1
|
Jeon H, Han AR, Oh S, Park JG, Namkoong M, Bang KM, Kim HM, Kim NK, Hwang KY, Hur K, Lee BJ, Heo J, Kim S, Song HK, Cho H, Lee IG. Polymorphic Self-Assembly with Procedural Flexibility for Monodisperse Quaternary Protein Structures of DegQ Enzymes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2308837. [PMID: 38351715 DOI: 10.1002/adma.202308837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/08/2024] [Indexed: 02/29/2024]
Abstract
As large molecular tertiary structures, some proteins can act as small robots that find, bind, and chaperone target protein clients, showing the potential to serve as smart building blocks in self-assembly fields. Instead of using such intrinsic functions, most self-assembly methodologies for proteins aim for de novo-designed structures with accurate geometric assemblies, which can limit procedural flexibility. Here, a strategy enabling polymorphic clustering of quaternary proteins, exhibiting simplicity and flexibility of self-assembling paths for proteins in forming monodisperse quaternary cage particles is presented. It is proposed that the enzyme protomer DegQ, previously solved at low resolution, may potentially be usable as a threefold symmetric building block, which can form polyhedral cages incorporated by the chaperone action of DegQ in the presence of protein clients. To obtain highly monodisperse cage particles, soft, and hence, less resistive client proteins, which can program the inherent chaperone activity of DegQ to efficient formations of polymorphic cages, depending on the size of clients are utilized. By reconstructing the atomic resolution cryogenic electron microscopy DegQ structures using obtained 12- and 24-meric clusters, the polymorphic clustering of DegQ enzymes is validated in terms of soft and rigid domains, which will provide effective routes for protein self-assemblies with procedural flexibility.
Collapse
Affiliation(s)
- Hanul Jeon
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Ah-Reum Han
- Center for Biomolecular and Cellular Structure, Life Science Cluster, Institute for Basic Science (IBS), 55, Expo-ro, Daejeon, 34126, Republic of Korea
| | - Sangmin Oh
- Extreme Materials Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Jin-Gyeong Park
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Myeong Namkoong
- Extreme Materials Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Kyeong-Mi Bang
- Advanced Analysis Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
- Department of Life Science, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Ho Min Kim
- Center for Biomolecular and Cellular Structure, Life Science Cluster, Institute for Basic Science (IBS), 55, Expo-ro, Daejeon, 34126, Republic of Korea
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291, Daehak-ro, Daejeon, 34126, Republic of Korea
| | - Nak-Kyoon Kim
- Advanced Analysis Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Kwang Yeon Hwang
- Department of Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Kahyun Hur
- Extreme Materials Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Science, Seoul National University, 599, Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
- College of Pharmacy, Ajou University, 206, Worldcup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 16499, Republic of Korea
| | - Jeongyun Heo
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Sehoon Kim
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Hyun Kyu Song
- Department of Life Science, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Hyesung Cho
- Extreme Materials Research Center, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - In-Gyun Lee
- Biomedical Research Division, Korea Institute of Science and Technology, 5, Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| |
Collapse
|
2
|
Vargas-Gasca F, Franco B, Vargas-Maya NI, Vicente-Gómez M, Olmedo-Monfil V. Pseudomonas environmental strain produces a DegQ-derived and PDZ domain containing peptide with protease activity. Antonie Van Leeuwenhoek 2024; 117:41. [PMID: 38400879 DOI: 10.1007/s10482-024-01939-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 01/28/2024] [Indexed: 02/26/2024]
Abstract
In the search of new enzymatic activities with a possible industrial application, we focused on those microorganisms and their molecular mechanisms that allow them to succeed in the environment, particularly in the proteolytic activity and its central role in the microorganisms' successful permanence. The use of highly active serine proteases for industrial applications is a modern need, especially for the formulation of detergents, protein processing, and hair removal from animal skins. This report provides the isolation and identification of a highly proteolytic fragment derived from DegQ produced by a Pseudomonas fluorescens environmental strain isolated from a frog carcass. Zymograms demonstrate that a 10 kDa protein mainly generates the total proteolytic activity of this strain, which is enhanced by the detergent SDS. Mass spectroscopy analysis revealed that the protein derived a couple of peptides, the ones showing the highest coverage belonging to DegQ. Interestingly, this small protein fragment contains a PDZ domain but no obvious residues indicating that it is a protease. Protein model analysis shows that this fragment corresponds to the main PDZ domain from DegQ, and its unique sequence and structure render a proteolytic peptide. The results presented here indicate that a novel DegQ fragment is sufficient for obtaining high protease activity highlighting that the analysis of environmental microorganisms can render new strains or enzymes with helpful biotechnological characteristics.
Collapse
Affiliation(s)
- Francisco Vargas-Gasca
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Noria Alta S/N, 36050, Guanajuato, GTO, México
| | - Bernardo Franco
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Noria Alta S/N, 36050, Guanajuato, GTO, México
| | - Naurú Idalia Vargas-Maya
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Noria Alta S/N, 36050, Guanajuato, GTO, México
| | - Marcos Vicente-Gómez
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Noria Alta S/N, 36050, Guanajuato, GTO, México
| | - Vianey Olmedo-Monfil
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Noria Alta S/N, 36050, Guanajuato, GTO, México.
| |
Collapse
|
3
|
Luo H, Qu X, Deng X, He L, Wu Y, Liu Y, He D, Yin J, Wang B, Gan F, Tang B, Tang XF. HtrAs are essential for the survival of the haloarchaeon Natrinema gari J7-2 in response to heat, high salinity, and toxic substances. Appl Environ Microbiol 2024; 90:e0204823. [PMID: 38289131 PMCID: PMC10880668 DOI: 10.1128/aem.02048-23] [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: 11/13/2023] [Accepted: 12/24/2023] [Indexed: 02/22/2024] Open
Abstract
Bacterial and eukaryotic HtrAs can act as an extracytoplasmic protein quality control (PQC) system to help cells survive in stress conditions, but the functions of archaeal HtrAs remain unknown. Particularly, haloarchaea route most secretory proteins to the Tat pathway, enabling them to fold properly in well-controlled cytoplasm with cytosolic PQC systems before secretion. It is unclear whether HtrAs are required for haloarchaeal survival and stress response. The haloarchaeon Natrinema gari J7-2 encodes three Tat signal peptide-bearing HtrAs (NgHtrA, NgHtrB, and NgHtrC), and the signal peptides of NgHtrA and NgHtrC contain a lipobox. Here, the in vitro analysis reveals that the three HtrAs show different profiles of temperature-, salinity-, and metal ion-dependent proteolytic activities and could exhibit chaperone-like activities to prevent the aggregation of reduced lysozyme when their proteolytic activities are inhibited at low temperatures or the active site is disrupted. The gene deletion and complementation assays reveal that NgHtrA and NgHtrC are essential for the survival of strain J7-2 at elevated temperature and/or high salinity and contribute to the resistance of this haloarchaeon to zinc and inhibitory substances generated from tryptone. Mutational analysis shows that the lipobox mediates membrane anchoring of NgHtrA or NgHtrC, and both the membrane-anchored and free extracellular forms of the two enzymes are involved in the stress resistance of strain J7-2, depending on the stress conditions. Deletion of the gene encoding NgHtrB in strain J7-2 causes no obvious growth defect, but NgHtrB can functionally substitute for NgHtrA or NgHtrC under some conditions.IMPORTANCEHtrA-mediated protein quality control plays an important role in the removal of aberrant proteins in the extracytoplasmic space of living cells, and the action mechanisms of HtrAs have been extensively studied in bacteria and eukaryotes; however, information about the function of archaeal HtrAs is scarce. Our results demonstrate that three HtrAs of the haloarchaeon Natrinema gari J7-2 possess both proteolytic and chaperone-like activities, confirming that the bifunctional nature of HtrAs is conserved across all three domains of life. Moreover, we found that NgHtrA and NgHtrC are essential for the survival of strain J7-2 under stress conditions, while NgHtrB can serve as a substitute for the other two HtrAs under certain circumstances. This study provides the first biochemical and genetic evidence of the importance of HtrAs for the survival of haloarchaea in response to stresses.
