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Piibor J, Waldmann A, Prasadani M, Kavak A, Andronowska A, Klein C, Kodithuwakku S, Fazeli A. Investigation of Uterine Fluid Extracellular Vesicles' Proteomic Profiles Provides Novel Diagnostic Biomarkers of Bovine Endometritis. Biomolecules 2024; 14:626. [PMID: 38927030 PMCID: PMC11202259 DOI: 10.3390/biom14060626] [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: 04/24/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Cow uterine infections pose a challenge in dairy farming, resulting in reproductive disorders. Uterine fluid extracellular vesicles (UF-EVs) play a key role in cell-to-cell communication in the uterus, potentially holding the signs of aetiology for endometritis. We used mass spectrometry-based quantitative shotgun proteomics to compare UF-EV proteomic profiles in healthy cows (H), cows with subclinical (SE) or clinical endometritis (CLE) sampled at 28-35 days postpartum. Functional analysis was performed on embryo cultures with the exposure to different EV types. A total of 248 UF-EV proteins exhibited differential enrichment between the groups. Interestingly, in SE, EV protein signature suggests a slight suppression of inflammatory response compared to CLE-UF-EVs, clustering closer with healthy cows' profile. Furthermore, CLE-UF-EVs proteomic profile highlighted pathways associated with cell apoptosis and active inflammation aimed at pathogen elimination. In SE-UF-EVs, the regulation of normal physiological status was aberrant, showing cell damage and endometrial repair at the same time. Serine peptidase HtrA1 (HTRA1) emerged as a potential biomarker for SE. Supplementation of CLE- and SE-derived UF-EVs reduced the embryo developmental rates and quality. Therefore, further research is warranted to elucidate the precise aetiology of SE in cattle, and HTRA1 should be further explored as a potential diagnostic biomarker.
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Affiliation(s)
- Johanna Piibor
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia; (J.P.); (A.W.); (M.P.); (A.K.); (S.K.)
| | - Andres Waldmann
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia; (J.P.); (A.W.); (M.P.); (A.K.); (S.K.)
- Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, LV-3004 Jelgava, Latvia
| | - Madhusha Prasadani
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia; (J.P.); (A.W.); (M.P.); (A.K.); (S.K.)
| | - Ants Kavak
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia; (J.P.); (A.W.); (M.P.); (A.K.); (S.K.)
| | - Aneta Andronowska
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Juliana Tuwima 10, 10-748 Olsztyn, Poland;
| | - Claudia Klein
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Höltystr. 10, 31535 Neustadt, Germany;
| | - Suranga Kodithuwakku
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia; (J.P.); (A.W.); (M.P.); (A.K.); (S.K.)
- Department of Animal Sciences, Faculty of Agriculture, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Alireza Fazeli
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia; (J.P.); (A.W.); (M.P.); (A.K.); (S.K.)
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila St. 14b, 50411 Tartu, Estonia
- Division of Clinical Medicine, School of Medicine & Population Health, University of Sheffield, Level 4, Jessop Wing, Tree Root Walk, Sheffield S10 2SF, UK
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Li Y, Wei Y, Ultsch M, Li W, Tang W, Tombling B, Gao X, Dimitrova Y, Gampe C, Fuhrmann J, Zhang Y, Hannoush RN, Kirchhofer D. Cystine-knot peptide inhibitors of HTRA1 bind to a cryptic pocket within the active site region. Nat Commun 2024; 15:4359. [PMID: 38777835 PMCID: PMC11111691 DOI: 10.1038/s41467-024-48655-w] [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: 09/28/2023] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
Cystine-knot peptides (CKPs) are naturally occurring peptides that exhibit exceptional chemical and proteolytic stability. We leveraged the CKP carboxypeptidase A1 inhibitor as a scaffold to construct phage-displayed CKP libraries and subsequently screened these collections against HTRA1, a trimeric serine protease implicated in age-related macular degeneration and osteoarthritis. The initial hits were optimized by using affinity maturation strategies to yield highly selective and potent picomolar inhibitors of HTRA1. Crystal structures, coupled with biochemical studies, reveal that the CKPs do not interact in a substrate-like manner but bind to a cryptic pocket at the S1' site region of HTRA1 and abolish catalysis by stabilizing a non-competent active site conformation. The opening and closing of this cryptic pocket is controlled by the gatekeeper residue V221, and its movement is facilitated by the absence of a constraining disulfide bond that is typically present in trypsin fold serine proteases, thereby explaining the remarkable selectivity of the CKPs. Our findings reveal an intriguing mechanism for modulating the activity of HTRA1, and highlight the utility of CKP-based phage display platforms in uncovering potent and selective inhibitors against challenging therapeutic targets.
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Affiliation(s)
- Yanjie Li
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yuehua Wei
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Mark Ultsch
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Wei Li
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Wanjian Tang
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Benjamin Tombling
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Xinxin Gao
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yoana Dimitrova
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Christian Gampe
- Department of Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jakob Fuhrmann
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yingnan Zhang
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Rami N Hannoush
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Daniel Kirchhofer
- Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
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Chen S, Puri A, Bell B, Fritsche J, Palacios HH, Balch M, Sprunger ML, Howard MK, Ryan JJ, Haines JN, Patti GJ, Davis AA, Jackrel ME. HTRA1 disaggregates α-synuclein amyloid fibrils and converts them into non-toxic and seeding incompetent species. Nat Commun 2024; 15:2436. [PMID: 38499535 PMCID: PMC10948756 DOI: 10.1038/s41467-024-46538-8] [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: 02/09/2023] [Accepted: 03/01/2024] [Indexed: 03/20/2024] Open
Abstract
Parkinson's disease (PD) is closely linked to α-synuclein (α-syn) misfolding and accumulation in Lewy bodies. The PDZ serine protease HTRA1 degrades fibrillar tau, which is associated with Alzheimer's disease, and inactivating mutations to mitochondrial HTRA2 are implicated in PD. Here, we report that HTRA1 inhibits aggregation of α-syn as well as FUS and TDP-43, which are implicated in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. The protease domain of HTRA1 is necessary and sufficient for inhibiting aggregation, yet this activity is proteolytically-independent. Further, HTRA1 disaggregates preformed α-syn fibrils, rendering them incapable of seeding aggregation of endogenous α-syn, while reducing HTRA1 expression promotes α-syn seeding. HTRA1 remodels α-syn fibrils by targeting the NAC domain, the key domain catalyzing α-syn amyloidogenesis. Finally, HTRA1 detoxifies α-syn fibrils and prevents formation of hyperphosphorylated α-syn accumulations in primary neurons. Our findings suggest that HTRA1 may be a therapeutic target for a range of neurodegenerative disorders.
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Affiliation(s)
- Sheng Chen
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Anuradhika Puri
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Braxton Bell
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Joseph Fritsche
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Hector H Palacios
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Maurie Balch
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Macy L Sprunger
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Matthew K Howard
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Jeremy J Ryan
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
| | - Jessica N Haines
- Department of Neurology, Washington University, St. Louis, MO, 63130, USA
| | - Gary J Patti
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA
- Department of Medicine, Washington University, St. Louis, MO, 63130, USA
| | - Albert A Davis
- Department of Neurology, Washington University, St. Louis, MO, 63130, USA
| | - Meredith E Jackrel
- Department of Chemistry, Washington University, St. Louis, MO, 63130, USA.
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Merle DA, Sen M, Armento A, Stanton CM, Thee EF, Meester-Smoor MA, Kaiser M, Clark SJ, Klaver CCW, Keane PA, Wright AF, Ehrmann M, Ueffing M. 10q26 - The enigma in age-related macular degeneration. Prog Retin Eye Res 2023; 96:101154. [PMID: 36513584 DOI: 10.1016/j.preteyeres.2022.101154] [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: 09/14/2022] [Revised: 11/21/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022]
Abstract
Despite comprehensive research efforts over the last decades, the pathomechanisms of age-related macular degeneration (AMD) remain far from being understood. Large-scale genome wide association studies (GWAS) were able to provide a defined set of genetic aberrations which contribute to disease risk, with the strongest contributors mapping to distinct regions on chromosome 1 and 10. While the chromosome 1 locus comprises factors of the complement system with well-known functions, the role of the 10q26-locus in AMD-pathophysiology remains enigmatic. 10q26 harbors a cluster of three functional genes, namely PLEKHA1, ARMS2 and HTRA1, with most of the AMD-associated genetic variants mapping to the latter two genes. High linkage disequilibrium between ARMS2 and HTRA1 has kept association studies from reliably defining the risk-causing gene for long and only very recently the genetic risk region has been narrowed to ARMS2, suggesting that this is the true AMD gene at this locus. However, genetic associations alone do not suffice to prove causality and one or more of the 14 SNPs on this haplotype may be involved in long-range control of gene expression, leaving HTRA1 and PLEKHA1 still suspects in the pathogenic pathway. Both, ARMS2 and HTRA1 have been linked to extracellular matrix homeostasis, yet their exact molecular function as well as their role in AMD pathogenesis remains to be uncovered. The transcriptional regulation of the 10q26 locus adds an additional level of complexity, given, that gene-regulatory as well as epigenetic alterations may influence expression levels from 10q26 in diseased individuals. Here, we provide a comprehensive overview on the 10q26 locus and its three gene products on various levels of biological complexity and discuss current and future research strategies to shed light on one of the remaining enigmatic spots in the AMD landscape.
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Affiliation(s)
- David A Merle
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Department for Ophthalmology, University Eye Clinic, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Department of Ophthalmology, Medical University of Graz, 8036, Graz, Austria.
| | - Merve Sen
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany
| | - Angela Armento
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany
| | - Chloe M Stanton
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Eric F Thee
- Department of Ophthalmology, Erasmus University Medical Center, 3015GD, Rotterdam, Netherlands; Department of Epidemiology, Erasmus University Medical Center, 3015CE, Rotterdam, Netherlands
| | - Magda A Meester-Smoor
- Department of Ophthalmology, Erasmus University Medical Center, 3015GD, Rotterdam, Netherlands; Department of Epidemiology, Erasmus University Medical Center, 3015CE, Rotterdam, Netherlands
| | - Markus Kaiser
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, 45117, Essen, Germany
| | - Simon J Clark
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Department for Ophthalmology, University Eye Clinic, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus University Medical Center, 3015GD, Rotterdam, Netherlands; Department of Epidemiology, Erasmus University Medical Center, 3015CE, Rotterdam, Netherlands; Department of Ophthalmology, Radboudumc, 6525EX, Nijmegen, Netherlands; Institute of Molecular and Clinical Ophthalmology Basel, CH-4031, Basel, Switzerland
| | - Pearse A Keane
- Institute for Health Research, Biomedical Research Centre for Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, UCL Institute of Ophthalmology, London, EC1V 2PD, UK
| | - Alan F Wright
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Michael Ehrmann
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, 45117, Essen, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research, Department for Ophthalmology, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany; Department for Ophthalmology, University Eye Clinic, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany.
