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Christensen LF, Høie MH, Bang-Berthelsen CH, Marcatili P, Hansen EB. Comparative Structure Analysis of the Multi-Domain, Cell Envelope Proteases of Lactic Acid Bacteria. Microorganisms 2023; 11:2256. [PMID: 37764099 PMCID: PMC10535647 DOI: 10.3390/microorganisms11092256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Lactic acid bacteria (LAB) have an extracellular proteolytic system that includes a multi-domain, cell envelope protease (CEP) with a subtilisin homologous protease domain. These CEPs have different proteolytic activities despite having similar protein sequences. Structural characterization has previously been limited to CEP homologs of dairy- and human-derived LAB strains, excluding CEPs of plant-derived LAB strains. CEP structures are a challenge to determine experimentally due to their large size and attachment to the cell envelope. This study aims to clarify the prevalence and structural diversity of CEPs by using the structure prediction software AlphaFold 2. Domain boundaries are clarified based on a comparative analysis of 21 three-dimensional structures, revealing novel domain architectures of CEP homologs that are not necessarily restricted to specific LAB species or ecological niches. The C-terminal flanking region of the protease domain is divided into fibronectin type-III-like domains with various structural traits. The analysis also emphasizes the existence of two distinct domains for cell envelope attachment that are preceded by an intrinsically disordered cell wall spanning domain. The domain variants and their combinations provide CEPs with different stability, proteolytic activity, and potentially adhesive properties, making CEPs targets for steering proteolytic activity with relevance for both food development and human health.
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Affiliation(s)
- Lise Friis Christensen
- National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800 Kongens Lyngby, Denmark
| | - Magnus Haraldson Høie
- Department of Health Technology, Technical University of Denmark, Ørsteds Plads, DK-2800 Kongens Lyngby, Denmark
| | | | - Paolo Marcatili
- Department of Health Technology, Technical University of Denmark, Ørsteds Plads, DK-2800 Kongens Lyngby, Denmark
| | - Egon Bech Hansen
- National Food Institute, Technical University of Denmark, Kemitorvet, DK-2800 Kongens Lyngby, Denmark
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2
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Auto- and Hetero-Catalytic Processing of the N-Terminal Propeptide Promotes the C-Terminal Fibronectin Type III Domain-Mediated Dimerization of a Thermostable Vpr-like Protease. Appl Environ Microbiol 2022; 88:e0150322. [PMID: 36250702 PMCID: PMC9642013 DOI: 10.1128/aem.01503-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial Vpr-like proteases are extracellular multidomain subtilases with diverse functions and can form oligomers, but their maturation and oligomerization mechanisms remain to be elucidated. Here, we report a novel Vpr-like protease (BTV) from thermophilic bacterium Brevibacillus sp. WF146. The BTV precursor comprises a signal peptide, an N-terminal propeptide, a subtilisin-like catalytic domain with an inserted protease-associated (PA) domain, two tandem fibronectin type III domains (Fn1 and Fn2), and a C-terminal propeptide. The BTV proform (pro-BTV) could be autoprocessed into the mature form (mBTV) via two intermediates lacking the N- or C-terminal propeptide, respectively, and the C-terminal propeptide delays the autocatalytic maturation of the enzyme. By comparison, pro-BTV is more efficiently processed into mBTV by protease TSS from strain WF146. Purified mBTV is a Ca2+-dependent thermostable protease, showing optimal activity at 60°C and retaining more than 60% of activity after incubation at 60°C for 8 h. The PA domain is important for enzyme stability and contributes to the substrate specificity of BTV by restricting the access of protein substrates to the active site. The proform and mature form of BTV exist as a monomer and a homodimer, respectively, and the dimerization is mediated by the Fn1 and Fn2 domains. The N-terminal propeptide of BTV not only acts as intramolecular chaperone and enzymatic inhibitor but also inhibits the homodimerization of the enzyme. The removal of the N-terminal propeptide leads to a structural adjustment of the enzyme and thus promotes enzyme dimerization. IMPORTANCE Vpr-like proteases are widely distributed in bacteria and fungi and are involved in processing lantibiotics, degrading collagen, keratin, and fibrin, and pathogenesis of microbes. The dissection of the roles of individual domains in enzyme maturation and oligomerization is crucial for understanding the action mechanisms of these multidomain proteases. Our results demonstrate that hetero-catalytic maturation of the extracellular Vpr-like protease BTV of Brevibacillus sp. WF146 is more efficient than autocatalytic maturation of the enzyme. Moreover, we found that the C-terminal tandem fibronectin type III domains rather than the PA domain mediate the dimerization of mature BTV, while the N-terminal propeptide inhibits the dimerization of the BTV proform. This study provides new insight into the activation and oligomerization mechanisms of Vpr-like proteases.