Collapse
Affiliation(s)
- Hongyi Luo
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaoyi Qu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xi Deng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Liping He
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yi Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yang Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Dan He
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jing Yin
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Bingxue Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Fei Gan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
- Cooperative Innovation Center of Industrial Fermentation, Ministry of Education and Hubei Province, Wuhan, China
| | - Bing Tang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Cooperative Innovation Center of Industrial Fermentation, Ministry of Education and Hubei Province, Wuhan, China
| | - Xiao-Feng Tang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
- Cooperative Innovation Center of Industrial Fermentation, Ministry of Education and Hubei Province, Wuhan, China
| |
Collapse
|
4
|
Kim JH, Lee GH, Jeong JH, Kim YG, Park HH. The structure of MucD from Pseudomonas syringae revealed N-terminal loop-mediated trimerization of HtrA-like serine protease. Biochem Biophys Res Commun 2023; 688:149175. [PMID: 37976815 DOI: 10.1016/j.bbrc.2023.149175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/19/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
Abstract
Protein quality control mechanisms are essential for maintaining cellular integrity, and the HtrA family of serine proteases plays a crucial role in handling folding stress in prokaryotic periplasm. Escherichia coli harbors three HtrA members, namely, DegS, DegP, and DegQ, which share a common domain structure. MucD, a putative HtrA family member that resembles DegP, is involved in alginate biosynthesis regulation and the stress response. Pseudomonas syringae causes plant diseases and opportunistic infections in humans. This study presents the high-resolution structure of MucD from Pseudomonas syringae (psMucD), revealing its composition as a typical HtrA family serine protease with protease and PDZ domains. Its findings suggest that psMucD containing one PDZ domain is a trimer in solution, and psMucD trimerization is mediated by its N-terminal loop. Sequence and structural analyses revealed similarities and differences with other HtrA family members. Additionally, this study provides a model of psMucD's catalytic process, comparing it with other members of the HtrA family of serine proteases.
Collapse
Affiliation(s)
- Ju Hyeong Kim
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Gwan Hee Lee
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jae-Hee Jeong
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, 790-784, Republic of Korea
| | - Yeon-Gil Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, 790-784, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, 06974, Republic of Korea.
| |
Collapse
|
5
|
González LJ, Bahr G, González MM, Bonomo RA, Vila AJ. In-cell kinetic stability is an essential trait in metallo-β-lactamase evolution. Nat Chem Biol 2023; 19:1116-1126. [PMID: 37188957 DOI: 10.1038/s41589-023-01319-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/21/2023] [Indexed: 05/17/2023]
Abstract
Protein stability is an essential property for biological function. In contrast to the vast knowledge on protein stability in vitro, little is known about the factors governing in-cell stability. Here we show that the metallo-β-lactamase (MBL) New Delhi MBL-1 (NDM-1) is a kinetically unstable protein on metal restriction that has evolved by acquiring different biochemical traits that optimize its in-cell stability. The nonmetalated (apo) NDM-1 is degraded by the periplasmic protease Prc that recognizes its partially unstructured C-terminal domain. Zn(II) binding renders the protein refractory to degradation by quenching the flexibility of this region. Membrane anchoring makes apo-NDM-1 less accessible to Prc and protects it from DegP, a cellular protease degrading misfolded, nonmetalated NDM-1 precursors. NDM variants accumulate substitutions at the C terminus that quench its flexibility, enhancing their kinetic stability and bypassing proteolysis. These observations link MBL-mediated resistance with the essential periplasmic metabolism, highlighting the importance of the cellular protein homeostasis.
Collapse
Affiliation(s)
- Lisandro J González
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina
- Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina
- Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Mariano M González
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina
- Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Robert A Bonomo
- Research Service, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, OH, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Medical Service and GRECC, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, OH, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina.
- Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA.
| |
Collapse
|
6
|
Frantz R, Gwozdzinski K, Gisch N, Doijad SP, Hudel M, Wille M, Abu Mraheil M, Schwudke D, Imirzalioglu C, Falgenhauer L, Ehrmann M, Chakraborty T. A Single Residue within the MCR-1 Protein Confers Anticipatory Resilience. Microbiol Spectr 2023; 11:e0359222. [PMID: 37071007 PMCID: PMC10269488 DOI: 10.1128/spectrum.03592-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/21/2023] [Indexed: 04/19/2023] Open
Abstract
The envelope stress response (ESR) of Gram-negative enteric bacteria senses fluctuations in nutrient availability and environmental changes to avert damage and promote survival. It has a protective role toward antimicrobials, but direct interactions between ESR components and antibiotic resistance genes have not been demonstrated. Here, we report interactions between a central regulator of ESR viz., the two-component signal transduction system CpxRA (conjugative pilus expression), and the recently described mobile colistin resistance protein (MCR-1). Purified MCR-1 is specifically cleaved within its highly conserved periplasmic bridge element, which links its N-terminal transmembrane domain with the C-terminal active-site periplasmic domain, by the CpxRA-regulated serine endoprotease DegP. Recombinant strains harboring cleavage site mutations in MCR-1 are either protease resistant or degradation susceptible, with widely differing consequences for colistin resistance. Transfer of the gene encoding a degradation-susceptible mutant to strains that lack either DegP or its regulator CpxRA restores expression and colistin resistance. MCR-1 production in Escherichia coli imposes growth restriction in strains lacking either DegP or CpxRA, effects that are reversed by transactive expression of DegP. Excipient allosteric activation of the DegP protease specifically inhibits growth of isolates carrying mcr-1 plasmids. As CpxRA directly senses acidification, growth of strains at moderately low pH dramatically increases both MCR-1-dependent phosphoethanolamine (PEA) modification of lipid A and colistin resistance levels. Strains expressing MCR-1 are also more resistant to antimicrobial peptides and bile acids. Thus, a single residue external to its active site induces ESR activity to confer resilience in MCR-1-expressing strains to commonly encountered environmental stimuli, such as changes in acidity and antimicrobial peptides. Targeted activation of the nonessential protease DegP can lead to the elimination of transferable colistin resistance in Gram-negative bacteria. IMPORTANCE The global presence of transferable mcr genes in a wide range of Gram-negative bacteria from clinical, veterinary, food, and aquaculture environments is disconcerting. Its success as a transmissible resistance factor remains enigmatic, because its expression imposes fitness costs and imparts only moderate levels of colistin resistance. Here, we show that MCR-1 triggers regulatory components of the envelope stress response, a system that senses fluctuations in nutrient availability and environmental changes, to promote bacterial survival in low pH environments. We identify a single residue within a highly conserved structural element of mcr-1 distal to its catalytic site that modulates resistance activity and triggers the ESR. Using mutational analysis, quantitative lipid A profiling and biochemical assays, we determined that growth in low pH environments dramatically increases colistin resistance levels and promotes resistance to bile acids and antimicrobial peptides. We exploited these findings to develop a targeted approach that eliminates mcr-1 and its plasmid carriers.
Collapse
Affiliation(s)
- Renate Frantz
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Konrad Gwozdzinski
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Swapnil Prakash Doijad
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Martina Hudel
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Maria Wille
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Mobarak Abu Mraheil
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Dominik Schwudke
- Division of Bioanalytical Chemistry, Priority Area Infections, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site: Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Airway Research Center North, Partner Site: Research Center Borstel, Borstel, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Linda Falgenhauer
- Institute of Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
- Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| | - Michael Ehrmann
- Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- Hessian University Competence Center for Hospital Hygiene, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research, Partner Site: Giessen-Marburg-Langen, Giessen, Germany
| |
Collapse
|
7
|
Cui L, Shi X, Li H, Wang S, Guo L, Lan Z, Dai Y, Zhang Q, Wu Y, Liu W. Crystal structures and solution conformations of HtrA from Helicobacter pylori reveal pH-dependent oligomeric conversion and conformational rearrangements. Int J Biol Macromol 2023:125274. [PMID: 37301353 DOI: 10.1016/j.ijbiomac.2023.125274] [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: 03/03/2023] [Revised: 05/06/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
Abstract
Helicobacter pylori is a Gram-negative microaerophilic bacterium that infects over 50 % of the world's population, making it a major risk factor for chronic gastritis, ulcer diseases of the stomach and duodenum, MALT lymphoma, and gastric cancer. The clinical consequences of H. pylori infection are closely linked with the expression of virulence factors secreted by the bacterium. One such virulence factor is high temperature requirement A (HtrA), which possesses chaperone and serine protease activity. In the host stomach, HtrA secreted from H. pylori (HpHtrA) disrupts intercellular adhesions by cleaving epithelial adhesion proteins including E-cadherin and desmoglein-2. This disruption causes intercellular junctions to open, allowing the bacterium to pass through the epithelial barrier, access the intercellular space, and colonize the gastric mucosa. HtrA proteases are well known for their structural complexity, reflected in their diverse oligomer forms and multi-tasking activities in both prokaryotes and eukaryotes. In this study, we determined crystal structures and solution conformations of HpHtrA monomer and trimer, which revealed large domain rearrangements between them. Notably, this is the first report of a monomeric structure in the HtrA family. We further found a pH-dependent dynamic trimer-to-monomer conversion and concurrent conformational changes that seem closely linked with a pH-sensing ability through the protonation of certain Asp residues. These results advance our understanding of the functional roles and the related mechanisms of this protease in bacterial infection, which may shed light on the development of HtrA-targeted therapies for H. pylori-associated diseases.