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5
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Chen S, Puri A, Bell B, Fritsche J, Palacios H, Balch M, Sprunger M, Howard M, Patterson J, Patti G, Davis A, Jackrel M. HtrA1 prevents and reverses α-synuclein aggregation, rendering it non-toxic and seeding incompetent. RESEARCH SQUARE 2023:rs.3.rs-2570571. [PMID: 37674720 PMCID: PMC10479434 DOI: 10.21203/rs.3.rs-2570571/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Parkinson disease (PD) is closely linked to the misfolding and accumulation of α-synuclein (α-syn) into Lewy bodies. HtrA1 is a PDZ serine protease that degrades fibrillar tau, which is associated with Alzheimer disease (AD). Further, inactivating mutations to mitochondrial HtrA2 have been implicated in PD. Here, we establish that HtrA1 inhibits the aggregation of α-syn as well as FUS and TDP-43, which are implicated in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). We demonstrate that the protease domain of HtrA1 is necessary and sufficient for inhibition of aggregation, yet this activity is independent of HtrA1 proteolytic activity. Further, we find that HtrA1 also disaggregates preformed α-syn fibrils, which may promote their clearance. Treatment of α-syn fibrils with HtrA1 renders α-syn incapable of seeding the aggregation of endogenous α-syn in mammalian biosensor cells. We find that HtrA1 remodels α-syn by specifically targeting the NAC domain, which is the key domain that catalyzes α-syn oligomerization and fibrillization. Finally, in a primary neuron model of α-syn aggregation, we show that HtrA1 and its proteolytically inactive form both detoxify α-syn and prevent the formation of hyperphosphorylated α-syn accumulations. Our findings suggest that HtrA1 prevents aggregation and promotes disaggregation of multiple disease-associated proteins, and may be a therapeutic target for treating a range of neurodegenerative disorders.
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6
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Romero-Molina S, Ruiz-Blanco YB, Mieres-Perez J, Harms M, Münch J, Ehrmann M, Sanchez-Garcia E. PPI-Affinity: A Web Tool for the Prediction and Optimization of Protein-Peptide and Protein-Protein Binding Affinity. J Proteome Res 2022; 21:1829-1841. [PMID: 35654412 PMCID: PMC9361347 DOI: 10.1021/acs.jproteome.2c00020] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Virtual screening
of protein–protein and protein–peptide
interactions is a challenging task that directly impacts the processes
of hit identification and hit-to-lead optimization in drug design
projects involving peptide-based pharmaceuticals. Although several
screening tools designed to predict the binding affinity of protein–protein
complexes have been proposed, methods specifically developed to predict
protein–peptide binding affinity are comparatively scarce.
Frequently, predictors trained to score the affinity of small molecules
are used for peptides indistinctively, despite the larger complexity
and heterogeneity of interactions rendered by peptide binders. To
address this issue, we introduce PPI-Affinity, a tool that leverages
support vector machine (SVM) predictors of binding affinity to screen
datasets of protein–protein and protein–peptide complexes,
as well as to generate and rank mutants of a given structure. The
performance of the SVM models was assessed on four benchmark datasets,
which include protein–protein and protein–peptide binding
affinity data. In addition, we evaluated our model on a set of mutants
of EPI-X4, an endogenous peptide inhibitor of the chemokine receptor
CXCR4, and on complexes of the serine proteases HTRA1 and HTRA3 with
peptides. PPI-Affinity is freely accessible at https://protdcal.zmb.uni-due.de/PPIAffinity.
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Affiliation(s)
- Sandra Romero-Molina
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Joel Mieres-Perez
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Mirja Harms
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany.,Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm 89081, Germany
| | - Michael Ehrmann
- Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
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Interplay between HTRA1 and classical signalling pathways in organogenesis and diseases. Saudi J Biol Sci 2022; 29:1919-1927. [PMID: 35531175 PMCID: PMC9072889 DOI: 10.1016/j.sjbs.2021.11.056] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/05/2021] [Accepted: 11/17/2021] [Indexed: 11/20/2022] Open
Abstract
The high temperature requirement factor A1 (HTRA1) is a serine protease which modulates an array of signalling pathways driving basal biological processes. HTRA1 plays a significant role in cell proliferation, migration and fate determination, in addition to controlling protein aggregates through refolding, translocation or degradation. The mutation of HTRA1 has been implicated in a plethora of disorders and this has also led to its growing interest as drug therapy target. This review details the involvement of HTRA1 in certain signalling pathways, namely the transforming growth factor beta (TGF-β), canonical Wingless/Integrated (WNT) and NOTCH signalling pathways during organogenesis and various disease pathogenesis such as preeclampsia, age-related macular degeneration (AMD), small vessel disease and cancer. We have also explored possible avenues of exploiting the serine proteases for therapeutic management of these disorders.
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Vecchio FL, Bisceglia P, Imbimbo BP, Lozupone M, Latino RR, Resta E, Leone M, Solfrizzi V, Greco A, Daniele A, Watling M, Panza F, Seripa D. Are apolipoprotein E fragments a promising new therapeutic target for Alzheimer’s disease? Ther Adv Chronic Dis 2022; 13:20406223221081605. [PMID: 35321401 PMCID: PMC8935560 DOI: 10.1177/20406223221081605] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/28/2022] [Indexed: 11/17/2022] Open
Abstract
Human apolipoprotein E (ApoE) is a 299-amino acid secreted glycoprotein that binds cholesterol and phospholipids. ApoE exists as three common isoforms (ApoE2, ApoE3, and ApoE4) and heterozygous carriers of the ε4 allele of the gene encoding ApoE (APOE) have a fourfold greater risk of developing Alzheimer’s disease (AD). The enzymes thrombin, cathepsin D, α-chymotrypsin-like serine protease, and high-temperature requirement serine protease A1 are responsible for ApoE proteolytic processing resulting in bioactive C-terminal-truncated fragments that vary depending on ApoE isoforms, brain region, aging, and neural injury. The objectives of the present narrative review were to describe ApoE processing, discussing current hypotheses about the potential role of various ApoE fragments in AD pathophysiology, and reviewing the current development status of different anti-ApoE drugs. The exact mechanism by which APOE gene variants increase/decrease AD risk and the role of ApoE fragments in the deposition are not fully understood, but APOE is known to directly affect tau-mediated neurodegeneration. ApoE fragments co-localize with neurofibrillary tangles and amyloid β (Aβ) plaques, and may cause neurodegeneration. Among anti-ApoE approaches, a fascinating strategy may be to therapeutically overexpress ApoE2 in APOE ε4/ε4 carriers through vector administration or liposomal delivery systems. Another approach involves reducing ApoE4 expression by intracerebroventricular antisense oligonucleotides that significantly decreased Aβ pathology in transgenic mice. Differences in the proteolytic processing of distinct ApoE isoforms and the use of ApoE fragments as mimetic peptides in AD treatment are also under investigation. Treatment with peptides that mimic the structural and biological properties of native ApoE may reduce Aβ deposition, tau hyperphosphorylation, and glial activation in mouse models of Aβ pathology. Alternative strategies involve the use of ApoE4 structure correctors, passive immunization to target a certain form of ApoE, conversion of the ApoE4 aminoacid sequence into that of ApoE3 or ApoE2, and inhibition of the ApoE-Aβ interaction.
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Affiliation(s)
- Filomena Lo Vecchio
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia 71013, Italy
| | - Paola Bisceglia
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | | | - Madia Lozupone
- Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Raffaela Rita Latino
- Complex Structure of Neurology, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Emanuela Resta
- Translational Medicine and Management of Health Systems, University of Foggia, Foggia, Italy
| | - Maurizio Leone
- Complex Structure of Neurology, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Vincenzo Solfrizzi
- ‘Cesare Frugoni’ Internal and Geriatric Medicine and Memory Unit, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Antonio Greco
- Department of Neuroscience, Catholic University of the Sacred Heart, Rome, Italy; Neurology Unit, IRCCS Fondazione Policlinico Universitario A. Gemelli, Rome, Italy
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | | | - Mark Watling
- CNS & Pain Department, TranScrip Ltd, Reading, UK
| | - Francesco Panza
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Foggia, Italy
- Population Health Unit, Healthy Aging Phenotypes Research Unit, ‘Salus in Apulia Study’, National Institute of Gastroenterology ‘Saverio de Bellis’, Research Hospital, Castellana Grotte, Bari 70013, Italy
| | - Davide Seripa
- Research Laboratory, Complex Structure of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Hematology and Stem Cell Transplant Unit, ‘Vito Fazzi’ Hospital, Lecce, Italy
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9
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Overview of Human HtrA Family Proteases and Their Distinctive Physiological Roles and Unique Involvement in Diseases, Especially Cancer and Pregnancy Complications. Int J Mol Sci 2021; 22:ijms221910756. [PMID: 34639128 PMCID: PMC8509474 DOI: 10.3390/ijms221910756] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/27/2021] [Accepted: 10/02/2021] [Indexed: 12/25/2022] Open
Abstract
The mammalian high temperature requirement A (HtrA) proteins are a family of evolutionarily conserved serine proteases, consisting of four homologs (HtrA1-4) that are involved in many cellular processes such as growth, unfolded protein stress response and programmed cell death. In humans, while HtrA1, 2 and 3 are widely expressed in multiple tissues with variable levels, HtrA4 expression is largely restricted to the placenta with the protein released into maternal circulation during pregnancy. This limited expression sets HtrA4 apart from the rest of the family. All four HtrAs are active proteases, and their specific cellular and physiological roles depend on tissue type. The dysregulation of HtrAs has been implicated in many human diseases such as cancer, arthritis, neurogenerative ailments and reproductive disorders. This review first discusses HtrAs broadly and then focuses on the current knowledge of key molecular characteristics of individual human HtrAs, their similarities and differences and their reported physiological functions. HtrAs in other species are also briefly mentioned in the context of understanding the human HtrAs. It then reviews the distinctive involvement of each HtrA in various human diseases, especially cancer and pregnancy complications. It is noteworthy that HtrA4 expression has not yet been reported in any primary tumour samples, suggesting an unlikely involvement of this HtrA in cancer. Collectively, we accentuate that a better understanding of tissue-specific regulation and distinctive physiological and pathological roles of each HtrA will improve our knowledge of many processes that are critical for human health.
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10
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Al-Rabadi LF, Caza T, Trivin-Avillach C, Rodan AR, Andeen N, Hayashi N, Williams B, Revelo MP, Clayton F, Abraham J, Lin E, Liou W, Zou CJ, Ramkumar N, Cummins T, Wilkey DW, Kawalit I, Herzog C, Storey A, Edmondson R, Sjoberg R, Yang T, Chien J, Merchant M, Arthur J, Klein J, Larsen C, Beck LH. Serine Protease HTRA1 as a Novel Target Antigen in Primary Membranous Nephropathy. J Am Soc Nephrol 2021; 32:1666-1681. [PMID: 33952630 PMCID: PMC8425645 DOI: 10.1681/asn.2020101395] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/21/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Identification of target antigens PLA2R, THSD7A, NELL1, or Semaphorin-3B can explain the majority of cases of primary membranous nephropathy (MN). However, target antigens remain unidentified in 15%-20% of patients. METHODS A multipronged approach, using traditional and modern technologies, converged on a novel target antigen, and capitalized on the temporal variation in autoantibody titer for biomarker discovery. Immunoblotting of human glomerular proteins followed by differential immunoprecipitation and mass spectrometric analysis was complemented by laser-capture microdissection followed by mass spectrometry, elution of immune complexes from renal biopsy specimen tissue, and autoimmune profiling on a protein fragment microarray. RESULTS These approaches identified serine protease HTRA1 as a novel podocyte antigen in a subset of patients with primary MN. Sera from two patients reacted by immunoblotting with a 51-kD protein within glomerular extract and with recombinant human HTRA1, under reducing and nonreducing conditions. Longitudinal serum samples from these patients seemed to correlate with clinical disease activity. As in PLA2R- and THSD7A- associated MN, anti-HTRA1 antibodies were predominantly IgG4, suggesting a primary etiology. Analysis of sera collected during active disease versus remission on protein fragment microarrays detected significantly higher titers of anti-HTRA1 antibody in active disease. HTRA1 was specifically detected within immune deposits of HTRA1-associated MN in 14 patients identified among three cohorts. Screening of 118 "quadruple-negative" (PLA2R-, THSD7A-, NELL1-, EXT2-negative) patients in a large repository of MN biopsy specimens revealed a prevalence of 4.2%. CONCLUSIONS Conventional and more modern techniques converged to identify serine protease HTRA1 as a target antigen in MN.