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Jain M, Teçza M, Kagawa TF, Cooney JC. Exosite binding modulates the specificity of the immunomodulatory enzyme ScpA, a C5a inactivating bacterial protease. Comput Struct Biotechnol J 2022; 20:4860-4869. [PMID: 36147677 PMCID: PMC9464890 DOI: 10.1016/j.csbj.2022.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/07/2022] [Accepted: 08/07/2022] [Indexed: 11/03/2022] Open
Abstract
C5a, the human complement protein is implicated in COVID-19 and sepsis. Proteolytic inactivation of C5a by ScpA involves interactions with a novel exosite. High affinity binding of C5a is shown to involve D783 of the ScpA Fn2 domain. Activity and affinity of ScpA is tuned by residues approx 50 Å from the active site. The data supports a complex dynamic process in ScpA substrate recognition.
The C5a peptidase from Streptococcus pyogenes (ScpA) is a highly specific enzyme with potential therapeutic value. ScpA is a good model for studying determinants of specificity in the multidomain immunomodulatory enzymes (IMEs), which comprise a large family of bacterial surface proteases. The surface exposed region of ScpA has 5 main domains which includes 3 C-terminal Fn3-like domains (Fn1, Fn2 and Fn3) (Kagawa et al. 2009). Progressive deletion of the Fn3-like domains from the C-ter resulted in loss of enzyme activity and showed an important role for the Fn2 domain in enzyme function. Functional investigation of specific acidic residues on the Fn2 domain identified 3 residues 30–50 Å from the catalytic site (D783, E864 and D889) which impacted to differing degrees on binding and on catalysis, supporting the presence of an exosite on the Fn2. In particular, residue D783 was observed to impact on both substrate binding affinity and the activity of ScpA. A double mutant cycle analysis showed energetic coupling between the targeted ScpA residues and residues in the core portion (residues 1–67) of the C5a substrate. The data supports the presence of a communication network between the active site and the exosite on Fn2. These findings provide a basis for rational engineering of this important enzyme family to enhance stability, activity and/or specificity.
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Teçza M, Kagawa TF, Jain M, Cooney JC. Enzyme kinetic and binding studies identify determinants of specificity for the immunomodulatory enzyme ScpA, a C5a inactivating bacterial protease. Comput Struct Biotechnol J 2021; 19:2356-2365. [PMID: 33897974 PMCID: PMC8052502 DOI: 10.1016/j.csbj.2021.04.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 11/30/2022] Open
Abstract
The human complement protein C5a is implicated in immunomodulatory diseases. ScpA, a C5a inactivating protease, represents a novel enzymatic approach to therapy. High-affinity ScpA specificity for C5a is driven by C5a core-exosite interactions. 3 Arginines in the C5a core, and electrostatic interactions contribute to binding. These studies are first steps in the development of novel immunomodulatory therapies.
