISSN	0169-2607
DOI	10.1016/j.cmpb.2017.10.025
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Article ; Online: Delineation of the pH-Responsive Regulon Controlled by the Helicobacter pylori ArsRS Two-Component System.

Loh, John T / Shum, Miranda V / Jossart, Scott D R / Campbell, Anne M / Sawhney, Neha / McDonald, W Hayes / Scholz, Matthew B / McClain, Mark S / Forsyth, Mark H / Cover, Timothy L

Infection and immunity

2021 Volume 89, Issue 4

Abstract: Helicobacter ... ...

Abstract	Helicobacter pylori
MeSH term(s)	Computational Biology/methods ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Helicobacter pylori/physiology ; Humans ; Hydrogen-Ion Concentration ; Mutation ; Proteome ; Proteomics/methods ; Response Elements ; Trans-Activators/metabolism ; Transcription, Genetic
Chemical Substances	Proteome ; Trans-Activators
Language	English
Publishing date	2021-03-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	218698-6
ISSN	1098-5522 ; 0019-9567
ISSN (online)	1098-5522
ISSN	0019-9567
DOI	10.1128/IAI.00597-20
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Article: Summary of the Pharmacology of Sulfanilamide and Related Compounds.

Cutting, W C / Cover, W L

California and western medicine

2008 Volume 52, Issue 3, Page(s) 110–113

Language	English
Publishing date	2008-08-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	2255398-8
ISSN	2380-9922 ; 0093-4038
ISSN (online)	2380-9922
ISSN	0093-4038
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Article ; Online: Effect of environmental salt concentration on the Helicobacter pylori exoproteome.

Caston, Rhonda R / Loh, John T / Voss, Bradley J / McDonald, W Hayes / Scholz, Matthew B / McClain, Mark S / Cover, Timothy L

Journal of proteomics

2019 Volume 202, Page(s) 103374

Abstract: Helicobacter pylori infection and a high salt diet are each risk factors for gastric cancer. In this study, we tested the hypothesis that environmental salt concentration influences the composition of the H. pylori exoproteome. H. pylori was cultured in ... ...

Abstract	Helicobacter pylori infection and a high salt diet are each risk factors for gastric cancer. In this study, we tested the hypothesis that environmental salt concentration influences the composition of the H. pylori exoproteome. H. pylori was cultured in media containing varying concentrations of sodium chloride, and aliquots were fractionated and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). We identified proteins that were selectively released into the extracellular space, and we identified selectively released proteins that were differentially abundant in culture supernatants, depending on the environmental salt concentration. We also used RNA-seq analysis to identify genes that were differentially expressed in response to environmental salt concentration. The salt-responsive proteins identified by proteomic analysis and salt-responsive genes identified by RNA-seq analysis were mostly non-concordant, but the secreted toxin VacA was salt-responsive in both analyses. Western blot analysis confirmed that VacA levels in the culture supernatant were increased in response to high salt conditions, and quantitative RT-qPCR experiments confirmed that vacA transcription was upregulated in response to high salt conditions. These results indicate that environmental salt concentration influences the composition of the H. pylori exoproteome, which could contribute to the increased risk of gastric cancer associated with a high salt diet. SIGNIFICANCE: Helicobacter pylori-induced alterations in the gastric mucosa have been attributed, at least in part, to the actions of secreted H. pylori proteins. In this study, we show that H. pylori growth in high salt concentrations leads to increased levels of a secreted VacA toxin. Salt-induced alterations in the composition of the H. pylori exoproteome is relevant to the increased risk of gastric cancer associated with consumption of a high salt diet.
MeSH term(s)	Bacterial Proteins/biosynthesis ; Dose-Response Relationship, Drug ; Gene Expression Regulation, Bacterial/drug effects ; Helicobacter pylori/metabolism ; Proteome/biosynthesis ; Proteomics ; Sodium Chloride, Dietary/pharmacology
Chemical Substances	Bacterial Proteins ; Proteome ; Sodium Chloride, Dietary
Language	English
Publishing date	2019-05-04
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2400835-7
ISSN	1876-7737 ; 1874-3919
ISSN (online)	1876-7737
ISSN	1874-3919
DOI	10.1016/j.jprot.2019.05.002
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Article ; Online: Bacterial Energetic Requirements for Helicobacter pylori Cag Type IV Secretion System-Dependent Alterations in Gastric Epithelial Cells.

Lin, Aung Soe / Dooyema, Samuel D R / Frick-Cheng, Arwen E / Harvey, M Lorena / Suarez, Giovanni / Loh, John T / McDonald, W Hayes / McClain, Mark S / Peek, Richard M / Cover, Timothy L

Infection and immunity

2020 Volume 88, Issue 2

Abstract: Helicobacter ... ...

Abstract	Helicobacter pylori
MeSH term(s)	Antigens, Bacterial/genetics ; Antigens, Bacterial/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Biological Transport ; DNA, Bacterial/metabolism ; Epithelial Cells/microbiology ; Helicobacter pylori/genetics ; Helicobacter pylori/metabolism ; Humans ; Interleukin-8/metabolism ; Lipopolysaccharides/metabolism ; NF-kappa B/metabolism ; Peptidoglycan/metabolism ; Toll-Like Receptor 9/metabolism ; Type IV Secretion Systems/genetics ; Type IV Secretion Systems/metabolism ; Virulence Factors/genetics ; Virulence Factors/metabolism
Chemical Substances	Antigens, Bacterial ; Bacterial Proteins ; DNA, Bacterial ; Interleukin-8 ; Lipopolysaccharides ; NF-kappa B ; Peptidoglycan ; Toll-Like Receptor 9 ; Type IV Secretion Systems ; Virulence Factors ; cagA protein, Helicobacter pylori
Language	English
Publishing date	2020-01-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	218698-6
ISSN	1098-5522 ; 0019-9567
ISSN (online)	1098-5522
ISSN	0019-9567
DOI	10.1128/IAI.00790-19
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Article: Supporting data for analysis of the Helicobacter pylori exoproteome.

Snider, Christina A / Voss, Bradley J / McDonald, W Hayes / Cover, Timothy L

Data in brief

2015 Volume 5, Page(s) 560–563

Abstract: The goal of this research was to analyze the composition of the Helicobacter pylori exoproteome at multiple phases of bacterial growth (Snider et al., 2015) [1]. H. pylori was grown in a serum-free medium and at serial time points, aliquots were ... ...

Abstract	The goal of this research was to analyze the composition of the Helicobacter pylori exoproteome at multiple phases of bacterial growth (Snider et al., 2015) [1]. H. pylori was grown in a serum-free medium and at serial time points, aliquots were centrifuged and fractionated to yield culture supernatant, a soluble cellular fraction, and a membrane fraction. Samples were analyzed by single dimensional LC-MS/MS analyses and multidimensional protein identification technology (MudPIT). Here we present data showing the numbers of assigned spectra and proportional abundance of individual proteins in each of the samples analyzed, along with a calculation of the level of enrichment of individual proteins in the supernatant compared to the soluble cellular fraction.
Language	English
Publishing date	2015-10-17
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2015.10.008
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