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Affiliation(s)
- Laith Farah Al-Rabadi
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah Health, Salt Lake City, Utah
| | | | - Claire Trivin-Avillach
- Section of Nephrology, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts
| | - Aylin R. Rodan
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah Health, Salt Lake City, Utah,Molecular Medicine Program, University of Utah Health, Salt Lake City, Utah,Department of Human Genetics, University of Utah Health, Salt Lake City, Utah,Medical Service, Veterans Affairs Salt Lake City Health Care System, Salt Lake City, Utah
| | - Nicole Andeen
- Department of Pathology, Oregon Health and Science University, Portland, Oregon
| | - Norifumi Hayashi
- Section of Nephrology, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts,Kanazawa Medical University, Ishikawa, Japan
| | - Brandi Williams
- Moran Eye Center, University of Utah Health, Salt Lake City, Utah
| | - Monica P. Revelo
- Department of Pathology, University of Utah Health, Salt Lake City, Utah
| | - Fred Clayton
- Department of Pathology, University of Utah Health, Salt Lake City, Utah
| | - Jo Abraham
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah Health, Salt Lake City, Utah
| | - Edwin Lin
- Department of Human Genetics, University of Utah Health, Salt Lake City, Utah
| | - Willisa Liou
- Department of Pathology, University of Utah Health, Salt Lake City, Utah
| | - Chang-Jiang Zou
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah Health, Salt Lake City, Utah
| | - Nirupama Ramkumar
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah Health, Salt Lake City, Utah
| | - Tim Cummins
- Clinical Proteomics Laboratory, Division of Nephrology and Hypertension, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky
| | - Daniel W. Wilkey
- Clinical Proteomics Laboratory, Division of Nephrology and Hypertension, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky
| | - Issa Kawalit
- International Renal Care Association, Amman, Jordan
| | - Christian Herzog
- Nephrology Division, Internal Medicine Department, University of Arkansas for Medical Science, Little Rock, Arkansas
| | - Aaron Storey
- Nephrology Division, Internal Medicine Department, University of Arkansas for Medical Science, Little Rock, Arkansas
| | - Rick Edmondson
- Nephrology Division, Internal Medicine Department, University of Arkansas for Medical Science, Little Rock, Arkansas
| | - Ronald Sjoberg
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Tianxin Yang
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah Health, Salt Lake City, Utah,Medical Service, Veterans Affairs Salt Lake City Health Care System, Salt Lake City, Utah
| | - Jeremy Chien
- Department of Biochemistry and Molecular Medicine, University of California Davis Health, Davis, California
| | - Michael Merchant
- Clinical Proteomics Laboratory, Division of Nephrology and Hypertension, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky
| | - John Arthur
- Nephrology Division, Internal Medicine Department, University of Arkansas for Medical Science, Little Rock, Arkansas
| | - Jon Klein
- Clinical Proteomics Laboratory, Division of Nephrology and Hypertension, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky,Robley Rex Veterans Administration Medical Center, Louisville, Kentucky
| | | | - Laurence H. Beck
- Section of Nephrology, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts
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11
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Liang CT, Roscow OMA, Zhang W. Recent developments in engineering protein-protein interactions using phage display. Protein Eng Des Sel 2021; 34:6297171. [PMID: 34117768 DOI: 10.1093/protein/gzab014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/09/2021] [Accepted: 05/18/2021] [Indexed: 12/14/2022] Open
Abstract
Targeted inhibition of misregulated protein-protein interactions (PPIs) has been a promising area of investigation in drug discovery and development for human diseases. However, many constraints remain, including shallow binding surfaces and dynamic conformation changes upon interaction. A particularly challenging aspect is the undesirable off-target effects caused by inherent structural similarity among the protein families. To tackle this problem, phage display has been used to engineer PPIs for high-specificity binders with improved binding affinity and greatly reduced undesirable interactions with closely related proteins. Although general steps of phage display are standardized, library design is highly variable depending on experimental contexts. Here in this review, we examined recent advances in the structure-based combinatorial library design and the advantages and limitations of different approaches. The strategies described here can be explored for other protein-protein interactions and aid in designing new libraries or improving on previous libraries.
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Affiliation(s)
- Chen T Liang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G2W1, Canada
| | - Olivia M A Roscow
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G2W1, Canada
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G2W1, Canada.,CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, MaRS Centre West Tower, 661 University Avenue, Toronto, Ontario M5G1M1, Canada
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12
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Nam HY, Song D, Eo J, Choi NE, Hong JA, Hong KT, Lee JS, Seo J, Lee J. Activity-Based Probes for the High Temperature Requirement A Serine Proteases. ACS Chem Biol 2020; 15:2346-2354. [PMID: 32786264 DOI: 10.1021/acschembio.0c00279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The high temperature requirement A (HTRA) family of serine proteases mediates protein quality control. These proteins process misfolded proteins in several diseases including Alzheimer's disease (AD) and Parkinson's disease (PD). While their structures and activation mechanisms have been studied, the precise details of the regulation of their activity under physiological conditions have not been completely elucidated, partly due to the lack of suitable chemical probes. In the present study, we developed novel activity-based probes (ABPs) targeting the HTRAs and demonstrated their utility in the monitoring and quantification of changes in enzyme activity in live cells. Using our probes, we found the activity of HTRA1 to be highly elevated in an AD-like cell-based model. We also observed the active HTRA2 in live cells by using a mitochondrion-targeted probe. We believe that our probes can serve as a useful tool to study the role of human HTRAs in neurodegenerative diseases.
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Affiliation(s)
- Ho Yeon Nam
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Dasom Song
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Jinny Eo
- Department of Global Medical Science, Sungshin University, Seoul 01133, Republic of Korea
| | - Na-Eun Choi
- Department of Global Medical Science, Sungshin University, Seoul 01133, Republic of Korea
| | - Jong-Ah Hong
- Department of Global Medical Science, Sungshin University, Seoul 01133, Republic of Korea
| | - Kyung Tae Hong
- Molecular Recognition Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Jun-Seok Lee
- Molecular Recognition Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Jiwon Seo
- Department of Chemistry, School of Physics and Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Jiyoun Lee
- Department of Global Medical Science, Sungshin University, Seoul 01133, Republic of Korea
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13
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Nielsen NS, Poulsen ET, Lukassen MV, Chao Shern C, Mogensen EH, Weberskov CE, DeDionisio L, Schauser L, Moore TC, Otzen DE, Hjortdal J, Enghild JJ. Biochemical mechanisms of aggregation in TGFBI-linked corneal dystrophies. Prog Retin Eye Res 2020; 77:100843. [DOI: 10.1016/j.preteyeres.2020.100843] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/17/2020] [Accepted: 01/23/2020] [Indexed: 12/22/2022]
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14
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A distinct concerted mechanism of structural dynamism defines activity of human serine protease HtrA3. Biochem J 2020; 477:407-429. [PMID: 31899476 PMCID: PMC6993860 DOI: 10.1042/bcj20190706] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 12/20/2019] [Accepted: 01/03/2020] [Indexed: 12/20/2022]
Abstract
Human HtrA3 (high-temperature requirement protease A3) is a trimeric multitasking propapoptotic serine protease associated with critical cellular functions and pathogenicity. Implicated in diseases including cancer and pre-eclampsia, its role as a tumor suppressor and potential therapeutic target cannot be ignored. Therefore, elucidating its mode of activation and regulatory switch becomes indispensable towards modulating its functions with desired effects for disease intervention. Using computational, biochemical and biophysical tools, we delineated the role of all domains, their combinations and the critical phenylalanine residues in regulating HtrA3 activity, oligomerization and specificity. Our findings underline the crucial roles of the N-terminus as well as the PDZ domain in oligomerization and formation of a catalytically competent enzyme, thus providing new insights into its structure–function coordination. Our study also reports an intricate ligand-induced allosteric switch, which redefines the existing hypothesis of HtrA3 activation besides opening up avenues for modulating protease activity favorably through suitable effector molecules.
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15
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Kiptiyah K, Widodo W, Ciptadi G, Aulanni'Am A, Widodo MA, Sumitro SB. 10-gingerol induces oxidative stress through HTR1A in cumulus cells: in-vitro and in-silico studies. JOURNAL OF COMPLEMENTARY & INTEGRATIVE MEDICINE 2020; 17:/j/jcim.ahead-of-print/jcim-2019-0042/jcim-2019-0042.xml. [PMID: 32284444 DOI: 10.1515/jcim-2019-0042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 10/24/2019] [Indexed: 01/04/2023]
Abstract
Background We investigated whether 10-gingerol is able to induce oxidative stress in cumulus cells. Methods For the in-vitro research, we used a cumulus cell culture in M199, containing 10-gingerol in various concentrations (0, 12, 16, and 20 µM), and detected oxidative stress through superoxide dismutase (SOD) activity and malondialdehyde (MDA) concentrations, with incubation periods of 24, 48, 72, and 96 h. The obtained results were confirmed by in-silico studies. Results The in-vitro data revealed that SOD activity and MDA concentration increased with increasing incubation periods: SOD activity at 0 µM (1.39 ± 0.24i), 12 µM (16.42 ± 0.35ab), 16 µM (17.28 ± 0.55ab), 20 µM (17.81 ± 0.12a), with a contribution of 71.1%. MDA concentration at 0 µM (17.82 ± 1.39 l), 12 µM (72.99 ± 0.31c), 16 µM (79.77 ± 4.19b), 20 µM (85.07 ± 2.57a), with a contribution of 73.1%. Based on this, the in-silico data uncovered that 10-gingerol induces oxidative stress in cumulus cells by inhibiting HTR1A functions and inactivating GSK3B and AKT-1. Conclusions 10-gingerol induces oxidative stress in cumulus cells through enhancing SOD activity and MDA concentration by inhibiting HTR1A functions and inactivating GSK3B and AKT-1.
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Affiliation(s)
- Kiptiyah Kiptiyah
- Department of Biology, Maulana Malik Ibrahim Islamic State University of Malang, Malang 65144, Indonesia
| | - Widodo Widodo
- Department of Biology, Brawijaya University of Malang, Malang, Indonesia
| | - Gatot Ciptadi
- Husbandry Faculty, Brawijaya University of Malang, Malang, Indonesia
| | | | - Mohammad A Widodo
- Biomedical Study Programme, Brawijaya University of Malang, Malang, Indonesia
| | - Sutiman B Sumitro
- Department of Biology, Brawijaya University of Malang, Malang, Indonesia
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16
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Amacher JF, Brooks L, Hampton TH, Madden DR. Specificity in PDZ-peptide interaction networks: Computational analysis and review. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100022. [PMID: 32289118 PMCID: PMC7138185 DOI: 10.1016/j.yjsbx.2020.100022] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/26/2020] [Accepted: 02/29/2020] [Indexed: 01/03/2023]
Abstract
Globular PDZ domains typically serve as protein-protein interaction modules that regulate a wide variety of cellular functions via recognition of short linear motifs (SLiMs). Often, PDZ mediated-interactions are essential components of macromolecular complexes, and disruption affects the entire scaffold. Due to their roles as linchpins in trafficking and signaling pathways, PDZ domains are attractive targets: both for controlling viral pathogens, which bind PDZ domains and hijack cellular machinery, as well as for developing therapies to combat human disease. However, successful therapeutic interventions that avoid off-target effects are a challenge, because each PDZ domain interacts with a number of cellular targets, and specific binding preferences can be difficult to decipher. Over twenty-five years of research has produced a wealth of data on the stereochemical preferences of individual PDZ proteins and their binding partners. Currently the field lacks a central repository for this information. Here, we provide this important resource and provide a manually curated, comprehensive list of the 271 human PDZ domains. We use individual domain, as well as recent genomic and proteomic, data in order to gain a holistic view of PDZ domains and interaction networks, arguing this knowledge is critical to optimize targeting selectivity and to benefit human health.