The Streptococcal C5a peptidase (ScpA) specifically inactivates the human complement factor hC5a, a potent anaphylatoxin recently identified as a therapeutic target for treatment of COVID-19 infections. Biologics used to modulate hC5a are predominantly monoclonal antibodies. Here we present data to support an alternative therapeutic approach based on the specific inactivation of hC5a by ScpA in studies using recombinant hC5a (rhC5a). Initial characterization of ScpA confirmed activity in human serum and against rhC5a desArg (rhC5adR), the predominant hC5a form in blood. A new FRET based enzyme assay showed that ScpA cleaved rhC5a at near physiological concentrations (Km 185 nM). Surface Plasmon Resonance (SPR) and Isothermal Titration Calorimetry (ITC) studies established a high affinity ScpA-rhC5a interaction (KD 34 nM, KDITC 30.8 nM). SPR analyses also showed that substrate binding is dominated (88% of ΔG°bind) by interactions with the bulky N-ter cleavage product (PN, ’core’ residues 1–67) with interactions involving the C-ter R74 contributing most of the remaining ΔG°bind. Furthermore, reduced binding affinity following mutation of a subset of positively charged Arginine residues of PN and in the presence of higher salt concentrations, highlighted the importance of electrostatic interactions. These data provide the first in-depth study of the ScpA-C5a interaction and indicate that ScpA’s ability to efficiently cleave physiological concentrations of C5a is driven by electrostatic interactions between an exosite on the enzyme and the ‘core’ of C5a. The results and methods described herein will facilitate engineering of ScpA to enhance its potential as a therapeutic for excessive immune response to infectious disease.
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Affiliation(s)
- Malgorzata Teçza
- Department of Chemical Sciences, University of Limerick, Limerick, Ireland
| | - Todd F Kagawa
- Department of Biological Sciences, University of Limerick, Limerick, Ireland.,SSPC, University of Limerick, Ireland
| | - Monica Jain
- Department of Biological Sciences, University of Limerick, Limerick, Ireland
| | - Jakki C Cooney
- Department of Biological Sciences, University of Limerick, Limerick, Ireland.,Bernal Institute, University of Limerick, Limerick, Ireland.,SSPC, University of Limerick, Ireland
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5
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Hansen EB, Marcatili P. Modeled Structure of the Cell Envelope Proteinase of Lactococcus lactis. Front Bioeng Biotechnol 2021; 8:613986. [PMID: 33415101 PMCID: PMC7783315 DOI: 10.3389/fbioe.2020.613986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 12/02/2020] [Indexed: 11/23/2022] Open
Abstract
The cell envelope proteinase (CEP) of Lactococcus lactis is a large extracellular protease covalently linked to the peptidoglycan of the cell wall. Strains of L. lactis are typically auxotrophic for several amino acids and in order to grow to high cell densities in milk they need an extracellular protease. The structure of the entire CEP enzyme is difficult to determine experimentally due to the large size and due to the attachment to the cell surface. We here describe the use of a combination of structure prediction tools to create a structural model for the entire CEP enzyme of Lactococcus lactis. The model has implications for how the bacterium interacts with casein micelles during growth in milk, and it has implications regarding the energetics of the proteolytic system. Our model for the CEP indicates that the catalytic triad is activated through a structural change caused by interaction with the substrate. The CEP of L. lactis might become a useful model for the mode of action for enzymes belonging to the large class of S8 proteinases with a PA (protease associated) domain and a downstream fibronectin like domain.
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Affiliation(s)
- Egon Bech Hansen
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Demark
| | - Paolo Marcatili
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Demark
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6
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Naumann TA, Naldrett MJ, Price NPJ. Kilbournase, a protease-associated domain subtilase secreted by the fungal corn pathogen Stenocarpella maydis. Fungal Genet Biol 2020; 141:103399. [PMID: 32387407 DOI: 10.1016/j.fgb.2020.103399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/23/2020] [Accepted: 04/30/2020] [Indexed: 10/24/2022]
Abstract
Subtilases are a large family of serine proteases that occur throughout biology. A small subset contain protease-associated (PA) domains that are structurally separate from but encoded within the active site. In bacteria, subtilase PA domains function to recruit specific protein substrates. Here we demonstrate that a protease secreted by the fungal corn pathogen Stenocarpella maydis, which truncates corn ChitA chitinase, is a PA domain subtilase. Protease was purified from S. maydis cultures and tryptic peptides were analyzed by LC-MS/MS. Ions were mapped to two predicted PA domain subtilases. Yeast strains were engineered to express each protease. One failed to produce recombinant protein while the other secreted protease that truncated ChitA. This protease, that we named kilbournase, was purified and characterized. It cleaved multiple peptide bonds in the amino-terminal chitin binding domain of ChitA while leaving the catalytic domain intact. Kilbournase was more active on the ChitA-B73 alloform compared to ChitA-LH82 and did not cleave AtChitIV3, a homolog from Arabidopsis thaliana, indicating a high level of specificity. Truncation of corn ChitA by kilbournase resembles truncation of human C5a by Streptococcus pyogenes ScpA, arguing that PA domain proteases in bacteria and fungi may commonly target specific host proteins.