Collapse
Affiliation(s)
- Liwei Cui
- Institute of Immunology, PLA, Army Medical University, Chongqing 400038, China; Department of Tropical Medicine and Infectious Diseases, Hainan Hospital of Chinese PLA General Hospital, Sanya, Hainan 572000, China
| | - Xiangrui Shi
- Department of Obstetrics and Gynecology, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Huiling Li
- Department of Tropical Medicine and Infectious Diseases, Hainan Hospital of Chinese PLA General Hospital, Sanya, Hainan 572000, China
| | - Sheng Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Avenue, Wuhan, Hubei 430074, China
| | - Ling Guo
- Institute of Immunology, PLA, Army Medical University, Chongqing 400038, China; Center for drug evaluation and inspection of Chongqing Medical Products Administration, Chongqing 401120, China
| | - Zhu Lan
- Institute of Immunology, PLA, Army Medical University, Chongqing 400038, China
| | - Yujie Dai
- Department of Obstetrics and Gynecology, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Qinghua Zhang
- Department of Obstetrics and Gynecology, Daping Hospital, Army Medical University, Chongqing 400042, China.
| | - Yuzhang Wu
- Institute of Immunology, PLA, Army Medical University, Chongqing 400038, China.
| | - Wei Liu
- Institute of Immunology, PLA, Army Medical University, Chongqing 400038, China.
| |
Collapse
|
8
|
Rong Y, Jensen SI, Lindorff-Larsen K, Nielsen AT. Folding of heterologous proteins in bacterial cell factories: Cellular mechanisms and engineering strategies. Biotechnol Adv 2023; 63:108079. [PMID: 36528238 DOI: 10.1016/j.biotechadv.2022.108079] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/20/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
The expression of correctly folded and functional heterologous proteins is important in many biotechnological production processes, whether it is enzymes, biopharmaceuticals or biosynthetic pathways for production of sustainable chemicals. For industrial applications, bacterial platform organisms, such as E. coli, are still broadly used due to the availability of tools and proven suitability at industrial scale. However, expression of heterologous proteins in these organisms can result in protein aggregation and low amounts of functional protein. This review provides an overview of the cellular mechanisms that can influence protein folding and expression, such as co-translational folding and assembly, chaperone binding, as well as protein quality control, across different model organisms. The knowledge of these mechanisms is then linked to different experimental methods that have been applied in order to improve functional heterologous protein folding, such as codon optimization, fusion tagging, chaperone co-production, as well as strain and protein engineering strategies.
Collapse
Affiliation(s)
- Yixin Rong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
| |
Collapse
|
9
|
Kidera A, Moritsugu K, Ekimoto T, Ikeguchi M. Functional dynamics of SARS-CoV-2 3C-like protease as a member of clan PA. Biophys Rev 2022; 14:1473-1485. [PMID: 36474932 PMCID: PMC9716165 DOI: 10.1007/s12551-022-01020-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
SARS-CoV-2 3C-like protease (3CLpro), a potential therapeutic target for COVID-19, consists of a chymotrypsin fold and a C-terminal α-helical domain (domain III), the latter of which mediates dimerization required for catalytic activation. To gain further understanding of the functional dynamics of SARS-CoV-2 3CLpro, this review extends the scope to the comparative study of many crystal structures of proteases having the chymotrypsin fold (clan PA of the MEROPS database). First, the close correspondence between the zymogen-enzyme transformation in chymotrypsin and the allosteric dimerization activation in SARS-CoV-2 3CLpro is illustrated. Then, it is shown that the 3C-like proteases of family Coronaviridae (the protease family C30), which are closely related to SARS-CoV-2 3CLpro, have the same homodimeric structure and common activation mechanism via domain III mediated dimerization. The survey extended to order Nidovirales reveals that all 3C-like proteases belonging to Nidovirales have domain III, but with various chain lengths, and 3CLpro of family Mesoniviridae (family C107) has the same homodimeric structure as that of C30, even though they have no sequence similarity. As a reference, monomeric 3C proteases belonging to the more distant family Picornaviridae (family C3) lacking domain III are compared with C30, and it is shown that the 3C proteases are rigid enough to maintain their structures in the active state. Supplementary Information The online version contains supplementary material available at 10.1007/s12551-022-01020-x.
Collapse
Affiliation(s)
- Akinori Kidera
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-Cho, Tsurumi, Yokohama 230-0045 Japan
| | - Kei Moritsugu
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-Cho, Tsurumi, Yokohama 230-0045 Japan ,Present Address: Graduate School of Science, Osaka Metropolitan University, 1-1 Gakuen-Cho, Nakaku, Sakai, Osaka 599-8570 Japan
| | - Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-Cho, Tsurumi, Yokohama 230-0045 Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-Cho, Tsurumi, Yokohama 230-0045 Japan
| |
Collapse
|
10
|
Song Y, Ke Y, Kang M, Bao R. Function, molecular mechanisms, and therapeutic potential of bacterial HtrA proteins: An evolving view. Comput Struct Biotechnol J 2022; 20:40-49. [PMID: 34976310 PMCID: PMC8671199 DOI: 10.1016/j.csbj.2021.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/24/2021] [Accepted: 12/04/2021] [Indexed: 02/05/2023] Open
Abstract
Members of the high temperature requirement A (HtrA) protein family are widely distributed amongst prokaryotic and eukaryotic species. HtrA proteins have ATP-independent dual chaperone-protease activity and mediate protein quality control. Emerging evidence indicates that HtrA family members are vital for establishing infections and bacterial survival under stress conditions. Bacterial HtrA proteins are increasingly thought of as important new targets for antibacterial drug development. Recent literature suggests that HtrA protein AlgW from Pseudomonas aeruginosa has distinct structural, functional, and regulatory characteristics. The novel dual-signal activation mechanism seen in AlgW is required to modulate stress and drug responses in bacteria, prompting us to review our understanding of the many HtrA proteins found in microorganisms. Here, we describe the distribution of HtrA gene orthologues in pathogenic bacteria, discuss their structure–function relationships, outline the molecular mechanisms exhibited by different bacterial HtrA proteins in bacteria under selective pressure, and review the significance of recently developed small molecule inhibitors targeting HtrA in pathogenic bacteria.
Collapse
Affiliation(s)
- Yingjie Song
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Yitao Ke
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Mei Kang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- Corresponding authors.
| | - Rui Bao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
- Corresponding authors.
| |
Collapse
|
11
|
Šulskis D, Thoma J, Burmann BM. Structural basis of DegP protease temperature-dependent activation. SCIENCE ADVANCES 2021; 7:eabj1816. [PMID: 34878848 PMCID: PMC8654288 DOI: 10.1126/sciadv.abj1816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/16/2021] [Indexed: 05/21/2023]
Abstract
Protein quality control is an essential cellular function mainly executed by a vast array of different proteases and molecular chaperones. One of the bacterial high temperature requirement A (HtrA) protein family members, the homo-oligomeric DegP protease, plays a crucial role in the Escherichia coli protein quality control machinery by removing unfolded proteins or preventing their aggregation and chaperoning them to their final folded state within the periplasm. DegP contains two regulatory PDZ domains, which play key roles in substrate recognition and in the transformation of DegP between inactive hexameric and proteolytic active cage-like structures. Here, we analyze the interaction and dynamics of the DegP PDZ domains underlying this transformation by high-resolution NMR spectroscopy complemented with biochemical cleavage assays. We identify an interdomain molecular lock, which controls the interactions between the two PDZ domains, regulated by fine-tuned temperature-dependent protein dynamics, and which is potentially conserved in proteins harboring tandem PDZ domains.