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Affiliation(s)
- Jeanine F Amacher
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.,Department of Chemistry, Western Washington University, Bellingham, WA 98225, USA
| | - Lionel Brooks
- Department of Biology, Western Washington University, Bellingham, WA 98225, USA
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Dean R Madden
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
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17
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Tao S, Zhou T, Saelao P, Wang Y, Zhu Y, Li T, Zhou H, Wang J. Intrauterine Growth Restriction Alters the Genome-Wide DNA Methylation Profiles in Small Intestine, Liver and Longissimus Dorsi Muscle of Newborn Piglets. Curr Protein Pept Sci 2019; 20:713-726. [PMID: 30678618 DOI: 10.2174/1389203720666190124165243] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 12/30/2018] [Accepted: 01/01/2019] [Indexed: 01/20/2023]
Abstract
Intrauterine growth restriction (IUGR) remains a major problem in swine production since the associated low birth weight leads to high rates of pre-weaning morbidity and mortality, and permanent retardation of growth and development. The underlying regulatory mechanisms from the aspects of epigenetic modification has received widespread attention. Studies explore the changes in genome wide methylation in small intestine (SI), liver and longissimus dorsi muscle (LDM) between IUGR and normal birth weight (NBW) newborn piglets using a methylated DNA immunoprecipitation-sequencing (MeDIP-Seq) approach. The data demonstrated that methylated peaks were prominently distributed in distal intergenic regions and the quantities of peaks in IUGR piglets were more than that of NBW piglets. IUGR piglets had relatively high methylated level in promoters, introns and coding exons in all the three tissues. Through KEGG pathway analysis of differentially methylated genes found that 33, 54 and 5 differentially methylated genes in small intestine, liver and longissimus dorsi muscle between NBW and IUGR piglets, respectively, which are related to development and differentiation, carbohydrate and energy metabolism, lipid metabolism, protein turnover, immune response, detoxification, oxidative stress and apoptosis pathway. The objective of this review is to assess the impact of differentially methylation status on developmental delay, metabolic disorders and immune deficiency of IUGR piglets.
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Affiliation(s)
- Shiyu Tao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Tianjiao Zhou
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Perot Saelao
- Department of Animal Science, University of California, Davis, CA 95616, United States
| | - Ying Wang
- Department of Animal Science, University of California, Davis, CA 95616, United States
| | - Yuhua Zhu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Tiantian Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA 95616, United States
| | - Junjun Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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18
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Valgardson J, Cosbey R, Houser P, Rupp M, Van Bronkhorst R, Lee M, Jagodzinski F, Amacher JF. MotifAnalyzer-PDZ: A computational program to investigate the evolution of PDZ-binding target specificity. Protein Sci 2019; 28:2127-2143. [PMID: 31599029 DOI: 10.1002/pro.3741] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 12/15/2022]
Abstract
Recognition of short linear motifs (SLiMs) or peptides by proteins is an important component of many cellular processes. However, due to limited and degenerate binding motifs, prediction of cellular targets is challenging. In addition, many of these interactions are transient and of relatively low affinity. Here, we focus on one of the largest families of SLiM-binding domains in the human proteome, the PDZ domain. These domains bind the extreme C-terminus of target proteins, and are involved in many signaling and trafficking pathways. To predict endogenous targets of PDZ domains, we developed MotifAnalyzer-PDZ, a program that filters and compares all motif-satisfying sequences in any publicly available proteome. This approach enables us to determine possible PDZ binding targets in humans and other organisms. Using this program, we predicted and biochemically tested novel human PDZ targets by looking for strong sequence conservation in evolution. We also identified three C-terminal sequences in choanoflagellates that bind a choanoflagellate PDZ domain, the Monsiga brevicollis SHANK1 PDZ domain (mbSHANK1), with endogenously-relevant affinities, despite a lack of conservation with the targets of a homologous human PDZ domain, SHANK1. All three are predicted to be signaling proteins, with strong sequence homology to cytosolic and receptor tyrosine kinases. Finally, we analyzed and compared the positional amino acid enrichments in PDZ motif-satisfying sequences from over a dozen organisms. Overall, MotifAnalyzer-PDZ is a versatile program to investigate potential PDZ interactions. This proof-of-concept work is poised to enable similar types of analyses for other SLiM-binding domains (e.g., MotifAnalyzer-Kinase). MotifAnalyzer-PDZ is available at http://motifAnalyzerPDZ.cs.wwu.edu.
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Affiliation(s)
- Jordan Valgardson
- Department of Computer Science, Western Washington University, Bellingham, Washington.,Department of Chemistry, Western Washington University, Bellingham, Washington
| | - Robin Cosbey
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Paul Houser
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Milo Rupp
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Raiden Van Bronkhorst
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Michael Lee
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Filip Jagodzinski
- Department of Computer Science, Western Washington University, Bellingham, Washington
| | - Jeanine F Amacher
- Department of Chemistry, Western Washington University, Bellingham, Washington
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19
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Discerning the mechanism of action of HtrA4: a serine protease implicated in the cell death pathway. Biochem J 2019; 476:1445-1463. [PMID: 31036715 DOI: 10.1042/bcj20190224] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/23/2019] [Accepted: 04/26/2019] [Indexed: 11/17/2022]
Abstract
High-temperature requirement protease A4 (HtrA4) is a secretary serine protease whose expression is up-regulated in pre-eclampsia (PE) and hence is a possible biomarker of PE. It has also been altered in cancers such as glioblastoma, breast carcinoma, and prostate cancer making it an emerging therapeutic target. Among the human HtrAs, HtrA4 is the least characterized protease pertaining to both structure and its functions. Although the members of human HtrA family share a significant structural and functional conservation, subtle structural changes have been associated with certain distinct functional requirements. Therefore, intricate dissection of HtrA4 structural and functional properties becomes imperative to understand its role in various biological and pathophysiological processes. Here, using inter-disciplinary approaches including in silico, biochemical and biophysical studies, we have done a domain-wise dissection of HtrA4 to delineate the roles of the domains in regulating oligomerization, stability, protease activity, and specificity. Our findings distinctly demonstrate the importance of the N-terminal region in oligomerization, stability and hence the formation of a functional enzyme. In silico structural comparison of HtrA4 with other human HtrAs, enzymology studies and cleavage assays with X-linked inhibitor of apoptosis protein (XIAP) show overall structural conservation and allosteric mode of protease activation, which suggest functional redundancy within this protease family. However, significantly lower protease activity as compared with HtrA2 indicates an additional mode of regulation of the protease activity in the cellular milieu. Overall, these studies provide first-hand information on HtrA4 and its interaction with antiapoptotic XIAP thus implicating its involvement in the apoptotic pathway.
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20
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Structural Dissection and Optimization of a Cation–π–π Stacking System in Human Pregnancy-Related Serine Protease–Peptide Complex. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09866-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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21
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Zhang D, He D, Pan X, Xu Y, Liu L. Structural analysis and rational design of orthogonal stacking system in an E. coli DegP PDZ1–peptide complex. CHEMICAL PAPERS 2019. [DOI: 10.1007/s11696-019-00797-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Abstract
The HTRA1 gene encoding an evolutionary conserved protein quality-control factor can be epigenetically silenced or inactivated by mutation under pathologic conditions such as cancer. Recent evidence suggests that the loss of HTRA1 function causes multiple phenotypes, including the acceleration of cell growth, delayed onset of senescence, centrosome amplification, and polyploidy, suggesting an implication in the regulation of the cell cycle. To address this model, we performed a large-scale proteomics study to correlate the abundance of proteins and HTRA1 levels in various cell cycle phases using label-free-quantification mass spectrometry. These data indicate that the levels of 4723 proteins fluctuated in a cell-cycle-dependent manner, 2872 in a HTRA1-dependent manner, and 1530 in a cell-cycle- and HTRA1-dependent manner. The large number of proteins affected by the modulation of HTRA1 levels supports its general role in protein homeostasis. Moreover, the detected changes in protein abundance, in combination with pull-down data, implicate HTRA1 in various cell cycle events such as DNA replication, chromosome segregation, and cell-cycle-dependent apoptosis. These results highlight the wide implications of HTRA1 in cellular physiology.
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Affiliation(s)
- Jasmin Schillinger
- Centre of Medical Biotechnology, Faculty of Biology , University Duisburg-Essen, Universitaetsstrasse , 45141 Essen , Germany
| | - Katharina Severin
- Centre of Medical Biotechnology, Faculty of Biology , University Duisburg-Essen, Universitaetsstrasse , 45141 Essen , Germany
| | - Farnusch Kaschani
- Centre of Medical Biotechnology, Faculty of Biology , University Duisburg-Essen, Universitaetsstrasse , 45141 Essen , Germany
| | - Markus Kaiser
- Centre of Medical Biotechnology, Faculty of Biology , University Duisburg-Essen, Universitaetsstrasse , 45141 Essen , Germany
| | - Michael Ehrmann
- Centre of Medical Biotechnology, Faculty of Biology , University Duisburg-Essen, Universitaetsstrasse , 45141 Essen , Germany
- School of Biosciences , Cardiff University , Cardiff CF10 3US , United Kingdom
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23
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Sun ML, Sun LM, Wang YQ. Peptide selectivity between the PDZ domains of human pregnancy-related serine proteases (HtrA1, HtrA2, HtrA3, and HtrA4) can be reshaped by different halogen probes. J Mol Recognit 2018; 31:e2698. [PMID: 29266444 DOI: 10.1002/jmr.2698] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/23/2017] [Accepted: 11/29/2017] [Indexed: 01/01/2023]
Abstract
The human HtrA family of serine proteases (HtrA1, HtrA2, HtrA3, and HtrA4) are the key enzymes associated with pregnancy and closely related to the development and progression of many pathological events. Previously, it was found that halogen substitution at the indole moiety of peptide Trp-1 residue can form a geometrically satisfactory halogen bond with the Drosophila discs large, zona occludens-1 (PDZ) domain of HtrA proteases. Here, we attempt to systematically investigate the effect of substitution with 4 halogen types and 2 indole positions on the binding affinity and specificity of peptide ligands to the 4 HtrA PDZ domains. The complex structures, interaction energies, halogen-bonding strength, and binding affinity of domain-peptide systems were modeled, analyzed, and measured via computational modeling and fluorescence-based assay. It is revealed that there is a compromise between the local rearrangement of halogen bond involving different halogen atoms and the global optimization of domain-peptide interaction; the substitution position is fundamentally important for peptide-binding affinity, while the halogen type can effectively shift peptide selectivity between the 4 domains. The HtrA1-PDZ and HtrA4-PDZ as well as HtrA2-PDZ and HtrA3-PDZ respond similarly to different halogen substitutions of peptide; -Br substitution at R2-position and -I substitution at R4-position are most effective in improving peptide selectivity for HtrA1-PDZ/HtrA4-PDZ and HtrA2-PDZ/HtrA3-PDZ, respectively; -F substitution would not address substantial effect on peptide selectivity for all the 4 domains. Consequently, the binding affinities of a native peptide ligand DSRIWWV-COOH as well as its 4 R2-halogenated counterparts were determined as 1.9, 1.4, 0.5, 0.27, and 0.92 μM, which are basically consistent with computational analysis. This study would help to rationally design selective peptide inhibitors of HtrA family members by using different halogen substitutions.
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Affiliation(s)
- Mei-Ling Sun
- Department of Obstetrics, Rizhao People's Hospital, Rizhao, China
| | - Li-Mei Sun
- Department of Obstetrics, Rizhao People's Hospital, Rizhao, China
| | - Yong-Qing Wang
- Department of Obstetrics, Rizhao People's Hospital, Rizhao, China
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Muñoz SS, Li H, Ruberu K, Chu Q, Saghatelian A, Ooi L, Garner B. The serine protease HtrA1 contributes to the formation of an extracellular 25-kDa apolipoprotein E fragment that stimulates neuritogenesis. J Biol Chem 2018; 293:4071-4084. [PMID: 29414786 PMCID: PMC5857987 DOI: 10.1074/jbc.ra117.001278] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/24/2018] [Indexed: 12/31/2022] Open
Abstract
Apolipoprotein-E (apoE) is a glycoprotein highly expressed in the brain, where it appears to play a role in lipid transport, β-amyloid clearance, and neuronal signaling. ApoE proteolytic fragments are also present in the brain, but the enzymes responsible for apoE fragmentation are unknown, and the biological activity of specific apoE fragments remains to be determined. Here we utilized SK-N-SH neuroblastoma cells differentiated into neurons with all-trans-retinoic acid (ATRA) to study extracellular apoE proteolysis. ApoE fragments were detectable in culture supernatants after 3 days, and their levels were increased for up to 9 days in the presence of ATRA. The concentration of apoE fragments was positively correlated with levels of the neuronal maturation markers (PSD95 and SMI32). The most abundant apoE fragments were 25- and 28-kDa N-terminal fragments that both contained sialylated glycosylation and bound to heparin. We detected apoE fragments only in the extracellular milieu and not in cell lysates, suggesting that an extracellular protease contributes to apoE fragmentation. Of note, siRNA-mediated knockdown of high-temperature requirement serine peptidase A1 (HtrA1) and a specific HtrA1 inhibitor reduced apoE 25-kDa fragment formation by 41 and 86%, respectively. Recombinant 25-kDa fragment apoE and full-length apoE both stimulated neuritogenesis in vitro, increasing neuroblastoma neurite growth by more than 2-fold over a 6-day period. This study provides a cellular model for assessing apoE proteolysis, indicates that HtrA1 regulates apoE 25-kDa fragment formation under physiological conditions, and reveals a new neurotrophic function for the apoE 25-kDa fragment.
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Affiliation(s)
- Sonia Sanz Muñoz
- From the Illawarra Health and Medical Research Institute and
- the School of Biological Sciences, University of Wollongong, New South Wales 2522, Australia and
| | - Hongyun Li
- From the Illawarra Health and Medical Research Institute and
- the School of Biological Sciences, University of Wollongong, New South Wales 2522, Australia and
| | - Kalani Ruberu
- From the Illawarra Health and Medical Research Institute and
- the School of Biological Sciences, University of Wollongong, New South Wales 2522, Australia and
| | - Qian Chu
- the Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Alan Saghatelian
- the Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Lezanne Ooi
- From the Illawarra Health and Medical Research Institute and
- the School of Biological Sciences, University of Wollongong, New South Wales 2522, Australia and
| | - Brett Garner
- From the Illawarra Health and Medical Research Institute and
- the School of Biological Sciences, University of Wollongong, New South Wales 2522, Australia and
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25
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Wysocka M, Sychowska K, Gruba N, Winiarski Ł, Skoreński M, Psurski M, Makowska J, Giełdoń A, Wenta T, Jarząb M, Glaza P, Zdancewicz J, Sieńczyk M, Lipińska B, Lesner A. Selection of Effective HTRA3 Activators Using Combinatorial Chemistry. ACS COMBINATORIAL SCIENCE 2017; 19:565-573. [PMID: 28741928 DOI: 10.1021/acscombsci.7b00051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Herein, we report selection, synthesis, and enzymatic evaluation of a peptidomimetic library able to increase proteolytic activity of HtrA3 (high temperature requirement A) protease. Iterative deconvolution in solution of synthesized modified pentapeptides yielded two potent HtrA3 activators acting in the micromolar range (HCOO-CH2O-C6H4-OCH2-CO-Tyr-Asn-Phe-His-Asn-OH and HCOO-CH2O-C6H4-OCH2-CO-Tyr-Asn-Phe-His-Glu-OH). Both compounds increased proteolysis of an artificial HtrA3 substrate over 40-fold in a selective manner. On the basis of molecular modeling, the selected compounds bind strongly to the PDZ domain.
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Affiliation(s)
| | - Kamila Sychowska
- Faculty
of Chemistry, University of Gdansk, PL80952 Gdansk, Poland
| | - Natalia Gruba
- Faculty
of Chemistry, University of Gdansk, PL80952 Gdansk, Poland
| | - Łukasz Winiarski
- Faculty
of Chemistry, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Marcin Skoreński
- Faculty
of Chemistry, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Mateusz Psurski
- Department
of Experimental Oncology, Hirszfeld Institute of Immunology and Experimental
Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland
| | - Joanna Makowska
- Faculty
of Chemistry, University of Gdansk, PL80952 Gdansk, Poland
| | - Artur Giełdoń
- Faculty
of Chemistry, University of Gdansk, PL80952 Gdansk, Poland
| | - Tomasz Wenta
- Faculty
of Biology, University of Gdansk, PL80952 Gdansk, Poland
| | - Mirosław Jarząb
- Faculty
of Biology, University of Gdansk, PL80952 Gdansk, Poland
| | - Przemysław Glaza
- Faculty
of Biology, University of Gdansk, PL80952 Gdansk, Poland
| | | | - Marcin Sieńczyk
- Faculty
of Chemistry, Wroclaw University of Science and Technology, 50-370 Wroclaw, Poland
| | - Barbara Lipińska
- Faculty
of Biology, University of Gdansk, PL80952 Gdansk, Poland
| | - Adam Lesner
- Faculty
of Chemistry, University of Gdansk, PL80952 Gdansk, Poland
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26
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Wenta T, Glaza P, Jarząb M, Zarzecka U, Żurawa-Janicka D, Lesner A, Skórko-Glonek J, Lipińska B. The role of the LB structural loop and its interactions with the PDZ domain of the human HtrA3 protease. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017. [DOI: 10.1016/j.bbapap.2017.06.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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10-Gingerol as an inducer of apoptosis through HTR1A in cumulus cells: In-vitro and in-silico studies. J Taibah Univ Med Sci 2017; 12:397-406. [PMID: 31435270 PMCID: PMC6695051 DOI: 10.1016/j.jtumed.2017.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 05/17/2017] [Accepted: 05/21/2017] [Indexed: 12/20/2022] Open
Abstract
Objectives Cumulus cells play a crucial role as essential mediators in the maturation of ova. Ginger contains 10-gingerol, which induces apoptosis in colon cancer cells. Based on this hypothesis, this study aimed to determine whether 10-gingerol is able to induce apoptosis in normal cells, namely, cumulus cells. Methods This study used an in vitro analysis by culturing Cumulus cells in M199 containing 10-gingerol in various concentrations (12, 16, and 20 μM) and later detected early apoptotic activity using an Annexin V-FITC detection kit. Result The in vitro data revealed that the number of apoptosis cells increased along with the period of incubation as follows: 12 μM (63.71% ± 2.192%); 16 μM (74.51% ± 4.596%); and 20 μM (78.795% ± 1.435%). The substance 10-gingerol induces apoptosis in cumulus cells by inhibiting HTR1A functions and inactivating GSK3B and AKT-1. Conclusions These findings indicate that further examination is warranted for 10-gingerol as a contraception agent.
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Key Words
- 10-Gingerol
- ARG, arginine
- Apoptosis
- Cumulus cells
- FOXO, forkhead box
- GLU, glutamine
- GLY, glycine
- GSK3B, glycogen synthase kinase-3β
- HTR1A
- HTR1A, 5-hydroxytryptamine receptor 1 A
- ILE, ileusine
- ILK, integrin-linked kinase
- In silico
- In vitro
- LYS, lysine
- MDM2, murine double minute clone 2
- MET, methionine
- NO, nitric oxide
- NOS3, nitric oxide synthase 3
- PTEN, phosphatase and tensin homologue delete on chromosome ten
- RICTOR, rapamycin-insensitive companion of mTOR
- TYR, tyrosine
- eNOS, endothelial nitric oxide synthase
- mTOR, mammalian target of rapamycin
- mTORC1, mTOR complex 1
- mTORC2, mTOR complex 2
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Zurawa-Janicka D, Wenta T, Jarzab M, Skorko-Glonek J, Glaza P, Gieldon A, Ciarkowski J, Lipinska B. Structural insights into the activation mechanisms of human HtrA serine proteases. Arch Biochem Biophys 2017; 621:6-23. [PMID: 28396256 DOI: 10.1016/j.abb.2017.04.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 12/21/2022]
Abstract
Human HtrA1-4 proteins belong to the HtrA family of evolutionarily conserved serine proteases and function as important modulators of many physiological processes, including maintenance of mitochondrial homeostasis, cell signaling and apoptosis. Disturbances in their action are linked to severe diseases, including oncogenesis and neurodegeneration. The HtrA1-4 proteins share structural and functional features of other members of the HtrA protein family, however there are several significant differences in structural architecture and mechanisms of action which makes each of them unique. Our goal is to present recent studies regarding human HtrAs. We focus on their physiological functions, structure and regulation, and describe current models of activation mechanisms. Knowledge of molecular basis of the human HtrAs' action is a subject of great interest; it is crucial for understanding their relevance in cellular physiology and pathogenesis as well as for using them as targets in future therapies of diseases such as neurodegenerative disorders and cancer.
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Affiliation(s)
- Dorota Zurawa-Janicka
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland.
| | - Tomasz Wenta
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Miroslaw Jarzab
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Joanna Skorko-Glonek
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Przemyslaw Glaza
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Artur Gieldon
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Jerzy Ciarkowski
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Barbara Lipinska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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29
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Characterization of a metagenome-derived protease from contaminated agricultural soil microorganisms and its random mutagenesis. Folia Microbiol (Praha) 2017; 62:499-508. [PMID: 28382524 DOI: 10.1007/s12223-017-0522-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 03/17/2017] [Indexed: 12/28/2022]
Abstract
Proteases are typical key enzymes that hydrolyze proteins into amino acids and peptides. Numerous proteases have been studied, but the discovery of metagenome-derived proteases is still significant for both commercial applications and basic research. An unexplored protease gene sep1A was identified by function-based screening from a plasmid metagenomic library derived from uncultured contaminated agricultural soil microorganisms. The putative protease gene was subcloned into pET-32a (+) vector and overexpressed in E. coli BL21(DE3) pLysS, then the recombinant protein was purified to homogeneity. The detailed biochemical characterization of the Sep1A protein was performed, including its molecular characterization, specific activity, pH-activity profile, metal ion-activity profile, and enzyme kinetic assays. Furthermore, the protein engineering approach of random mutagenesis via error-prone PCR was applied on the original Sep1A protein. Biochemical characterization demonstrated that the purified recombinant Ep48 protein could hydrolyze casein. Compared with the original Sep1A protein, the best variant of Ep48 in the random mutagenesis library, with the Gln307Leu and Asp391Gly changes, exhibited 2.62-fold activity at the optimal reaction conditions of 50 °C and pH 9.0. These results are the first step toward a better understanding of the properties of Sep1A protein. Protein engineering with error-prone PCR paves the way toward the metagenome-derived genes for biotechnological applications.
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30
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Hershey DM, Browne PJ, Iavarone AT, Teyra J, Lee EH, Sidhu SS, Komeili A. Magnetite Biomineralization in Magnetospirillum magneticum Is Regulated by a Switch-like Behavior in the HtrA Protease MamE. J Biol Chem 2016; 291:17941-52. [PMID: 27302060 DOI: 10.1074/jbc.m116.731000] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 11/06/2022] Open
Abstract
Magnetotactic bacteria are aquatic organisms that produce subcellular magnetic particles in order to orient in the earth's geomagnetic field. MamE, a predicted HtrA protease required to produce magnetite crystals in the magnetotactic bacterium Magnetospirillum magneticum AMB-1, was recently shown to promote the proteolytic processing of itself and two other biomineralization factors in vivo Here, we have analyzed the in vivo processing patterns of three proteolytic targets and used this information to reconstitute proteolysis with a purified form of MamE. MamE cleaves a custom peptide substrate with positive cooperativity, and its autoproteolysis can be stimulated with exogenous substrates or peptides that bind to either of its PDZ domains. A misregulated form of the protease that circumvents specific genetic requirements for proteolysis causes biomineralization defects, showing that proper regulation of its activity is required during magnetite biosynthesis in vivo Our results represent the first reconstitution of the proteolytic activity of MamE and show that its behavior is consistent with the previously proposed checkpoint model for biomineralization.
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Affiliation(s)
| | | | - Anthony T Iavarone
- the California Institute for Quantitative Biosciences, and the QB3/Chemistry Mass Spectrometry Facility, and the University of California, Berkeley, California 94720 and
| | - Joan Teyra
- the Department of Molecular Genetics, Terrance Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | | | - Sachdev S Sidhu
- the Department of Molecular Genetics, Terrance Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Arash Komeili
- From the Departments of Plant and Microbial Biology and the California Institute for Quantitative Biosciences, and Molecular and Cell Biology,
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31
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Dou SF, Liu H, Cao TM, Wen QL, Li J, Shao QC. Structure-Based Design of a Br Halogen Bond at the Complex Interface of the Human Placental HtrA1 PDZ Domain with Its Heptapeptide Ligand. Arch Pharm (Weinheim) 2016; 349:302-7. [PMID: 26972470 DOI: 10.1002/ardp.201500466] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 11/06/2022]
Abstract
The shock-induced serine protease HtrA1 is a potential regulator of human placenta development during pregnancy. The protein contains a functional PDZ domain that has been solved in complex with a phage display-derived heptapeptide: Asp-6 Ser-5 Arg-4 Ile-3 Trp-2 Trp-1 Val0 . In this study, a rationally designed halogen bond was introduced to the domain-peptide complex based on its NMR structure in solution. We computationally compared the stabilization energies and hindrance effects due to the presence of different halogens X (X = F, Cl, Br, or I), using a hybrid quantum mechanics/molecular mechanics (QM/MM) approach, and found that the Br atom could considerably promote the peptide binding free energy (ΔΔG = -5.2 kcal/mol). Fluorescence assays confirmed that the peptide affinity to the HtrA1 PDZ domain was improved by approximately sevenfold upon bromination. Structural analysis identified a geometrically perfect halogen bond between the Br atom of the peptide Trp-1 residue and the carbonyl O atom of the HtrA1 Ile385 residue, with a bond length and an interaction energy of d = 3.20 Å and ΔE = -3.7 kcal/mol, respectively.
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Affiliation(s)
- Shuo-Fen Dou
- Catheter Room, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Hong Liu
- Department of Obstetrics, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Tong-Mei Cao
- Department of Obstetrics, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Qing-Li Wen
- Department of Obstetrics, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Jie Li
- Department of Obstetrics, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Qing-Chun Shao
- Department of Obstetrics, Affiliated Hospital of Weifang Medical University, Weifang, China
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32
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Solution structure of Q388A3 PDZ domain from Trypanosoma brucei. J Struct Biol 2016; 194:214-7. [PMID: 26917351 DOI: 10.1016/j.jsb.2016.02.018] [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: 01/27/2016] [Revised: 02/18/2016] [Accepted: 02/20/2016] [Indexed: 11/23/2022]
Abstract
PDZ domains are abundant protein interaction modules that often recognize short amino acid motifs at the C-termini of target proteins and regulate multiple biological processes. So far, no PDZ domain in Trypanosoma brucei, an eukaryotic parasite causing sleeping sickness, has been studied. Q388A3, conserved in the related kinetoplastid parasites, is a 1634-residue protein containing a PDZ domain at its C-terminus. In this work, the solution structure of Q388A3 PDZ domain was solved by NMR spectroscopy. Q388A3 PDZ domain adopts a PDZ-like fold composed by a five-stranded β-sheet capped by two α-helices, which is similar to the PDZ domains from HtrA family proteins. Meanwhile, Q388A3 PDZ domain shows some structural features quite different from HtrA PDZ domain.
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33
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Liu H, Dou SF, Zhang X, Wang Y, Wen QL, Mu YN. Rational Improvement of Peptide Affinity to Human Pregnancy-Related Serine Protease HtrA3 PDZ Domain by Introducing a Halogen Bond to the Domain–Peptide Complex Interface. Int J Pept Res Ther 2016. [DOI: 10.1007/s10989-016-9516-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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34
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Maksimchuk KR, Alser KA, Mou R, Valdivia RH, McCafferty DG. The Chlamydia trachomatis Protease CPAF Contains a Cryptic PDZ-Like Domain with Similarity to Human Cell Polarity and Tight Junction PDZ-Containing Proteins. PLoS One 2016; 11:e0147233. [PMID: 26829550 PMCID: PMC4734761 DOI: 10.1371/journal.pone.0147233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/30/2015] [Indexed: 12/31/2022] Open
Abstract
The need for more effective anti-chlamydial therapeutics has sparked research efforts geared toward further understanding chlamydial pathogenesis mechanisms. Recent studies have implicated the secreted chlamydial serine protease, chlamydial protease-like activity factor (CPAF) as potentially important for chlamydial pathogenesis. By mechanisms that remain to be elucidated, CPAF is directed to a discrete group of substrates, which are subsequently cleaved or degraded. While inspecting the previously solved CPAF crystal structure, we discovered that CPAF contains a cryptic N-terminal PSD95 Dlg ZO-1 (PDZ) domain spanning residues 106–212 (CPAF106-212). This PDZ domain is unique in that it bears minimal sequence similarity to canonical PDZ-forming sequences and displays little sequence and structural similarity to known chlamydial PDZ domains. We show that the CPAF106-212 sequence is homologous to PDZ domains of human tight junction proteins.
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Affiliation(s)
- Kenneth R. Maksimchuk
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Katherine A. Alser
- Department of Chemistry, Duke University, Durham, North Carolina, United States of America
| | - Rui Mou
- Department of Chemistry, Duke University, Durham, North Carolina, United States of America
| | - Raphael H. Valdivia
- Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America
| | - Dewey G. McCafferty
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Chemistry, Duke University, Durham, North Carolina, United States of America
- * E-mail:
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35
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Ciferri C, Lipari MT, Liang WC, Estevez A, Hang J, Stawicki S, Wu Y, Moran P, Elliott M, Eigenbrot C, Katschke KJ, van Lookeren Campagne M, Kirchhofer D. The trimeric serine protease HtrA1 forms a cage-like inhibition complex with an anti-HtrA1 antibody. Biochem J 2015; 472:169-81. [PMID: 26385991 DOI: 10.1042/bj20150601] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 09/17/2015] [Indexed: 12/17/2022]
Abstract
High temperature requirement A1 (HtrA1) is a trypsin-fold serine protease implicated in the progression of age-related macular degeneration (AMD). Our interest in an antibody therapy to neutralize HtrA1 faces the complication that the target adopts a trimeric arrangement, with three active sites in close proximity. In the present study, we describe antibody 94, obtained from a human antibody phage display library, which forms a distinct macromolecular complex with HtrA1 and inhibits the enzymatic activity of recombinant and native HtrA1 forms. Using biochemical methods and negative-staining EM we were able to elucidate the molecular composition of the IgG94 and Fab94 complexes and the associated inhibition mechanism. The 246-kDa complex between the HtrA1 catalytic domain trimer (HtrA1_Cat) and Fab94 had a propeller-like organization with one Fab bound peripherally to each protomer. Low-resolution EM structures and epitope mapping indicated that the antibody binds to the surface-exposed loops B and C of the catalytic domain, suggesting an allosteric inhibition mechanism. The HtrA1_Cat-IgG94 complex (636 kDa) is a cage-like structure with three centrally located IgG94 molecules co-ordinating two HtrA1_Cat trimers and the six active sites pointing into the cavity of the cage. In both complexes, all antigen-recognition regions (paratopes) are found to bind one HtrA1 protomer and all protomers are bound by a paratope, consistent with the complete inhibition of enzyme activity. Therefore, in addition to its potential therapeutic usefulness, antibody 94 establishes a new paradigm of multimeric serine protease inhibition.
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Affiliation(s)
- Claudio Ciferri
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, U.S.A
| | - Michael T Lipari
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, U.S.A
| | - Wei-Ching Liang
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, U.S.A
| | - Alberto Estevez
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, U.S.A
| | - Julie Hang
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, U.S.A
| | - Scott Stawicki
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, U.S.A
| | - Yan Wu
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, U.S.A
| | - Paul Moran
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, U.S.A
| | - Mike Elliott
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, U.S.A
| | - Charles Eigenbrot
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, U.S.A
| | - Kenneth J Katschke
- Department of Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, U.S.A
| | | | - Daniel Kirchhofer
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, U.S.A.
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Glaza P, Osipiuk J, Wenta T, Zurawa-Janicka D, Jarzab M, Lesner A, Banecki B, Skorko-Glonek J, Joachimiak A, Lipinska B. Structural and Functional Analysis of Human HtrA3 Protease and Its Subdomains. PLoS One 2015; 10:e0131142. [PMID: 26110759 PMCID: PMC4481513 DOI: 10.1371/journal.pone.0131142] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/27/2015] [Indexed: 11/18/2022] Open
Abstract
Human HtrA3 protease, which induces mitochondria-mediated apoptosis, can be a tumor suppressor and a potential therapeutic target in the treatment of cancer. However, there is little information about its structure and biochemical properties. HtrA3 is composed of an N-terminal domain not required for proteolytic activity, a central serine protease domain and a C-terminal PDZ domain. HtrA3S, its short natural isoform, lacks the PDZ domain which is substituted by a stretch of 7 C-terminal amino acid residues, unique for this isoform. This paper presents the crystal structure of the HtrA3 protease domain together with the PDZ domain (ΔN-HtrA3), showing that the protein forms a trimer whose protease domains are similar to those of human HtrA1 and HtrA2. The ΔN-HtrA3 PDZ domains are placed in a position intermediate between that in the flat saucer-like HtrA1 SAXS structure and the compact pyramidal HtrA2 X-ray structure. The PDZ domain interacts closely with the LB loop of the protease domain in a way not found in other human HtrAs. ΔN-HtrA3 with the PDZ removed (ΔN-HtrA3-ΔPDZ) and an N-terminally truncated HtrA3S (ΔN-HtrA3S) were fully active at a wide range of temperatures and their substrate affinity was not impaired. This indicates that the PDZ domain is dispensable for HtrA3 activity. As determined by size exclusion chromatography, ΔN-HtrA3 formed stable trimers while both ΔN-HtrA3-ΔPDZ and ΔN-HtrA3S were monomeric. This suggests that the presence of the PDZ domain, unlike in HtrA1 and HtrA2, influences HtrA3 trimer formation. The unique C-terminal sequence of ΔN-HtrA3S appeared to have little effect on activity and oligomerization. Additionally, we examined the cleavage specificity of ΔN-HtrA3. Results reported in this paper provide new insights into the structure and function of ΔN-HtrA3, which seems to have a unique combination of features among human HtrA proteases.
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Affiliation(s)
- Przemyslaw Glaza
- Department of Biochemistry, Faculty of Biology, University of Gdansk, 80–308 Gdansk, Poland
| | - Jerzy Osipiuk
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, IL 60439, United States of America
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois, IL 60439, United States of America
| | - Tomasz Wenta
- Department of Biochemistry, Faculty of Biology, University of Gdansk, 80–308 Gdansk, Poland
| | - Dorota Zurawa-Janicka
- Department of Biochemistry, Faculty of Biology, University of Gdansk, 80–308 Gdansk, Poland
| | - Miroslaw Jarzab
- Department of Biochemistry, Faculty of Biology, University of Gdansk, 80–308 Gdansk, Poland
| | - Adam Lesner
- Department of Biochemistry, Faculty of Chemistry, University of Gdansk, 80–308 Gdansk, Poland
| | - Bogdan Banecki
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology of the University of Gdansk and the Medical University of Gdansk, 80–822 Gdansk, Poland
| | - Joanna Skorko-Glonek
- Department of Biochemistry, Faculty of Biology, University of Gdansk, 80–308 Gdansk, Poland
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois, IL 60439, United States of America
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois, IL 60439, United States of America
| | - Barbara Lipinska
- Department of Biochemistry, Faculty of Biology, University of Gdansk, 80–308 Gdansk, Poland
- * E-mail:
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A Structural Portrait of the PDZ Domain Family. J Mol Biol 2014; 426:3509-19. [DOI: 10.1016/j.jmb.2014.08.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 08/06/2014] [Accepted: 08/12/2014] [Indexed: 11/18/2022]
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38
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Singh H, Nero TL, Wang Y, Parker MW, Nie G. Activity-modulating monoclonal antibodies to the human serine protease HtrA3 provide novel insights into regulating HtrA proteolytic activities. PLoS One 2014; 9:e108235. [PMID: 25248123 PMCID: PMC4172569 DOI: 10.1371/journal.pone.0108235] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 08/27/2014] [Indexed: 11/18/2022] Open
Abstract
Mammalian HtrA (high temperature requirement factor A) proteases, comprising 4 multi-domain members HtrA1-4, play important roles in a number of normal cellular processes as well as pathological conditions such as cancer, arthritis, neurodegenerative diseases and pregnancy disorders. However, how HtrA activities are regulated is not well understood, and to date no inhibitors specific to individual HtrA proteins have been identified. Here we investigated five HtrA3 monoclonal antibodies (mAbs) that we have previously produced, and demonstrated that two of them regulated HtrA3 activity in an opposing fashion: one inhibited while the other stimulated. The inhibitory mAb also blocked HtrA3 activity in trophoblast cells and enhanced migration and invasion, confirming its potential in vivo utility. To understand how the binding of these mAbs modulated HtrA3 protease activity, their epitopes were visualized in relation to a 3-dimensional HtrA3 homology model. This model suggests that the inhibitory HtrA3 mAb blocks substrate access to the protease catalytic site, whereas the stimulatory mAb may bind to the PDZ domain alone or in combination with the N-terminal and protease domains. Since HtrA1, HtrA3 and HtrA4 share identical domain organization, our results establish important foundations for developing potential therapeutics to target these HtrA proteins specifically for the treatment of a number of diseases, including cancer and pregnancy disorders.
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Affiliation(s)
- Harmeet Singh
- MIMR-PHI Institute of Medical Research, Clayton, Victoria, Australia
- Monash University, Clayton, Victoria, Australia
- * E-mail: (GN); (HS)
| | - Tracy L. Nero
- ACRF Rational Drug Discovery Centre, St Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Yao Wang
- MIMR-PHI Institute of Medical Research, Clayton, Victoria, Australia
- Monash University, Clayton, Victoria, Australia
| | - Michael W. Parker
- ACRF Rational Drug Discovery Centre, St Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, the University of Melbourne, Parkville, Victoria, Australia
| | - Guiying Nie
- MIMR-PHI Institute of Medical Research, Clayton, Victoria, Australia
- Monash University, Clayton, Victoria, Australia
- * E-mail: (GN); (HS)
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Risør MW, Poulsen ET, Thomsen LR, Dyrlund T, Nielsen TA, Nielsen NC, Sanggaard KW, Enghild JJ. The autolysis of human HtrA1 is governed by the redox state of its N-terminal domain. Biochemistry 2014; 53:3851-7. [PMID: 24846539 PMCID: PMC4067144 DOI: 10.1021/bi401633w] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 05/20/2014] [Indexed: 01/07/2023]
Abstract
Human HtrA1 (high-temperature requirement protein A1) belongs to a conserved family of serine proteases involved in protein quality control and cell fate. The homotrimeric ubiquitously expressed protease has chymotrypsin-like specificity and primarily targets hydrophobic stretches in selected or misfolded substrate proteins. In addition, the enzyme is capable of exerting autolytic activity by removing the N-terminal insulin-like growth factor binding protein (IGFBP)/Kazal-like tandem motif without affecting the protease activity. In this study, we have addressed the mechanism governing the autolytic activity and find that it depends on the integrity of the disulfide bonds in the N-terminal IGFBP/Kazal-like domain. The specificity of the autolytic cleavage reveals a strong preference for cysteine in the P1 position of HtrA1, explaining the lack of autolysis prior to disulfide reduction. Significantly, the disulfides were reduced by thioredoxin, suggesting that autolysis of HtrA1 in vivo is linked to the endogenous redox balance and that the N-terminal domain acts as a redox-sensing switch.
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Affiliation(s)
- Michael W. Risør
- Department
of Molecular Biology and Genetics, Aarhus
University, DK-8000 Aarhus, Denmark
- Centre
for Insoluble Protein Structures (inSPIN), Aarhus University, DK-8000 Aarhus, Denmark
| | - Ebbe Toftgaard Poulsen
- Department
of Molecular Biology and Genetics, Aarhus
University, DK-8000 Aarhus, Denmark
| | - Line R. Thomsen
- Department
of Molecular Biology and Genetics, Aarhus
University, DK-8000 Aarhus, Denmark
| | - Thomas
F. Dyrlund
- Department
of Molecular Biology and Genetics, Aarhus
University, DK-8000 Aarhus, Denmark
| | - Tania A. Nielsen
- Department
of Molecular Biology and Genetics, Aarhus
University, DK-8000 Aarhus, Denmark
| | - Niels Chr. Nielsen
- Centre
for Insoluble Protein Structures (inSPIN), Aarhus University, DK-8000 Aarhus, Denmark
- Department
of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - Kristian W. Sanggaard
- Department
of Molecular Biology and Genetics, Aarhus
University, DK-8000 Aarhus, Denmark
| | - Jan J. Enghild
- Department
of Molecular Biology and Genetics, Aarhus
University, DK-8000 Aarhus, Denmark
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Holcomb J, Jiang Y, Guan X, Trescott L, Lu G, Hou Y, Wang S, Brunzelle J, Sirinupong N, Li C, Yang Z. Crystal structure of the NHERF1 PDZ2 domain in complex with the chemokine receptor CXCR2 reveals probable modes of PDZ2 dimerization. Biochem Biophys Res Commun 2014; 448:169-74. [PMID: 24768637 DOI: 10.1016/j.bbrc.2014.04.085] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 04/16/2014] [Indexed: 01/19/2023]
Abstract
The formation of CXCR2-NHERF1-PLCβ2 macromolecular complex in neutrophils regulates CXCR2 signaling and plays a key role in neutrophil chemotaxis and transepithelial neutrophilic migration. However, NHERF1 by itself, with only two PDZ domains, has a limited capacity in scaffolding the multiprotein-complex formation. Here we report the crystal structure of the NHERF1 PDZ2 domain in complex with the C-terminal CXCR2 sequence. The structure reveals that the PDZ2-CXCR2 binding specificity is achieved by numerous hydrogen bonds and hydrophobic contacts with the last four CXCR2 residues contributing to specific interactions. The structure also reveals two probable modes of PDZ2 dimerization where the two canonical ligand-binding pockets are well separated and orientated in a unique parallel fashion. This study provides not only the structural basis for the PDZ-mediated NHERF1-CXCR2 interaction, but also an additional example of how PDZ domains may dimerize, which both could prove valuable in understanding NHERF1 complex-scaffolding function in neutrophils.
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Affiliation(s)
- Joshua Holcomb
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Yuanyuan Jiang
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Xiaoqing Guan
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Laura Trescott
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Guorong Lu
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Yuning Hou
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Shuo Wang
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA
| | | | - Nualpun Sirinupong
- Nutraceuticals and Functional Food Research and Development Center, Prince of Songkla University, Hat-Yai, Songkhla, Thailand
| | - Chunying Li
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA.
| | - Zhe Yang
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA.
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41
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Crystallographic analysis of NHERF1–PLCβ3 interaction provides structural basis for CXCR2 signaling in pancreatic cancer. Biochem Biophys Res Commun 2014; 446:638-43. [PMID: 24642259 DOI: 10.1016/j.bbrc.2014.03.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 03/09/2014] [Indexed: 01/25/2023]
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42
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Holcomb J, Jiang Y, Lu G, Trescott L, Brunzelle J, Sirinupong N, Li C, Naren AP, Yang Z. Structural insights into PDZ-mediated interaction of NHERF2 and LPA(2), a cellular event implicated in CFTR channel regulation. Biochem Biophys Res Commun 2014; 446:399-403. [PMID: 24613836 DOI: 10.1016/j.bbrc.2014.02.128] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 02/27/2014] [Indexed: 12/22/2022]
Abstract
The formation of CFTR-NHERF2-LPA2 macromolecular complex in airway epithelia regulates CFTR channel function and plays an important role in compartmentalized cAMP signaling. We previously have shown that disruption of the PDZ-mediated NHERF2-LPA2 interaction abolishes the LPA inhibitory effect and augments CFTR Cl(-) channel activity in vitro and in vivo. Here we report the first crystal structure of the NHERF2 PDZ1 domain in complex with the C-terminal LPA2 sequence. The structure reveals that the PDZ1-LPA2 binding specificity is achieved by numerous hydrogen bonds and hydrophobic contacts with the last four LPA2 residues contributing to specific interactions. Comparison of the PDZ1-LPA2 structure to the structure of PDZ1 in complex with a different peptide provides insights into the diverse nature of PDZ1 substrate recognition and suggests that the conformational flexibility in the ligand binding pocket is involved in determining the broad substrate specificity of PDZ1. In addition, the structure reveals a small surface pocket adjacent to the ligand-binding site, which may have therapeutic implications. This study provides an understanding of the structural basis for the PDZ-mediated NHERF2-LPA2 interaction that could prove valuable in selective drug design against CFTR-related human diseases.
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Affiliation(s)
- Joshua Holcomb
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Yuanyuan Jiang
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Guorong Lu
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Laura Trescott
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA
| | | | - Nualpun Sirinupong
- Nutraceuticals and Functional Food Research and Development Center, Prince of Songkla University, Hat-Yai, Songkhla, Thailand
| | - Chunying Li
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Anjaparavanda P Naren
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
| | - Zhe Yang
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI, USA.
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43
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Mu Y, Cai P, Hu S, Ma S, Gao Y. Characterization of diverse internal binding specificities of PDZ domains by yeast two-hybrid screening of a special peptide library. PLoS One 2014; 9:e88286. [PMID: 24505465 PMCID: PMC3913781 DOI: 10.1371/journal.pone.0088286] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 01/09/2014] [Indexed: 01/07/2023] Open
Abstract
Protein-protein interactions (PPIs) are essential events to play important roles in a series of biological processes. There are probably more ways of PPIs than we currently realized. Structural and functional investigations of weak PPIs have lagged behind those of strong PPIs due to technical difficulties. Weak PPIs are often short-lived, which may result in more dynamic signals with important biological roles within and/or between cells. For example, the characteristics of PSD-95/Dlg/ZO-1 (PDZ) domain binding to internal sequences, which are primarily weak interactions, have not yet been systematically explored. In the present study, we constructed a nearly random octapeptide yeast two-hybrid library. A total of 24 PDZ domains were used as baits for screening the library. Fourteen of these domains were able to bind internal PDZ-domain binding motifs (PBMs), and PBMs screened for nine PDZ domains exhibited strong preferences. Among 11 PDZ domains that have not been reported their internal PBM binding ability, six were confirmed to bind internal PBMs. The first PDZ domain of LNX2, which has not been reported to bind C-terminal PBMs, was found to bind internal PBMs. These results suggest that the internal PBMs binding ability of PDZ domains may have been underestimated. The data provided diverse internal binding properties for several PDZ domains that may help identify their novel binding partners.
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Affiliation(s)
- Yi Mu
- National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, P.R. China
| | - Pengfei Cai
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Siqi Hu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Sucan Ma
- National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, P.R. China
| | - Youhe Gao
- National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, P.R. China
- * E-mail:
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44
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Jiang Y, Lu G, Trescott LR, Hou Y, Guan X, Wang S, Stamenkovich A, Brunzelle J, Sirinupong N, Li C, Yang Z. New conformational state of NHERF1-CXCR2 signaling complex captured by crystal lattice trapping. PLoS One 2013; 8:e81904. [PMID: 24339979 PMCID: PMC3858284 DOI: 10.1371/journal.pone.0081904] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 10/18/2013] [Indexed: 11/18/2022] Open
Abstract
NHERF1 is a PDZ adaptor protein that scaffolds the assembly of diverse signaling complexes and has been implicated in many cancers. However, little is known about the mechanism responsible for its scaffolding promiscuity or its ability to bind to multiple targets. Computational studies have indicated that PDZ promiscuity may be attributed to its conformational dynamics, but experimental evidence for this relationship remains very limited. Here we examine the conformational flexibility of the NHERF1 PDZ1 domain using crystal lattice trapping via solving PDZ1 structure of a new crystal form. The structure, together with prior PDZ1 structures of a different space group, reveals that 4 of 11 ligand-interacting residues undergo significant crystal packing-induced structural changes. Most of these residues correspond to the residues involved in allosteric transition when a peptide ligand binds. In addition, a subtle difference in ligand conformations causes the same peptide to bind in slightly different modes in different crystal forms. These findings indicate that substantial structural flexibility is present in the PDZ1 peptide-binding pocket, and the structural substate trapped in the present crystal form can be utilized to represent the conformational space accessible to the protein. Such knowledge will be critical for drug design against the NHERF1 PDZ1 domain, highlighting the continued need for experimentally determined PDZ1-ligand complexes.
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Affiliation(s)
- Yuanyuan Jiang
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Guorong Lu
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Laura R. Trescott
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Yuning Hou
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Xiaoqing Guan
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Shuo Wang
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Angelique Stamenkovich
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Joseph Brunzelle
- Advance Photon Source, Argonne National Lab, Argonne, Illinois, United States of America
| | - Nualpun Sirinupong
- Nutraceuticals and Functional Food Research and Development Center, Prince of Songkla University, Hat-Yai, Songkhla, Thailand
| | - Chunying Li
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- * E-mail: (ZY); (CL)
| | - Zhe Yang
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- * E-mail: (ZY); (CL)
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45
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Lu G, Wu Y, Jiang Y, Wang S, Hou Y, Guan X, Brunzelle J, Sirinupong N, Sheng S, Li C, Yang Z. Structural insights into neutrophilic migration revealed by the crystal structure of the chemokine receptor CXCR2 in complex with the first PDZ domain of NHERF1. PLoS One 2013; 8:e76219. [PMID: 24098448 PMCID: PMC3788737 DOI: 10.1371/journal.pone.0076219] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 08/21/2013] [Indexed: 11/17/2022] Open
Abstract
Neutrophil plays an essential role in host defense against infection, but uncontrolled neutrophilic infiltration can cause inflammation and severe epithelial damage. We recently showed that CXCR2 formed a signaling complex with NHERF1 and PLC-2, and that the formation of this complex was required for intracellular calcium mobilization and neutrophilic transepithelial migration. To uncover the structural basis of the complex formation, we report here the crystal structure of the NHERF1 PDZ1 domain in complex with the C-terminal sequence of CXCR2 at 1.16 Å resolution. The structure reveals that the CXCR2 peptide binds to PDZ1 in an extended conformation with the last four residues making specific side chain interactions. Remarkably, comparison of the structure to previously studied PDZ1 domains has allowed the identification of PDZ1 ligand-specific interactions and the mechanisms that govern PDZ1 target selection diversities. In addition, we show that CXCR2 can bind both NHERF1 PDZ1 and PDZ2 in pulldown experiments, consistent with the observation that the peptide binding pockets of these two PDZ domains are highly structurally conserved. The results of this study therefore provide structural basis for the CXCR2-mediated neutrophilic migration and could have important clinical applications in the prevention and treatment of numerous neutrophil-dependent inflammatory disorders.
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Affiliation(s)
- Guorong Lu
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
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Bejugam PR, Kuppili RR, Singh N, Gadewal N, Chaganti LK, Sastry GM, Bose K. Allosteric regulation of serine protease HtrA2 through novel non-canonical substrate binding pocket. PLoS One 2013; 8:e55416. [PMID: 23457469 PMCID: PMC3573033 DOI: 10.1371/journal.pone.0055416] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 12/22/2012] [Indexed: 11/24/2022] Open
Abstract
HtrA2, a trimeric proapoptotic serine protease is involved in several diseases including cancer and neurodegenerative disorders. Its unique ability to mediate apoptosis via multiple pathways makes it an important therapeutic target. In HtrA2, C-terminal PDZ domain upon substrate binding regulates its functions through coordinated conformational changes the mechanism of which is yet to be elucidated. Although allostery has been found in some of its homologs, it has not been characterized in HtrA2 so far. Here, with an in silico and biochemical approach we have shown that allostery does regulate HtrA2 activity. Our studies identified a novel non-canonical selective binding pocket in HtrA2 which initiates signal propagation to the distal active site through a complex allosteric mechanism. This non-classical binding pocket is unique among HtrA family proteins and thus unfolds a novel mechanism of regulation of HtrA2 activity and hence apoptosis.
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Affiliation(s)
- Pruthvi Raj Bejugam
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Raja R. Kuppili
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Nitu Singh
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Nikhil Gadewal
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | - Lalith K. Chaganti
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | | | - Kakoli Bose
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India
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47
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Koide S, Huang J. Generation of high-performance binding proteins for peptide motifs by affinity clamping. Methods Enzymol 2013; 523:285-302. [PMID: 23422435 DOI: 10.1016/b978-0-12-394292-0.00013-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
We describe concepts and methodologies for generating "Affinity Clamps," a new class of recombinant binding proteins that achieve high affinity and high specificity toward short peptide motifs of biological importance, which is a major challenge in protein engineering. The Affinity Clamping concept exploits the potential of nonhomologous recombination of protein domains in generating large changes in protein function and the inherent binding affinity and specificity of the so-called modular interaction domains toward short peptide motifs. Affinity Clamping creates a clamshell architecture that clamps onto a target peptide. The design processes involve (i) choosing a starting modular interaction domain appropriate for the target and applying structure-guided modifications; (ii) attaching a second domain, termed "enhancer domain"; and (iii) optimizing the peptide-binding site located between the domains by directed evolution. The two connected domains work synergistically to achieve high levels of affinity and specificity that are unattainable with either domain alone. Because of the simple and modular architecture, Affinity Clamps are particularly well suited as building blocks for designing more complex functionalities. Affinity Clamping represents a major advance in protein design that is broadly applicable to the recognition of peptide motifs.
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Affiliation(s)
- Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, USA.
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Wang LJ, Cheong ML, Lee YS, Lee MT, Chen H. High-temperature requirement protein A4 (HtrA4) suppresses the fusogenic activity of syncytin-1 and promotes trophoblast invasion. Mol Cell Biol 2012; 32:3707-17. [PMID: 22778138 PMCID: PMC3430202 DOI: 10.1128/mcb.00223-12] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 07/03/2012] [Indexed: 11/20/2022] Open
Abstract
Cell-cell fusion and cell invasion are essential for placental development. Human cytotrophoblasts in the chorionic villi may undergo cell-cell fusion to form syncytiotrophoblasts to facilitate nutrient-gas exchange or differentiate into extravillous trophoblasts (EVTs) to facilitate maternal-fetal circulation. The placental transcription factor glial cells missing 1 (GCM1) regulates syncytin-1 and -2 expression to mediate trophoblast fusion. Interestingly, GCM1 and syncytin-1 are also expressed in EVTs with unknown physiological functions. In this study, we performed chromatin immunoprecipitation-on-chip (ChIP-chip) analysis and identified the gene for high-temperature requirement protein A4 (HtrA4) as a GCM1 target gene, which encodes a serine protease facilitating cleavage of fibronectin and invasion of placental cells. Importantly, HtrA4 is immunolocalized in EVTs at the maternal-fetal interface, and its expression is decreased by hypoxia and in preeclampsia, a pregnancy complication associated with placental hypoxia and shallow trophoblast invasion. We further demonstrate that HtrA4 interacts with syncytin-1 and suppresses cell-cell fusion. Therefore, HtrA4 may be crucial for EVT differentiation by playing a dual role in prevention of cell-cell fusion of EVTs and promotion of their invasion into the uterus. Our study reveals a novel function of GCM1 and HtrA4 in regulation of trophoblast invasion and that abnormal HrtA4 expression may contribute to shallow trophoblast invasion in preeclampsia.
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Affiliation(s)
- Liang-Jie Wang
- Graduate Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Mei-Leng Cheong
- Graduate Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Department of Obstetrics and Gynecology, Cathay General Hospital, Taipei, Taiwan
| | - Yun-Shien Lee
- Department of Biotechnology, Ming Chuan University, Tao-Yuan, Taiwan
| | - Ming-Ting Lee
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei, Taiwan
| | - Hungwen Chen
- Graduate Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei, Taiwan
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Affiliation(s)
- David J Huggins
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Hills Road, Cambridge, CB2 0XZ, United Kingdom.
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Composition and proteolytic processing of corneal deposits associated with mutations in the TGFBI gene. Exp Eye Res 2011; 96:163-70. [PMID: 22155582 DOI: 10.1016/j.exer.2011.11.014] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 09/22/2011] [Accepted: 11/17/2011] [Indexed: 11/21/2022]
Abstract
Different types of granular corneal dystrophy (GCD) and lattice corneal dystrophy (LCD) are associated with mutations in the transforming growth factor beta induced gene (TGFBI). These dystrophies are characterized by the formation of non-amyloid granular deposits (GCDs) and amyloid (LCD type 1 and its variants) in the cornea. Typical corneal non-amyloid deposits from GCD type 2 (R124H), amyloid from a variant of LCD type 1 (V624M) and disease-free tissue controls were procured by laser capture microdissection and analyzed by tandem mass spectrometry. Label-free quantitative comparisons of deposits and controls suggested that the non-amyloid sample (R124H) specifically accumulated transforming growth factor beta induced protein (TGFBIp/keratoepithelin/βig-h3), serum amyloid P-component, clusterin, type III collagen, keratin 3, and histone H3-like protein. The amyloid (V624M) similarly accumulated serum amyloid P-component and clusterin but also a C-terminal fragment of TGFBIp containing residues Y571-R588 derived from the fourth fasciclin-1 domain (FAS1-4), apolipoprotein E and apolipoprotein A-IV. Significantly, analyses of the amyloid sample also revealed the presence of the serine protease Htr (High-temperature requirement) A1 and a number of proteolytic cleavage sites in the FAS1-4 domain of TGFBIp. These cleavage sites were consistent with the ligand binding and proteolytic activity of HtrA1 suggesting that it plays a role in the proteolytic processing of the amyloidogenic FAS1-4 domain. Taken together, the data suggest that the amyloidogenic-prone region of the fourth FAS1 domain of TGFBIp encompasses the Y571-R588 peptide and that HtrA1 is involved in the proteolytic processing of TGFBIp-derived amyloid in vivo.
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