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Affiliation(s)
- Todd A Naumann
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agriculture Utilization Research, Peoria, IL 61604, United States.
| | - Michael J Naldrett
- Nebraska Center for Biotechnology, Beadle Center, University of Nebraska-Lincoln, Lincoln, NE 68588, United States
| | - Neil P J Price
- Renewable Product Technology Research Unit, National Center for Agriculture Utilization Research, Peoria, IL 61604, United States
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Schaller A, Stintzi A, Rivas S, Serrano I, Chichkova NV, Vartapetian AB, Martínez D, Guiamét JJ, Sueldo DJ, van der Hoorn RAL, Ramírez V, Vera P. From structure to function - a family portrait of plant subtilases. THE NEW PHYTOLOGIST 2018; 218:901-915. [PMID: 28467631 DOI: 10.1111/nph.14582] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/13/2017] [Indexed: 05/20/2023]
Abstract
Contents Summary 901 I. Introduction 901 II. Biochemistry and structure of plant SBTs 902 III. Phylogeny of plant SBTs and family organization 903 IV. Physiological roles of plant SBTs 905 V. Conclusions and outlook 911 Acknowledgements 912 References 912 SUMMARY: Subtilases (SBTs) are serine peptidases that are found in all three domains of life. As compared with homologs in other Eucarya, plant SBTs are more closely related to archaeal and bacterial SBTs, with which they share many biochemical and structural features. However, in the course of evolution, functional diversification led to the acquisition of novel, plant-specific functions, resulting in the present-day complexity of the plant SBT family. SBTs are much more numerous in plants than in any other organism, and include enzymes involved in general proteolysis as well as highly specific processing proteases. Most SBTs are targeted to the cell wall, where they contribute to the control of growth and development by regulating the properties of the cell wall and the activity of extracellular signaling molecules. Plant SBTs affect all stages of the life cycle as they contribute to embryogenesis, seed development and germination, cuticle formation and epidermal patterning, vascular development, programmed cell death, organ abscission, senescence, and plant responses to their biotic and abiotic environments. In this article we provide a comprehensive picture of SBT structure and function in plants.
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Affiliation(s)
- Andreas Schaller
- Institute of Plant Physiology and Biotechnology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Annick Stintzi
- Institute of Plant Physiology and Biotechnology, University of Hohenheim, Stuttgart, 70593, Germany
| | - Susana Rivas
- Laboratoire des Interactions Plantes-Microorganismes, LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, 31326, France
| | - Irene Serrano
- Laboratoire des Interactions Plantes-Microorganismes, LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, 31326, France
| | - Nina V Chichkova
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Andrey B Vartapetian
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
| | - Dana Martínez
- Instituto de Fisiología Vegetal, Universidad Nacional de La Plata, La Plata, 1900, Argentina
| | - Juan J Guiamét
- Instituto de Fisiología Vegetal, Universidad Nacional de La Plata, La Plata, 1900, Argentina
| | - Daniela J Sueldo
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Vicente Ramírez
- Institute for Plant Cell Biology and Biotechnology, Heinrich-Heine University, Düsseldorf, 40225, Germany
| | - Pablo Vera
- Institute for Plant Molecular and Cell Biology, Universidad Politécnica de Valencia-CSIC, Valencia, 46022, Spain
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Li HJ, Tang BL, Shao X, Liu BX, Zheng XY, Han XX, Li PY, Zhang XY, Song XY, Chen XL. Characterization of a New S8 serine Protease from Marine Sedimentary Photobacterium sp. A5-7 and the Function of Its Protease-Associated Domain. Front Microbiol 2016; 7:2016. [PMID: 28066343 PMCID: PMC5177683 DOI: 10.3389/fmicb.2016.02016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/01/2016] [Indexed: 11/13/2022] Open
Abstract
Bacterial extracellular proteases are important for bacterial nutrition and marine sedimentary organic nitrogen degradation. However, only a few proteases from marine sedimentary bacteria have been characterized. Some subtilases have a protease-associated (PA) domain inserted in the catalytic domain. Although structural analysis and deletion mutation suggests that the PA domain in subtilases is involved in substrate binding, direct evidence to support this function is still absent. Here, a protease, P57, secreted by Photobacterium sp. A5-7 isolated from marine sediment was characterized. P57 could hydrolyze casein, gelatin and collagen. It showed the highest activity at 40°C and pH 8.0. P57 is a new subtilase, with 63% sequence identity to the closest characterized protease. Mature P57 contains a catalytic domain and an inserted PA domain. The recombinant PA domain from P57 was shown to have collagen-binding ability, and Phe349 and Tyr432 were revealed to be key residues for collagen binding in the PA domain. This study first shows direct evidence that the PA domain of a subtilase can bind substrate, which provides a better understanding of the function of the PA domain of subtilases and bacterial extracellular proteases from marine sediment.
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Affiliation(s)
- Hui-Juan Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
- College of Chemical and Environmental Engineering, Shandong University of Science and TechnologyQingdao, China
| | - Bai-Lu Tang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Xuan Shao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Bai-Xue Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Xiao-Yu Zheng
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Xiao-Xu Han
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Institute of Marine Science and Technology, Shandong UniversityJinan, China
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Zebisch M, Jones EY. ZNRF3/RNF43--A direct linkage of extracellular recognition and E3 ligase activity to modulate cell surface signalling. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 118:112-8. [PMID: 25937466 DOI: 10.1016/j.pbiomolbio.2015.04.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 01/16/2023]
Abstract
The interactions of extracellular ligands with single membrane spanning receptors, such as kinases, typically serve to agonise or antagonise the intracellular activation of signalling pathways. Within the cell, E3 ligases can act to alter the localisation and activity of proteins involved in signalling systems. Structural and functional characterisation of two closely related single membrane spanning molecules, RNF43 and ZNRF3, has recently revealed the receptor-like functionalities of a ligand-binding ectodomain combined with the intracellular architecture and activity of an E3 ligase. This direct link provides a hereto novel mechanism for extracellular control of ubiquitin ligase activity that is used for the modulation of Wnt signalling, a pathway of major importance in embryogenesis, stem cell biology and cancer. In this review we discuss recent findings for the structure and interactions of the extracellular region of RNF43/ZNRF3 and draw parallels with the properties and function of signalling receptor ectodomains.
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Affiliation(s)
- Matthias Zebisch
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom.
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Børsting M, Qvist K, Brockmann E, Vindeløv J, Pedersen T, Vogensen F, Ardö Y. Classification of Lactococcus lactis cell envelope proteinase based on gene sequencing, peptides formed after hydrolysis of milk, and computer modeling. J Dairy Sci 2015; 98:68-77. [DOI: 10.3168/jds.2014-8517] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 09/02/2014] [Indexed: 11/19/2022]
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Original features of cell-envelope proteinases of Lactobacillus helveticus. A review. Int J Food Microbiol 2011; 146:1-13. [DOI: 10.1016/j.ijfoodmicro.2011.01.039] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 01/24/2011] [Accepted: 01/26/2011] [Indexed: 11/23/2022]
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12
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Collagenolytic subtilisin-like protease from the deep-sea bacterium Alkalimonas collagenimarina AC40T. Appl Microbiol Biotechnol 2009; 86:589-98. [DOI: 10.1007/s00253-009-2324-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Revised: 10/18/2009] [Accepted: 10/19/2009] [Indexed: 10/20/2022]
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13
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Kagawa TF, O'Connell MR, Mouat P, Paoli M, O'Toole PW, Cooney JC. Model for Substrate Interactions in C5a Peptidase from Streptococcus pyogenes: A 1.9 Å Crystal Structure of the Active Form of ScpA. J Mol Biol 2009; 386:754-72. [DOI: 10.1016/j.jmb.2008.12.074] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Revised: 12/18/2008] [Accepted: 12/29/2008] [Indexed: 10/21/2022]
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14
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Lineberry N, Su L, Soares L, Fathman CG. The single subunit transmembrane E3 ligase gene related to anergy in lymphocytes (GRAIL) captures and then ubiquitinates transmembrane proteins across the cell membrane. J Biol Chem 2008; 283:28497-505. [PMID: 18713730 DOI: 10.1074/jbc.m805092200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ubiquitin E3 ligase gene related to anergy in lymphocytes (GRAIL) (Rnf128) is a type 1 transmembrane protein that induces T cell anergy through the ubiquitination activity of its cytosolic RING finger. GRAIL also contains an equally large luminal region consisting primarily of an uncharacterized protease-associated (PA) domain. Using two-hybrid technology to screen for proteins that bound the PA domain we identified CD151, a member of the tetraspanin family of membrane proteins. GRAIL bound to the luminal/extracellular portion of both CD151 and the related tetraspanin CD81 using its PA domain, which promoted ubiquitination of cytosolic lysine residues. GRAIL exhibited specificity for lysines only within the tetraspanin amino terminus even in the presence of other cytosolic lysine residues in the substrate. GRAIL-mediated ubiquitination promoted proteasomal degradation and cell surface down-regulation of tetraspanins via Lys-48 linkages. As a result, the juxtaposition of PA and RING finger domains across a lipid bilayer facilitates the capture of transmembrane substrates for subsequent ubiquitination. These findings identify for the first time a single subunit E3 ligase containing a substrate-binding domain spatially restricted by a membrane from its E2 recruitment domain as well as an E3 ligase for members of the tetraspanin family.
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Affiliation(s)
- Neil Lineberry
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California 94305, USA
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Pastar I, Tonic I, Golic N, Kojic M, van Kranenburg R, Kleerebezem M, Topisirovic L, Jovanovic G. Identification and genetic characterization of a novel proteinase, PrtR, from the human isolate Lactobacillus rhamnosus BGT10. Appl Environ Microbiol 2004; 69:5802-11. [PMID: 14532028 PMCID: PMC201213 DOI: 10.1128/aem.69.10.5802-5811.2003] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel proteinase, PrtR, produced by the human vaginal isolate Lactobacillus rhamnosus strain BGT10 was identified and genetically characterized. The prtR gene and flanking regions were cloned and sequenced. The deduced amino acid sequence of PrtR shares characteristics that are common for other cell envelope proteinases (CEPs) characterized to date, but in contrast to the other cell surface subtilisin-like serine proteinases, it has a smaller and somewhat different B domain and lacks the helix domain, and the anchor domain has a rare sorting signal sequence. Furthermore, PrtR lacks the insert domain, which otherwise is situated inside the catalytic serine protease domain of all CEPs, and has a different cell wall spacer (W) domain similar to that of the cell surface antigen I and II polypeptides expressed by oral and vaginal streptococci. Moreover, the PrtR W domain exhibits significant sequence homology to the consensus sequence that has been shown to be the hallmark of human intestinal mucin protein. According to its alpha(S1)- and beta-casein cleavage efficacy, PrtR is an efficient proteinase at pH 6.5 and is distributed throughout all L. rhamnosus strains tested. Proteinase extracts of the BGT10 strain obtained with Ca(2+)-free buffer at pH 6.5 were proteolytically active. The prtR promoter-like sequence was determined, and the minimal promoter region was defined by use of prtR-gusA operon fusions. The prtR expression is Casitone dependent, emphasizing that nitrogen depletion elevates its transcription. This is in correlation with the catalytic activity of the PrtR proteinase.
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Affiliation(s)
- Irena Pastar
- Institute of Molecular Genetics and Genetic Engineering, 11001 Belgrade, Serbia and Montenegro. Wageningen Centre for Food Sciences, 6700 AN Wageningen. NIZO Food Research, 6710 BA Ede, The Netherlands
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16
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Exterkate FA, Slangen C, Siezen RJ. Effect of genetically modified Lactococcus lactis cell-envelope proteinases with altered specificity on the course of casein degradation under cheese conditions. Int Dairy J 2001. [DOI: 10.1016/s0958-6946(01)00065-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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17
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Abstract
We have identified a similarity between the apical domain of the human transferrin receptor and several other protein families. This domain is found associated with two different families of peptidases. Therefore, we term it the PA domain for protease-associated domain. The PA domain is found inserted within a loop of the peptidase domain of family M8/M33 zinc peptidases. The PA domain is also found in a vacuolar sorting receptor and a ring finger protein of unknown function that may be a cell surface receptor. The PA domain may mediate substrate determination of peptidases or form protein-protein interactions.
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Affiliation(s)
- P Mahon
- Department of Biochemistry, University of Cambridge, United Kingdom
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18
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Bruinenberg PG, De Vos WM, Siezen RJ. Deletion of various carboxy-terminal domains of Lactococcus lactis SK11 proteinase: effects on activity, specificity, and stability of the truncated enzyme. Appl Environ Microbiol 2000; 66:2859-65. [PMID: 10877779 PMCID: PMC92084 DOI: 10.1128/aem.66.7.2859-2865.2000] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Lactococcus lactis SK11 cell envelope proteinase is an extracellular, multidomain protein of nearly 2,000 residues consisting of an N-terminal serine protease domain, followed by various other domains of largely unknown function. Using a strategy of deletion mutagenesis, we have analyzed the function of several C-terminal domains of the SK11 proteinase which are absent in cell envelope proteinases of other lactic acid bacteria. The various deletion mutants were functionally expressed in L. lactis and analyzed for enzyme stability, activity, (auto)processing, and specificity toward several substrates. C-terminal deletions of first the cell envelope W (wall) and AN (anchor) domains and then the H (helix) domain leads to fully active, secreted proteinases of unaltered specificity. Gradually increasing the C-terminal deletion into the so-called B domain leads to increasing instability and autoproteolysis and progressively less proteolytic activity. However, the mutant with the largest deletion (838 residues) from the C terminus and lacking the entire B domain still retains proteolytic activity. All truncated enzymes show unaltered proteolytic specificity toward various substrates. This suggests that the main role played by these domains is providing stability or protection from autoproteolysis (B domain), spacing away from the cell (H domain), and anchoring to the cell envelope (W and AN domains). In addition, this study allowed us to more precisely map the main C-terminal autoprocessing site of the SK11 proteinase and the epitope for binding of group IV monoclonal antibodies.
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19
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Pederson JA, Mileski GJ, Weimer BC, Steele JL. Genetic characterization of a cell envelope-associated proteinase from Lactobacillus helveticus CNRZ32. J Bacteriol 1999; 181:4592-7. [PMID: 10419958 PMCID: PMC103591 DOI: 10.1128/jb.181.15.4592-4597.1999] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A cell envelope-associated proteinase gene (prtH) was identified in Lactobacillus helveticus CNRZ32. The prtH gene encodes a protein of 1,849 amino acids and with a predicted molecular mass of 204 kDa. The deduced amino acid sequence of the prtH product has significant identity (45%) to that of the lactococcal PrtP proteinases. Southern blot analysis indicates that prtH is not broadly distributed within L. helveticus. A prtH deletion mutant of CNRZ32 was constructed to evaluate the physiological role of PrtH. PrtH is not required for rapid growth or fast acid production in milk by CNRZ32. Cell surface proteinase activity and specificity were determined by hydrolysis of alpha(s1)-casein fragment 1-23 by whole cells. A comparison of CNRZ32 and its prtH deletion mutant indicates that CNRZ32 has at least two cell surface proteinases that differ in substrate specificity.
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Affiliation(s)
- J A Pederson
- Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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20
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Kulakova L, Galkin A, Kurihara T, Yoshimura T, Esaki N. Cold-active serine alkaline protease from the psychrotrophic bacterium Shewanella strain ac10: gene cloning and enzyme purification and characterization. Appl Environ Microbiol 1999; 65:611-7. [PMID: 9925590 PMCID: PMC91069 DOI: 10.1128/aem.65.2.611-617.1999] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gene encoding serine alkaline protease (SapSh) of the psychrotrophic bacterium Shewanella strain Ac10 was cloned in Escherichia coli. The amino acid sequence deduced from the 2,442-bp nucleotide sequence revealed that the protein was 814 amino acids long and had an estimated molecular weight of 85,113. SapSh exhibited sequence similarities with members of the subtilisin family of proteases, and there was a high level of conservation in the regions around a putative catalytic triad consisting of Asp-30, His-65, and Ser-369. The amino acid sequence contained the following regions which were assigned on the basis of homology to previously described sequences: a signal peptide (26 residues), a propeptide (117 residues), and an extension up to the C terminus (about 250 residues). Another feature of SapSh is the fact that the space between His-65 and Ser-369 is approximately 150 residues longer than the corresponding spaces in other proteases belonging to the subtilisin family. SapSh was purified to homogeneity from the culture supernatant of E. coli recombinant cells by affinity chromatography with a bacitracin-Sepharose column. The recombinant SapSh (rSapSh) was found to have a molecular weight of about 44,000 and to be highly active in the alkaline region (optimum pH, around 9.0) when azocasein and synthetic peptides were used as substrates. rSapSh was characterized by its high levels of activity at low temperatures; it was five times more active than subtilisin Carlsberg at temperatures ranging from 5 to 15 degreesC. The activation energy for hydrolysis of azocasein by rSapSh was much lower than the activation energy for hydrolysis of azocasein by the subtilisin. However, rSapSh was far less stable than the subtilisin.
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Affiliation(s)
- L Kulakova
- Institute for Chemical Research, Kyoto University, Uji, Kyoto-Fu 611, Japan
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Abstract
Subtilases are members of the clan (or superfamily) of subtilisin-like serine proteases. Over 200 subtilases are presently known, more than 170 of which with their complete amino acid sequence. In this update of our previous overview (Siezen RJ, de Vos WM, Leunissen JAM, Dijkstra BW, 1991, Protein Eng 4:719-731), details of more than 100 new subtilases discovered in the past five years are summarized, and amino acid sequences of their catalytic domains are compared in a multiple sequence alignment. Based on sequence homology, a subdivision into six families is proposed. Highly conserved residues of the catalytic domain are identified, as are large or unusual deletions and insertions. Predictions have been updated for Ca(2+)-binding sites, disulfide bonds, and substrate specificity, based on both sequence alignment and three-dimensional homology modeling.
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Affiliation(s)
- R J Siezen
- Department of Biophysical Chemistry, NIZO, Ede, The Netherlands.
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22
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Exterkate FA. The lactococcal cell envelope proteinases: Differences, calcium-binding effects and role in cheese ripening. Int Dairy J 1995. [DOI: 10.1016/0958-6946(95)00042-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Bruinenberg PG, de Vos WM, Siezen RJ. Prevention of C-terminal autoprocessing of Lactococcus lactis SK11 cell-envelope proteinase by engineering of an essential surface loop. Biochem J 1994; 302 ( Pt 3):957-63. [PMID: 7945226 PMCID: PMC1137323 DOI: 10.1042/bj3020957] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The catalytic domain of the cell-envelope proteinase from Lactococcus lactis SK11 has various inserts, situated in external loops of the catalytic domain, compared with the related subtilisins. Protein engineering was employed to analyse the necessity and function of one of these extra loops (residues 205-219), that is predicted to be located in close proximity to the substrate-binding region and is susceptible to autoproteolysis. We constructed a deletion mutant which lacks 14 residues of this surface loop and subsequently introduced various insertion cassettes coding either for the original loop with three mutations (E205S/E218T/M219S: triple-mutant proteinase) or for neutral spacers (1, 4, 7 and 16 serine residues). Engineered proteinases were analysed for activity, (auto)processing, and cleavage specificity. The presence of residues 205-219 is shown to be essential for proteolytic activity, as only triple-mutant proteinase retained activity towards casein substrates. The triple-mutant proteinase was found to be defective in C-terminal autoprocessing, and subsequent release from the lactococcal cell envelope in a calcium-free medium, indicative of either an altered proteolytic specificity or altered accessibility of the processing site. The specificity change appears to be subtle, as only small differences were found between wild-type and triple-mutant proteinase in the breakdown of casein substrates.
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Affiliation(s)
- P G Bruinenberg
- Department of Biophysical Chemistry, NIZO, Ede, The Netherlands
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