Collapse
Affiliation(s)
- Darius Šulskis
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Göteborg, Sweden
| | - Johannes Thoma
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Göteborg, Sweden
| | - Björn M. Burmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Göteborg, Sweden
- Corresponding author.
| |
Collapse
|
12
|
Sučec I, Bersch B, Schanda P. How do Chaperones Bind (Partly) Unfolded Client Proteins? Front Mol Biosci 2021; 8:762005. [PMID: 34760928 PMCID: PMC8573040 DOI: 10.3389/fmolb.2021.762005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/06/2021] [Indexed: 01/03/2023] Open
Abstract
Molecular chaperones are central to cellular protein homeostasis. Dynamic disorder is a key feature of the complexes of molecular chaperones and their client proteins, and it facilitates the client release towards a folded state or the handover to downstream components. The dynamic nature also implies that a given chaperone can interact with many different client proteins, based on physico-chemical sequence properties rather than on structural complementarity of their (folded) 3D structure. Yet, the balance between this promiscuity and some degree of client specificity is poorly understood. Here, we review recent atomic-level descriptions of chaperones with client proteins, including chaperones in complex with intrinsically disordered proteins, with membrane-protein precursors, or partially folded client proteins. We focus hereby on chaperone-client interactions that are independent of ATP. The picture emerging from these studies highlights the importance of dynamics in these complexes, whereby several interaction types, not only hydrophobic ones, contribute to the complex formation. We discuss these features of chaperone-client complexes and possible factors that may contribute to this balance of promiscuity and specificity.
Collapse
Affiliation(s)
- Iva Sučec
- CEA, CNRS, Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, Grenoble, France
| | - Beate Bersch
- CEA, CNRS, Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, Grenoble, France
| | - Paul Schanda
- CEA, CNRS, Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, Grenoble, France.,Institute of Science and Technology Austria, Klosterneuburg, Austria
| |
Collapse
|
13
|
Oligomeric assembly regulating mitochondrial HtrA2 function as examined by methyl-TROSY NMR. Proc Natl Acad Sci U S A 2021; 118:2025022118. [PMID: 33692127 DOI: 10.1073/pnas.2025022118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Human High temperature requirement A2 (HtrA2) is a mitochondrial protease chaperone that plays an important role in cellular proteostasis and in regulating cell-signaling events, with aberrant HtrA2 function leading to neurodegeneration and parkinsonian phenotypes. Structural studies of the enzyme have established a trimeric architecture, comprising three identical protomers in which the active sites of each protease domain are sequestered to form a catalytically inactive complex. The mechanism by which enzyme function is regulated is not well understood. Using methyl transverse relaxation optimized spectroscopy (TROSY)-based solution NMR in concert with biochemical assays, a functional HtrA2 oligomerization/binding cycle has been established. In the absence of substrates, HtrA2 exchanges between a heretofore unobserved hexameric conformation and the canonical trimeric structure, with the hexamer showing much weaker affinity toward substrates. Both structures are substrate inaccessible, explaining their low basal activity in the absence of the binding of activator peptide. The binding of the activator peptide to each of the protomers of the trimer occurs with positive cooperativity and induces intrasubunit domain reorientations to expose the catalytic center, leading to increased proteolytic activity. Our data paint a picture of HtrA2 as a finely tuned, stress-protective enzyme whose activity can be modulated both by oligomerization and domain reorientation, with basal levels of catalysis kept low to avoid proteolysis of nontarget proteins.
Collapse
|
14
|
Zarzecka U, Matkowska D, Backert S, Skorko-Glonek J. Importance of two PDZ domains for the proteolytic and chaperone activities of Helicobacter pylori serine protease HtrA. Cell Microbiol 2020; 23:e13299. [PMID: 33277762 DOI: 10.1111/cmi.13299] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022]
Abstract
The Helicobacter pylori HtrA protein (HtrAHp ) is an important virulence factor involved in the infection process by proteolysis of components of the tight (claudin-8 and occludin) and adherens junctions (E-cadherin) between epithelial cells. As a protease and chaperone, HtrAHp is involved in protein quality control, which is particularly important under stress conditions. HtrAHp contains a protease domain and two C-terminal PDZ domains (PDZ1 and PDZ2). In the HtrA protein family, the PDZ domains are proposed to play important roles, including regulation of proteolytic activity. We therefore mutated the PDZ1 and PDZ2 domains in HtrAHp and studied the maintenance of proteolytic activity, assembly and rearrangement of the corresponding oligomeric forms. Our in vitro experiments demonstrated that at least PDZ1 is important for efficient substrate cleavage, while both PDZ domains are dispensable for the chaperone-like activity. However, in living H. pylori cells, only the mutant containing at least PDZ1, but not PDZ2, ensured bacterial growth under stressful conditions. Moreover, we can demonstrate that PDZ1 is crucial for HtrAHp oligomerization. Interestingly, all truncated proteolytically active HtrAHp variants were functional in the in vitro infection assay and caused damage to the E-cadherin-based adherens junctions. These findings provide valuable new insights into the function of HtrAHp in an important pathogen of humans.
Collapse
Affiliation(s)
- Urszula Zarzecka
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdańsk, Gdańsk, Poland.,Division of Microbiology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Dorota Matkowska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Steffen Backert
- Division of Microbiology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Joanna Skorko-Glonek
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| |
Collapse
|
15
|
Gu Y, Wang S, Huang L, Sa W, Li J, Huang J, Dai M, Cheng G. Development of Resistance in Escherichia coli ATCC25922 under Exposure of Sub-Inhibitory Concentration of Olaquindox. Antibiotics (Basel) 2020; 9:E791. [PMID: 33182563 PMCID: PMC7696260 DOI: 10.3390/antibiotics9110791] [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: 09/02/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 01/31/2023] Open
Abstract
Quinoxaline1,4-di-N-oxides (QdNOs) are a class of important antibacterial drugs of veterinary use, of which the drug resistance mechanism has not yet been clearly explained. This study investigated the molecular mechanism of development of resistance in Escherichia coli (E. coli) under the pressure of sub-inhibitory concentration (sub-MIC) of olaquindox (OLA), a representative QdNOs drug. In vitro challenge of E. coli with 1/100× MIC to 1/2× MIC of OLA showed that the bacteria needed a longer time to develop resistance and could only achieve low to moderate levels of resistance as well as form weak biofilms. The transcriptomic and genomic profiles of the resistant E. coli induced by sub-MIC of OLA demonstrated that genes involved in tricarboxylic acid cycle, oxidation-reduction process, biofilm formation, and efflux pumps were up-regulated, while genes involved in DNA repair and outer membrane porin were down-regulated. Mutation rates were significantly increased in the sub-MIC OLA-treated bacteria and the mutated genes were mainly involved in the oxidation-reduction process, DNA repair, and replication. The SNPs were found in degQ, ks71A, vgrG, bigA, cusA, and DR76-4702 genes, which were covered in both transcriptomic and genomic profiles. This study provides new insights into the resistance mechanism of QdNOs and increases the current data pertaining to the development of bacterial resistance under the stress of antibacterials at sub-MIC concentrations.
Collapse
Affiliation(s)
- Yufeng Gu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuge Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Lulu Huang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Sa
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
| | - Jun Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
| | - Junhong Huang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Menghong Dai
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
| | - Guyue Cheng
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (S.W.); (L.H.); (W.S.); (J.L.); (J.H.); (M.D.)
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
16
|
Cage-like polyhedrons of DegQ from Cytophaga hutchinsonii show stable proteolytic activity and strong chaperone activity. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
17
|
Wilmaerts D, Dewachter L, De Loose PJ, Bollen C, Verstraeten N, Michiels J. HokB Monomerization and Membrane Repolarization Control Persister Awakening. Mol Cell 2019; 75:1031-1042.e4. [DOI: 10.1016/j.molcel.2019.06.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/21/2019] [Accepted: 06/12/2019] [Indexed: 11/15/2022]
|
18
|
Pagani TD, Guimarães ACR, Waghabi MC, Corrêa PR, Kalume DE, Berrêdo-Pinho M, Degrave WM, Mendonça-Lima L. Exploring the Potential Role of Moonlighting Function of the Surface-Associated Proteins From Mycobacterium bovis BCG Moreau and Pasteur by Comparative Proteomic. Front Immunol 2019; 10:716. [PMID: 31080447 PMCID: PMC6497762 DOI: 10.3389/fimmu.2019.00716] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 03/18/2019] [Indexed: 12/14/2022] Open
Abstract
Surface-associated proteins from Mycobacterium bovis BCG Moreau RDJ are important components of the live Brazilian vaccine against tuberculosis. They are important targets during initial BCG vaccine stimulation and modulation of the host's immune response, especially in the bacterial-host interaction. These proteins might also be involved in cellular communication, chemical response to the environment, pathogenesis processes through mobility, colonization, and adherence to the host cell, therefore performing multiple functions. In this study, the proteomic profile of the surface-associated proteins from M. bovis BCG Moreau was compared to the BCG Pasteur reference strain. The methodology used was 2DE gel electrophoresis combined with mass spectrometry techniques (MALDI-TOF/TOF), leading to the identification of 115 proteins. Of these, 24 proteins showed differential expression between the two BCG strains. Furthermore, 27 proteins previously described as displaying moonlighting function were identified, 8 of these proteins showed variation in abundance comparing BCG Moreau to Pasteur and 2 of them presented two different domain hits. Moonlighting proteins are multifunctional proteins in which two or more biological functions are fulfilled by a single polypeptide chain. Therefore, the identification of such proteins with moonlighting predicted functions can contribute to a better understanding of the molecular mechanisms unleashed by live BCG Moreau RDJ vaccine components.
Collapse
Affiliation(s)
- Talita Duarte Pagani
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ana Carolina R Guimarães
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Mariana C Waghabi
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Paloma Rezende Corrêa
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Dário Eluan Kalume
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil.,Unidade de Espectrometria de Massas e Proteômica, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcia Berrêdo-Pinho
- Laboratório de Microbiologia Celular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Wim Maurits Degrave
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Leila Mendonça-Lima
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| |
Collapse
|
19
|
Zhang Z, Huang Q, Tao X, Song G, Zheng P, Li H, Sun H, Xia W. The unique trimeric assembly of the virulence factor HtrA from Helicobacter pylori occurs via N-terminal domain swapping. J Biol Chem 2019; 294:7990-8000. [PMID: 30936204 DOI: 10.1074/jbc.ra119.007387] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 03/27/2019] [Indexed: 12/12/2022] Open
Abstract
Knowledge of the molecular mechanisms of specific bacterial virulence factors can significantly contribute to antibacterial drug discovery. Helicobacter pylori is a Gram-negative microaerophilic bacterium that infects almost half of the world's population, leading to gastric disorders and even gastric cancer. H. pylori expresses a series of virulence factors in the host, among which high-temperature requirement A (HpHtrA) is a newly identified serine protease secreted by H. pylori. HpHtrA cleaves the extracellular domain of the epithelial cell surface adhesion protein E-cadherin and disrupts gastric epithelial cell junctions, allowing H. pylori to access the intercellular space. Here we report the first crystal structure of HpHtrA at 3.0 Å resolution. The structure revealed a new type of HtrA protease trimer stabilized by unique N-terminal domain swapping distinct from other known HtrA homologs. We further observed that truncation of the N terminus completely abrogates HpHtrA trimer formation as well as protease activity. In the presence of unfolded substrate, HpHtrA assembled into cage-like 12-mers or 24-mers. Combining crystallographic, biochemical, and mutagenic data, we propose a mechanistic model of how HpHtrA recognizes and cleaves the well-folded E-cadherin substrate. Our study provides a fundamental basis for the development of anti-H. pylori agents by using a previously uncharacterized HtrA protease as a target.
Collapse
Affiliation(s)
- Zhemin Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Qi Huang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xuan Tao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China
| | - Guobing Song
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hongyan Li
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Hongzhe Sun
- Department of Chemistry, University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Wei Xia
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou, 510275, China.
| |
Collapse
|
20
|
Fu X, Wang Y, Shao H, Ma J, Song X, Zhang M, Chang Z. DegP functions as a critical protease for bacterial acid resistance. FEBS J 2018; 285:3525-3538. [DOI: 10.1111/febs.14627] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 06/03/2018] [Accepted: 08/03/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Xinmiao Fu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
- Engineering Research Center of Industrial Microbiology of Ministry of Education College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
| | - Yan Wang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
- Engineering Research Center of Industrial Microbiology of Ministry of Education College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
| | - Heqi Shao
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
| | - Jing Ma
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
| | - Xinwen Song
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
| | - Meng Zhang
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
| | - Zengyi Chang
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
| |
Collapse
|
21
|
Albrecht N, Tegtmeyer N, Sticht H, Skórko-Glonek J, Backert S. Amino-Terminal Processing of Helicobacter pylori Serine Protease HtrA: Role in Oligomerization and Activity Regulation. Front Microbiol 2018; 9:642. [PMID: 29713313 PMCID: PMC5911493 DOI: 10.3389/fmicb.2018.00642] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/19/2018] [Indexed: 12/17/2022] Open
Abstract
The HtrA family of serine proteases is found in most bacteria, and plays an essential role in the virulence of the gastric pathogen Helicobacter pylori. Secreted H. pylori HtrA (HtrA Hp ) cleaves various junctional proteins such as E-cadherin disrupting the epithelial barrier, which is crucial for bacterial transmigration across the polarized epithelium. Recent studies indicated the presence of two characteristic HtrA Hp forms of 55 and 52 kDa (termed p55 and p52, respectively), in worldwide strains. In addition, p55 and p52 were produced by recombinant HtrA Hp , indicating auto-cleavage. However, the cleavage sites and their functional importance are yet unclear. Here, we determined the amino-terminal ends of p55 and p52 by Edman sequencing. Two proteolytic cleavage sites were identified (H46/D47 and K50/D51). Remarkably, the cleavage site sequences are conserved in HtrA Hp from worldwide isolates, but not in other Gram-negative pathogens, suggesting a highly specific assignment in H. pylori. We analyzed the role of the amino-terminal cleavage sites on activity, secretion and function of HtrA Hp . Three-dimensional modeling suggested a trimeric structure and a role of amino-terminal processing in oligomerization and regulation of proteolytic activity of HtrA Hp . Furthermore, point and deletion mutants of these processing sites were generated in the recently reported Campylobacter jejuni ΔhtrA/htrAHp genetic complementation system and the minimal sequence requirements for processing were determined. Polarized Caco-2 epithelial cells were infected with these strains and analyzed by immunofluorescence microscopy. The results indicated that HtrA Hp processing strongly affected the ability of the protease to disrupt the E-cadherin-based cell-to-cell junctions. Casein zymography confirmed that the amino-terminal region is required for maintaining the proteolytic activity of HtrA Hp . Furthermore, we demonstrated that this cleavage influences the secretion of HtrA Hp in the extracellular space as an important prerequisite for its virulence activity. Taken together, our data demonstrate that amino-terminal cleavage of HtrA Hp is conserved in this pathogen and affects oligomerization and thus, secretion and regulatory activities, suggesting an important role in the pathogenesis of H. pylori.
Collapse
Affiliation(s)
- Nicole Albrecht
- Division of Microbiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nicole Tegtmeyer
- Division of Microbiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Joanna Skórko-Glonek
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Steffen Backert
- Division of Microbiology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| |
Collapse
|
22
|
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: 51] [Impact Index Per Article: 7.3] [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.
Collapse
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
| |
Collapse
|
23
|
Zhu F, Yang X, Wu Y, Wang Y, Tang XF, Tang B. Release of an HtrA-Like Protease from the Cell Surface of Thermophilic Brevibacillus sp. WF146 via Substrate-Induced Autoprocessing of the N-terminal Membrane Anchor. Front Microbiol 2017; 8:481. [PMID: 28377763 PMCID: PMC5359297 DOI: 10.3389/fmicb.2017.00481] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 03/08/2017] [Indexed: 01/07/2023] Open
Abstract
High-temperature requirement A (HtrA)-like proteases participate in protein quality control in prokaryotes and eukaryotes by degrading damaged proteins; however, little is known about HtrAs produced by thermophiles. HtrAw is an HtrA-like protease of thermophilic Brevibacillus sp. WF146. The intact form of HtrAw (iHtrAw) consisting of a transmembrane segment-containing N-terminal domain, a trypsin-like protease domain, and a C-terminal PDZ domain was produced in Escherichia coli. Purified iHtrAw itself is unable to cleave the N-terminal domain, but requires protein substrates to autoprocess the N-terminal domain intermolecularly, yielding a short form (sHtrAw). Mutation at the substrate-binding site in the PDZ domain affects the conversion of iHtrAw to sHtrAw. Deletion analysis revealed that the N-terminal domain is not necessary for enzyme folding, activity, and thermostability. Compared with other known HtrAs, HtrAw contains an additional Ca2+-binding Dx[DN]xDG motif important for enzyme stability and/or activity. When produced in an htrA/htrB double deletion mutant of Bacillus subtilis, iHtrAw localized predominantly to the cell pellet, and the amount of sHtrAw in the culture supernatant increased at elevated temperatures. Moreover, HtrAw increased the heat resistance of the B. subtilis mutant. In strain WF146, HtrAw exists in both a cell-associated intact form and a cell-free short form; an increase in growth temperature enhanced HtrAw production and the amount of cell-free short form. Release of the short form of HtrAw from the membrane may have the advantage of allowing the enzyme to freely access and degrade damaged proteins surrounding the bacterium living at high temperatures.
Collapse
Affiliation(s)
- Fengtao Zhu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University Wuhan, China
| | - Xing Yang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University Wuhan, China
| | - Yan Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University Wuhan, China
| | - Yasi Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University Wuhan, China
| | - Xiao-Feng Tang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan UniversityWuhan, China; Hubei Provincial Cooperative Innovation Center of Industrial FermentationWuhan, China
| | - Bing Tang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan UniversityWuhan, China; Hubei Provincial Cooperative Innovation Center of Industrial FermentationWuhan, China
| |
Collapse
|
24
|
Zhang L, Wang X, Fan F, Wang HW, Wang J, Li X, Sui SF. Cryo-EM structure of Nma111p, a unique HtrA protease composed of two protease domains and four PDZ domains. Cell Res 2017; 27:582-585. [PMID: 28084331 DOI: 10.1038/cr.2017.5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Li Zhang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaojing Wang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fenghui Fan
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jiawei Wang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xueming Li
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| |
Collapse
|
25
|
Richa T, Ide S, Suzuki R, Ebina T, Kuroda Y. Fast H-DROP: A thirty times accelerated version of H-DROP for interactive SVM-based prediction of helical domain linkers. J Comput Aided Mol Des 2016; 31:237-244. [PMID: 28028736 DOI: 10.1007/s10822-016-9999-8] [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: 07/24/2016] [Accepted: 12/10/2016] [Indexed: 10/20/2022]
Abstract
Efficient and rapid prediction of domain regions from amino acid sequence information alone is often required for swift structural and functional characterization of large multi-domain proteins. Here we introduce Fast H-DROP, a thirty times accelerated version of our previously reported H-DROP (Helical Domain linker pRediction using OPtimal features), which is unique in specifically predicting helical domain linkers (boundaries). Fast H-DROP, analogously to H-DROP, uses optimum features selected from a set of 3000 ones by combining a random forest and a stepwise feature selection protocol. We reduced the computational time from 8.5 min per sequence in H-DROP to 14 s per sequence in Fast H-DROP on an 8 Xeon processor Linux server by using SWISS-PROT instead of Genbank non-redundant (nr) database for generating the PSSMs. The sensitivity and precision of Fast H-DROP assessed by cross-validation were 33.7 and 36.2%, which were merely ~2% lower than that of H-DROP. The reduced computational time of Fast H-DROP, without affecting prediction performances, makes it more interactive and user-friendly. Fast H-DROP and H-DROP are freely available from http://domserv.lab.tuat.ac.jp/ .
Collapse
Affiliation(s)
- Tambi Richa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 12-24-16 Nakamachi, Koganei-shi, Tokyo, 184-8588, Japan
| | - Soichiro Ide
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 12-24-16 Nakamachi, Koganei-shi, Tokyo, 184-8588, Japan
| | - Ryosuke Suzuki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 12-24-16 Nakamachi, Koganei-shi, Tokyo, 184-8588, Japan
| | - Teppei Ebina
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 12-24-16 Nakamachi, Koganei-shi, Tokyo, 184-8588, Japan.,Department of Physiology, Graduate school of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 12-24-16 Nakamachi, Koganei-shi, Tokyo, 184-8588, Japan.
| |
Collapse
|
26
|
Dong W, Wang J, Niu G, Zhao S, Liu L. Crystal structure of the zinc-bound HhoA protease from Synechocystis sp. PCC 6803. FEBS Lett 2016; 590:3435-3442. [PMID: 27616292 DOI: 10.1002/1873-3468.12416] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/04/2016] [Accepted: 09/05/2016] [Indexed: 11/05/2022]
Abstract
The high temperature requirement A (HtrA) proteases are oligomeric serine proteases essential for protein quality control. HtrA homolog A (HhoA) from the photosynthetic cyanobacterium Synechocystis sp. PCC 6803 assembles into a proteolytically active hexamer. Herein, we present the crystal structure of the hexameric HhoA in complex with the copurified peptide. Our data indicate the presence of three methionines in close proximity to the peptide-binding site of the PDZ domain. Unexpectedly, we observed that a zinc ion is accommodated within the central channel formed by a HhoA trimer. However, neither calcium nor magnesium showed affinity for HhoA. The role of the zinc ion in HhoA was tested in an in vitro proteolytic assay against the nonspecific substrate β-casein and was found to be inhibitory. Our findings provide insights into the regulation of HhoA by a redox-related mechanism involving methionine residues and by zinc ion-binding within the central channel.
Collapse
Affiliation(s)
- Wei Dong
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jia Wang
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guoqi Niu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Shun Zhao
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Lin Liu
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
27
|
Distinct 3D Architecture and Dynamics of the Human HtrA2(Omi) Protease and Its Mutated Variants. PLoS One 2016; 11:e0161526. [PMID: 27571206 PMCID: PMC5003398 DOI: 10.1371/journal.pone.0161526] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/08/2016] [Indexed: 11/19/2022] Open
Abstract
HtrA2(Omi) protease controls protein quality in mitochondria and plays a major role in apoptosis. Its HtrA2S306A mutant (with the catalytic serine routinely disabled for an X-ray study to avoid self-degradation) is a homotrimer whose subunits contain the serine protease domain (PD) and the regulatory PDZ domain. In the inactive state, a tight interdomain interface limits penetration of both PDZ-activating ligands and PD substrates into their respective target sites. We successfully crystalized HtrA2V226K/S306A, whose active counterpart HtrA2V226K has had higher proteolytic activity, suggesting higher propensity to opening the PD-PDZ interface than that of the wild type HtrA2. Yet, the crystal structure revealed the HtrA2V226K/S306A architecture typical of the inactive protein. To get a consistent interpretation of crystallographic data in the light of kinetic results, we employed molecular dynamics (MD). V325D inactivating mutant was used as a reference. Our simulations demonstrated that upon binding of a specific peptide ligand NH2-GWTMFWV-COOH, the PDZ domains open more dynamically in the wild type protease compared to the V226K mutant, whereas the movement is not observed in the V325D mutant. The movement relies on a PDZ vs. PD rotation which opens the PD-PDZ interface in a lid-like (budding flower-like in trimer) fashion. The noncovalent hinges A and B are provided by two clusters of interfacing residues, harboring V325D and V226K in the C- and N-terminal PD barrels, respectively. The opening of the subunit interfaces progresses in a sequential manner during the 50 ns MD simulation. In the systems without the ligand only minor PDZ shifts relative to PD are observed, but the interface does not open. Further activation-associated events, e.g. PDZ-L3 positional swap seen in any active HtrA protein (vs. HtrA2), were not observed. In summary, this study provides hints on the mechanism of activation of wtHtrA2, the dynamics of the inactive HtrA2V325D, but does not allow to explain an increased activity of HtrA2V226K.
Collapse
|
28
|
Tang-Siegel G, Bumgarner R, Ruiz T, Kittichotirat W, Chen W, Chen C. Human Serum-Specific Activation of Alternative Sigma Factors, the Stress Responders in Aggregatibacter actinomycetemcomitans. PLoS One 2016; 11:e0160018. [PMID: 27490177 PMCID: PMC4973924 DOI: 10.1371/journal.pone.0160018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/12/2016] [Indexed: 01/08/2023] Open
Abstract
Aggregatibacter actinomycetemcomitans, a known pathogen causing periodontal disease and infective endocarditis, is a survivor in the periodontal pocket and blood stream; both environments contain serum as a nutrient source. To screen for unknown virulence factors associated with this microorganism, A. actinomycetemcomitans was grown in serum-based media to simulate its in vivo environment. Different strains of A. actinomycetemcomitans showed distinct growth phenotypes only in the presence of human serum, and they were grouped into high- and low-responder groups. High-responders comprised mainly serotype c strains, and showed an unusual growth phenomenon, featuring a second, rapid increase in turbidity after 9-h incubation that reached a final optical density 2- to 7-fold higher than low-responders. Upon further investigation, the second increase in turbidity was not caused by cell multiplication, but by cell death. Whole transcriptomic analysis via RNA-seq identified 35 genes that were up-regulated by human serum, but not horse serum, in high-responders but not in low-responders, including prominently an alternative sigma factor rpoE (σE). A lacZ reporter construct driven by the 132-bp rpoE promoter sequence of A. actinomycetemcomitans responded dramatically to human serum within 90 min of incubation only when the construct was carried by a high responder strain. The rpoE promoter is 100% identical among high- and low-responder strains. Proteomic investigation showed potential interactions between human serum protein, e.g. apolipoprotein A1 (ApoA1) and A. actinomycetemcomitans. The data clearly indicated a different activation process for rpoE in high- versus low-responder strains. This differential human serum-specific activation of rpoE, a putative extra-cytoplasmic stress responder and global regulator, suggests distinct in vivo adaptations among different strains of A. actinomycetemcomitans.
Collapse
Affiliation(s)
- Gaoyan Tang-Siegel
- Department of Molecular Physiology and Biophysics, College of Medicine, University of Vermont, Burlington, VT, United States of America
| | - Roger Bumgarner
- Department of Microbiology, University of Washington, Seattle, WA, United States of America
| | - Teresa Ruiz
- Department of Molecular Physiology and Biophysics, College of Medicine, University of Vermont, Burlington, VT, United States of America
| | - Weerayuth Kittichotirat
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Weizhen Chen
- Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, United States of America
| | - Casey Chen
- Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, United States of America
- * E-mail:
| |
Collapse
|
29
|
De Geyter J, Tsirigotaki A, Orfanoudaki G, Zorzini V, Economou A, Karamanou S. Protein folding in the cell envelope of Escherichia coli. Nat Microbiol 2016; 1:16107. [PMID: 27573113 DOI: 10.1038/nmicrobiol.2016.107] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/02/2016] [Indexed: 11/09/2022]
Abstract
While the entire proteome is synthesized on cytoplasmic ribosomes, almost half associates with, localizes in or crosses the bacterial cell envelope. In Escherichia coli a variety of mechanisms are important for taking these polypeptides into or across the plasma membrane, maintaining them in soluble form, trafficking them to their correct cell envelope locations and then folding them into the right structures. The fidelity of these processes must be maintained under various environmental conditions including during stress; if this fails, proteases are called in to degrade mislocalized or aggregated proteins. Various soluble, diffusible chaperones (acting as holdases, foldases or pilotins) and folding catalysts are also utilized to restore proteostasis. These responses can be general, dealing with multiple polypeptides, with functional overlaps and operating within redundant networks. Other chaperones are specialized factors, dealing only with a few exported proteins. Several complex machineries have evolved to deal with binding to, integration in and crossing of the outer membrane. This complex protein network is responsible for fundamental cellular processes such as cell wall biogenesis; cell division; the export, uptake and degradation of molecules; and resistance against exogenous toxic factors. The underlying processes, contributing to our fundamental understanding of proteostasis, are a treasure trove for the development of novel antibiotics, biopharmaceuticals and vaccines.
Collapse
Affiliation(s)
- Jozefien De Geyter
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| | - Alexandra Tsirigotaki
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| | - Georgia Orfanoudaki
- Institute of Molecular Biology and Biotechnology, FORTH and Department of Biology, University of Crete, PO Box 1385, GR-711 10 Iraklio, Crete, Greece
| | - Valentina Zorzini
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| | - Anastassios Economou
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium.,Institute of Molecular Biology and Biotechnology, FORTH and Department of Biology, University of Crete, PO Box 1385, GR-711 10 Iraklio, Crete, Greece
| | - Spyridoula Karamanou
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000 Leuven, Belgium
| |
Collapse
|
30
|
Cheregi O, Wagner R, Funk C. Insights into the Cyanobacterial Deg/HtrA Proteases. FRONTIERS IN PLANT SCIENCE 2016; 7:694. [PMID: 27252714 PMCID: PMC4877387 DOI: 10.3389/fpls.2016.00694] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/05/2016] [Indexed: 06/05/2023]
Abstract
Proteins are the main machinery for all living processes in a cell; they provide structural elements, regulate biochemical reactions as enzymes, and are the interface to the outside as receptors and transporters. Like any other machinery proteins have to be assembled correctly and need maintenance after damage, e.g., caused by changes in environmental conditions, genetic mutations, and limitations in the availability of cofactors. Proteases and chaperones help in repair, assembly, and folding of damaged and misfolded protein complexes cost-effective, with low energy investment compared with neo-synthesis. Despite their importance for viability, the specific biological role of most proteases in vivo is largely unknown. Deg/HtrA proteases, a family of serine-type ATP-independent proteases, have been shown in higher plants to be involved in the degradation of the Photosystem II reaction center protein D1. The objective of this review is to highlight the structure and function of their cyanobacterial orthologs. Homology modeling was used to find specific features of the SynDeg/HtrA proteases of Synechocystis sp. PCC 6803. Based on the available data concerning their location and their physiological substrates we conclude that these Deg proteases not only have important housekeeping and chaperone functions within the cell, but also are needed for remodeling the cell exterior.
Collapse
|
31
|
Russell TM, Tang X, Goldstein JM, Bagarozzi D, Johnson BJB. The salt-sensitive structure and zinc inhibition of Borrelia burgdorferi protease BbHtrA. Mol Microbiol 2015; 99:586-96. [PMID: 26480895 DOI: 10.1111/mmi.13251] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2015] [Indexed: 11/28/2022]
Abstract
HtrA serine proteases are highly conserved and essential ATP-independent proteases with chaperone activity. Bacteria express a variable number of HtrA homologues that contribute to the virulence and pathogenicity of bacterial pathogens. Lyme disease spirochetes possess a single HtrA protease homologue, Borrelia burgdorferi HtrA (BbHtrA). Previous studies established that, like the human orthologue HtrA1, BbHtrA is proteolytically active against numerous extracellular proteins in vitro. In this study, we utilized size exclusion chromatography and blue native polyacrylamide gel electrophoresis (BN-PAGE) to demonstrate BbHtrA oligomeric structures that were substrate independent and salt sensitive. Examination of the influence of transition metals on the activity of BbHtrA revealed that this protease is inhibited by Zn(2+) > Cu(2+) > Mn(2+). Extending this analysis to two other HtrA proteases, E. coli DegP and HtrA1, revealed that all three HtrA proteases were reversibly inhibited by ZnCl2 at all micro molar concentrations examined. Commercial inhibitors for HtrA proteases are not available and physiologic HtrA inhibitors are unknown. Our observation of conserved zinc inhibition of HtrA proteases will facilitate structural and functional studies of additional members of this important class of proteases.
Collapse
Affiliation(s)
- Theresa M Russell
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Fort Collins, CO, USA
| | - Xiaoling Tang
- Division of Scientific Resources, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA, USA
| | - Jason M Goldstein
- Division of Scientific Resources, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA, USA
| | - Dennis Bagarozzi
- Division of Scientific Resources, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Atlanta, GA, USA
| | - Barbara J B Johnson
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Fort Collins, CO, USA
| |
Collapse
|
32
|
Schubert A, Wrase R, Hilgenfeld R, Hansen G. Structures of DegQ from Legionella pneumophila Define Distinct ON and OFF States. J Mol Biol 2015. [PMID: 26205420 DOI: 10.1016/j.jmb.2015.06.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HtrA (high-temperature requirement A) family proteins play important roles in protein-quality control processes in the bacterial periplasm. A common feature of all members of this family is their modular organization comprising a chymotrypsin-like protease domain and at least one PDZ (postsynaptic density of 95 kDa, disks large homolog 1 and zonula occludens 1) domain. All characterized HtrA proteins assemble into complex oligomers consisting of typically 3-24 monomers, which allow a tight regulation of proteolytic activity. Here, we provide evidence that the assembly of proteolytically active, higher-order complexes of DegQ from Legionella pneumophila is triggered by the binding of substrate-derived peptides. Crystal structures of inactive 3-mers and active 12-mers of DegQ reveal molecular details of elements of a conserved allosteric activation cascade that defines distinct protease ON and OFF states. Results from DegQ(Lp) variants harboring structure-based amino acid substitutions indicate that peptide binding to the PDZ1 domain is critical for proteolytic activity but not for the formation of higher-order oligomers. Combining structural, mutagenesis and biochemical data, we show that, in contrast to the proteolytic activity, the chaperone function of DegQ is not affected by the state of the activation cascade.
Collapse
Affiliation(s)
- Alexander Schubert
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - Robert Wrase
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany; German Center of Infection Research (DZIF), Hamburg Lübeck Borstel Site, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - Guido Hansen
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany.
| |
Collapse
|
33
|
Bakker D, Buckley AM, de Jong A, van Winden VJC, Verhoeks JPA, Kuipers OP, Douce GR, Kuijper EJ, Smits WK, Corver J. The HtrA-like protease CD3284 modulates virulence of Clostridium difficile. Infect Immun 2014; 82:4222-32. [PMID: 25047848 PMCID: PMC4187886 DOI: 10.1128/iai.02336-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 01/05/2023] Open
Abstract
In the past decade, Clostridium difficile has emerged as an important gut pathogen. Symptoms of C. difficile infection range from mild diarrhea to pseudomembranous colitis. Besides the two main virulence factors toxin A and toxin B, other virulence factors are likely to play a role in the pathogenesis of the disease. In other Gram-positive and Gram-negative pathogenic bacteria, conserved high-temperature requirement A (HtrA)-like proteases have been shown to have a role in protein homeostasis and quality control. This affects the functionality of virulence factors and the resistance of bacteria to (host-induced) environmental stresses. We found that the C. difficile 630 genome encodes a single HtrA-like protease (CD3284; HtrA) and have analyzed its role in vivo and in vitro through the creation of an isogenic ClosTron-based htrA mutant of C. difficile strain 630Δerm (wild type). In contrast to the attenuated phenotype seen with htrA deletion in other pathogens, this mutant showed enhanced virulence in the Golden Syrian hamster model of acute C. difficile infection. Microarray data analysis showed a pleiotropic effect of htrA on the transcriptome of C. difficile, including upregulation of the toxin A gene. In addition, the htrA mutant showed reduced spore formation and adherence to colonic cells. Together, our data show that htrA can modulate virulence in C. difficile.
Collapse
Affiliation(s)
- Dennis Bakker
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
| | - Anthony M Buckley
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Anne de Jong
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Vincent J C van Winden
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
| | - Joost P A Verhoeks
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands
| | - Gillian R Douce
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Ed J Kuijper
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen Corver
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
| |
Collapse
|
34
|
An H, Douillard FP, Wang G, Zhai Z, Yang J, Song S, Cui J, Ren F, Luo Y, Zhang B, Hao Y. Integrated transcriptomic and proteomic analysis of the bile stress response in a centenarian-originated probiotic Bifidobacterium longum BBMN68. Mol Cell Proteomics 2014; 13:2558-72. [PMID: 24965555 DOI: 10.1074/mcp.m114.039156] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bifidobacteria are natural inhabitants of the human gastrointestinal tract and well known for their health-promoting effects. Tolerance to bile stress is crucial for bifidobacteria to survive in the colon and to exert their beneficial actions. In this work, RNA-Seq transcriptomic analysis complemented with proteomic analysis was used to investigate the cellular response to bile in Bifidobacterium longum BBMN68. The transcript levels of 236 genes were significantly changed (≥ threefold, p < 0.001) and 44 proteins were differentially abundant (≥1.6-fold, p < 0.01) in B. longum BBMN68 when exposed to 0.75 g l(-1) ox-bile. The hemolysin-like protein and bile efflux systems were significantly over produced, which might prevent bile adsorption and exclude bile, respectively. The cell membrane composition was modified probably by an increase of cyclopropane fatty acid and a decrease of transmembrane proteins, resulting in a cell membrane more impermeable to bile salts. Our hypothesis was later confirmed by surface hydrophobicity assay. The transcription of genes related to xylose utilization and bifid shunt were up-regulated, which increased the production of ATP and reducing equivalents to cope with bile-induced damages in a xylan-rich colon environment. Bile salts signal the B. longum BBMN68 to gut entrance and enhance the expression of esterase and sortase associated with adhesion and colonization in intestinal tract, which was supported by a fivefold increased adhesion ability to HT-29 cells by BBMN68 upon bile exposure. Notably, bacterial one-hybrid and EMSA assay revealed that the two-component system senX3-regX3 controlled the expression of pstS in bifidobacteria and the role of this target gene in bile resistance was further verified by heterologous expression in Lactococcus lactis. Taken altogether, this study established a model for global response mechanisms in B. longum to bile.
Collapse
Affiliation(s)
- Haoran An
- From the ‡Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - François P Douillard
- §Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Guohong Wang
- From the ‡Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Zhengyuan Zhai
- From the ‡Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jin Yang
- ¶Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuhui Song
- ¶Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianyun Cui
- From the ‡Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Fazheng Ren
- From the ‡Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- From the ‡Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Bing Zhang
- ¶Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanling Hao
- From the ‡Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Municipality, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China;
| |
Collapse
|
35
|
Dolze E, Chigri F, Höwing T, Hierl G, Isono E, Vothknecht UC, Gietl C. Calmodulin-like protein AtCML3 mediates dimerization of peroxisomal processing protease AtDEG15 and contributes to normal peroxisome metabolism. PLANT MOLECULAR BIOLOGY 2013; 83:607-24. [PMID: 23943091 PMCID: PMC3830196 DOI: 10.1007/s11103-013-0112-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 07/17/2013] [Indexed: 05/22/2023]
Abstract
Matrix enzymes are imported into peroxisomes and glyoxysomes, a subclass of peroxisomes involved in lipid mobilization. Two peroxisomal targeting signals (PTS), the C-terminal PTS1 and the N-terminal PTS2, mediate the translocation of proteins into the organelle. PTS2 processing upon import is conserved in higher eukaryotes, and in watermelon the glyoxysomal processing protease (GPP) was shown to catalyse PTS2 processing. GPP and its ortholog, the peroxisomal DEG protease from Arabidopsis thaliana (AtDEG15), belong to the Deg/HtrA family of ATP-independent serine proteases with Escherichia coli DegP as their prototype. GPP existes in monomeric and dimeric forms. Their equilibrium is shifted towards the monomer upon Ca(2+)-removal and towards the dimer upon Ca(2+)-addition, which is accompanied by a change in substrate specificity from a general protease (monomer) to the specific cleavage of the PTS2 (dimer). We describe the Ca(2+)/calmodulin (CaM) mediated dimerization of AtDEG15. Dimerization is mediated by the CaM-like protein AtCML3 as shown by yeast two and three hybrid analyses. The binding of AtCML3 occurs within the first 25 N-terminal amino acids of AtDEG15, a domain containing a predicted CaM-binding motif. Biochemical analysis of AtDEG15 deletion constructs in planta support the requirement of the CaM-binding domain for PTS2 processing. Phylogenetic analyses indicate that the CaM-binding site is conserved in peroxisomal processing proteases of higher plants (dicots, monocots) but not present in orthologs of animals or cellular slime molds. Despite normal PTS2 processing activity, an atcml3 mutant exhibited reduced 2,4-DB sensitivity, a phenotype previously reported for the atdeg15 mutant, indicating similarly impaired peroxisome metabolism.
Collapse
Affiliation(s)
- Esther Dolze
- Institute of Botany, Center of Life and Food Sciences Weihenstephan, TU Munich, Emil-Ramann-Str. 4, 85350 Freising, Germany
| | - Fatima Chigri
- Department of Biology, Center of Integrated Protein Science, LMU Munich, 82152 Martinsried, Germany
| | - Timo Höwing
- Institute of Botany, Center of Life and Food Sciences Weihenstephan, TU Munich, Emil-Ramann-Str. 4, 85350 Freising, