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Overstreet AMC, Anderson B, Burge M, Zhu X, Tao Y, Cham CM, Michaud B, Horam S, Sangwan N, Dwidar M, Liu X, Santos A, Finney C, Dai Z, Leone VA, Messer JS. HMGB1 acts as an agent of host defense at the gut mucosal barrier. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542477. [PMID: 37398239 PMCID: PMC10312563 DOI: 10.1101/2023.05.30.542477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Mucosal barriers provide the first line of defense between internal body surfaces and microbial threats from the outside world. 1 In the colon, the barrier consists of two layers of mucus and a single layer of tightly interconnected epithelial cells supported by connective tissue and immune cells. 2 Microbes colonize the loose, outer layer of colonic mucus, but are essentially excluded from the tight, epithelial-associated layer by host defenses. 3 The amount and composition of the mucus is calibrated based on microbial signals and loss of even a single component of this mixture can destabilize microbial biogeography and increase the risk of disease. 4-7 However, the specific components of mucus, their molecular microbial targets, and how they work to contain the gut microbiota are still largely unknown. Here we show that high mobility group box 1 (HMGB1), the prototypical damage-associated molecular pattern molecule (DAMP), acts as an agent of host mucosal defense in the colon. HMGB1 in colonic mucus targets an evolutionarily conserved amino acid sequence found in bacterial adhesins, including the well-characterized Enterobacteriaceae adhesin FimH. HMGB1 aggregates bacteria and blocks adhesin-carbohydrate interactions, inhibiting invasion through colonic mucus and adhesion to host cells. Exposure to HMGB1 also suppresses bacterial expression of FimH. In ulcerative colitis, HMGB1 mucosal defense is compromised, leading to tissue-adherent bacteria expressing FimH. Our results demonstrate a new, physiologic role for extracellular HMGB1 that refines its functions as a DAMP to include direct, virulence limiting effects on bacteria. The amino acid sequence targeted by HMGB1 appears to be broadly utilized by bacterial adhesins, critical for virulence, and differentially expressed by bacteria in commensal versus pathogenic states. These characteristics suggest that this amino acid sequence is a novel microbial virulence determinant and could be used to develop new approaches to diagnosis and treatment of bacterial disease that precisely identify and target virulent microbes.
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Phage Display Libraries: From Binders to Targeted Drug Delivery and Human Therapeutics. Mol Biotechnol 2019; 61:286-303. [DOI: 10.1007/s12033-019-00156-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Pedrosa AG, Francisco T, Bicho D, Dias AF, Barros-Barbosa A, Hagmann V, Dodt G, Rodrigues TA, Azevedo JE. Peroxisomal monoubiquitinated PEX5 interacts with the AAA ATPases PEX1 and PEX6 and is unfolded during its dislocation into the cytosol. J Biol Chem 2018; 293:11553-11563. [PMID: 29884772 DOI: 10.1074/jbc.ra118.003669] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/28/2018] [Indexed: 11/06/2022] Open
Abstract
PEX1 and PEX6 are two members of the ATPases associated with diverse cellular activities (AAA) family and the core components of the receptor export module of the peroxisomal matrix protein import machinery. Their role is to extract monoubiquitinated PEX5, the peroxisomal protein-shuttling receptor, from the peroxisomal membrane docking/translocation module (DTM), so that a new cycle of protein transportation can start. Recent data have shown that PEX1 and PEX6 form a heterohexameric complex that unfolds substrates by processive threading. However, whether the natural substrate of the PEX1-PEX6 complex is monoubiquitinated PEX5 (Ub-PEX5) itself or some Ub-PEX5-interacting component(s) of the DTM remains unknown. In this work, we used an established cell-free in vitro system coupled with photoaffinity cross-linking and protein PEGylation assays to address this problem. We provide evidence suggesting that DTM-embedded Ub-PEX5 interacts directly with both PEX1 and PEX6 through its ubiquitin moiety and that the PEX5 polypeptide chain is globally unfolded during the ATP-dependent extraction event. These findings strongly suggest that DTM-embedded Ub-PEX5 is a bona fide substrate of the PEX1-PEX6 complex.
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Affiliation(s)
- Ana G Pedrosa
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - Tânia Francisco
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - Diana Bicho
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - Ana F Dias
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - Aurora Barros-Barbosa
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - Vera Hagmann
- Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe Seyler Strasse 4, 72076 Tübingen, Germany
| | - Gabriele Dodt
- Interfakultäres Institut für Biochemie, Universität Tübingen, Hoppe Seyler Strasse 4, 72076 Tübingen, Germany
| | - Tony A Rodrigues
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - Jorge E Azevedo
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal.
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Kao YT, Gonzalez KL, Bartel B. Peroxisome Function, Biogenesis, and Dynamics in Plants. PLANT PHYSIOLOGY 2018; 176:162-177. [PMID: 29021223 PMCID: PMC5761812 DOI: 10.1104/pp.17.01050] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/09/2017] [Indexed: 05/19/2023]
Abstract
Recent advances highlight understanding of the diversity of peroxisome contributions to plant biology and the mechanisms through which these essential organelles are generated.
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Affiliation(s)
- Yun-Ting Kao
- Department of Biosciences, Rice University, Houston, Texas 77005
| | - Kim L Gonzalez
- Department of Biosciences, Rice University, Houston, Texas 77005
| | - Bonnie Bartel
- Department of Biosciences, Rice University, Houston, Texas 77005
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Falkenberg KD, Braverman NE, Moser AB, Steinberg SJ, Klouwer FCC, Schlüter A, Ruiz M, Pujol A, Engvall M, Naess K, van Spronsen F, Körver-Keularts I, Rubio-Gozalbo ME, Ferdinandusse S, Wanders RJA, Waterham HR. Allelic Expression Imbalance Promoting a Mutant PEX6 Allele Causes Zellweger Spectrum Disorder. Am J Hum Genet 2017; 101:965-976. [PMID: 29220678 DOI: 10.1016/j.ajhg.2017.11.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/14/2017] [Indexed: 01/14/2023] Open
Abstract
Zellweger spectrum disorders (ZSDs) are autosomal-recessive disorders that are caused by defects in peroxisome biogenesis due to bi-allelic mutations in any of 13 different PEX genes. Here, we identified seven unrelated individuals affected with an apparent dominant ZSD in whom a heterozygous mutant PEX6 allele (c.2578C>T [p.Arg860Trp]) was overrepresented due to allelic expression imbalance (AEI). We demonstrated that AEI of PEX6 is a common phenomenon and is correlated with heterozygosity for a frequent variant in the 3' untranslated region (UTR) of the mutant allele, which disrupts the most distal of two polyadenylation sites. Asymptomatic parents, who were heterozygous for PEX c.2578C>T, did not show AEI and were homozygous for the 3' UTR variant. Overexpression models confirmed that the overrepresentation of the pathogenic PEX6 c.2578T variant compared to wild-type PEX6 c.2578C results in a peroxisome biogenesis defect and thus constitutes the cause of disease in the affected individuals. AEI promoting the overrepresentation of a mutant allele might also play a role in other autosomal-recessive disorders, in which only one heterozygous pathogenic variant is identified.
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Affiliation(s)
- Kim D Falkenberg
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Nancy E Braverman
- Department of Pediatrics and Human Genetics, Research Institute of the McGill University Health Center and McGill University, Montreal, QC H4A 3J1, Canada
| | - Ann B Moser
- Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Steven J Steinberg
- Institute of Genetic Medicine and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Femke C C Klouwer
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands; Department of Pediatric Neurology, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, Barcelona 08908, Spain; CIBERER U759, Center for Biomedical Research on Rare Diseases, Valencia 46010, Spain
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, Barcelona 08908, Spain; CIBERER U759, Center for Biomedical Research on Rare Diseases, Valencia 46010, Spain
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, Barcelona 08908, Spain; CIBERER U759, Center for Biomedical Research on Rare Diseases, Valencia 46010, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Barcelona 08010, Spain
| | - Martin Engvall
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm 171 77, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 171 76, Sweden
| | - Karin Naess
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm 171 77, Sweden; Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Stockholm 171 77, Sweden
| | - FrancJan van Spronsen
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Groningen 9700 RB, the Netherlands
| | - Irene Körver-Keularts
- Department of Pediatrics, Maastricht University Medical Center, Maastricht 6211 LK, the Netherlands
| | - M Estela Rubio-Gozalbo
- Department of Pediatrics, Maastricht University Medical Center, Maastricht 6211 LK, the Netherlands; Laboratory Genetic Metabolic Diseases, Maastricht University Medical Center, Maastricht 6211 LK, the Netherlands
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands.
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Reumann S, Bartel B. Plant peroxisomes: recent discoveries in functional complexity, organelle homeostasis, and morphological dynamics. CURRENT OPINION IN PLANT BIOLOGY 2016; 34:17-26. [PMID: 27500947 PMCID: PMC5161562 DOI: 10.1016/j.pbi.2016.07.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 07/15/2016] [Accepted: 07/20/2016] [Indexed: 05/20/2023]
Abstract
Peroxisomes are essential for life in plants. These organelles house a variety of metabolic processes that generate and inactivate reactive oxygen species. Our knowledge of pathways and mechanisms that depend on peroxisomes and their constituent enzymes continues to grow, and in this review we highlight recent advances in understanding the identity and biological functions of peroxisomal enzymes and metabolic processes. We also review how peroxisomal matrix and membrane proteins enter the organelle from their sites of synthesis. Peroxisome homeostasis is regulated by specific degradation mechanisms, and we discuss the contributions of specialized autophagy and a peroxisomal protease to the degradation of entire peroxisomes and peroxisomal enzymes that are damaged or superfluous. Finally, we review how peroxisomes can flexibly change their morphology to facilitate inter-organellar contacts.
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Affiliation(s)
- Sigrun Reumann
- Department of Plant Biochemistry and Infection Biology, Biocentre Klein Flottbek, University of Hamburg, D-22609 Hamburg, Germany; Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, N-4036 Stavanger, Norway
| | - Bonnie Bartel
- Department of BioSciences, Rice University, Houston, TX 77005, USA.
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A cell-free organelle-based in vitro system for studying the peroxisomal protein import machinery. Nat Protoc 2016; 11:2454-2469. [PMID: 27831570 DOI: 10.1038/nprot.2016.147] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Here we describe a protocol to dissect the peroxisomal matrix protein import pathway using a cell-free in vitro system. The system relies on a postnuclear supernatant (PNS), which is prepared from rat/mouse liver, to act as a source of peroxisomes and cytosolic components. A typical in vitro assay comprises the following steps: (i) incubation of the PNS with an in vitro-synthesized 35S-labeled reporter protein; (ii) treatment of the organelle suspension with a protease that degrades reporter proteins that have not associated with peroxisomes; and (iii) SDS-PAGE/autoradiography analysis. To study transport of proteins into peroxisomes, it is possible to use organelle-resident proteins that contain a peroxisomal targeting signal (PTS) as reporters in the assay. In addition, a receptor (PEX5L/S or PEX5L.PEX7) can be used to report the dynamics of shuttling proteins that mediate the import process. Thus, different but complementary perspectives on the mechanism of this pathway can be obtained. We also describe strategies to fortify the system with recombinant proteins to increase import yields and block specific parts of the machinery at a number of steps. The system recapitulates all the steps of the pathway, including mono-ubiquitination of PEX5L/S at the peroxisome membrane and its ATP-dependent export back into the cytosol by PEX1/PEX6. An in vitro import(/export) experiment can be completed in 24 h.
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Abstract
The import of proteins into peroxisomes possesses many unusual features such as the ability to import folded proteins, and a surprising diversity of targeting signals with differing affinities that can be recognized by the same receptor. As understanding of the structure and function of many components of the protein import machinery has grown, an increasingly complex network of factors affecting each step of the import pathway has emerged. Structural studies have revealed the presence of additional interactions between cargo proteins and the PEX5 receptor that affect import potential, with a subtle network of cargo-induced conformational changes in PEX5 being involved in the import process. Biochemical studies have also indicated an interdependence of receptor-cargo import with release of unloaded receptor from the peroxisome. Here, we provide an update on recent literature concerning mechanisms of protein import into peroxisomes.
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Affiliation(s)
- Alison Baker
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology and Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Thomas Lanyon-Hogg
- Institute of Chemical Biology, Department of Chemistry, Imperial College London, London SW7 2AZ, U.K
| | - Stuart L Warriner
- School of Chemistry, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
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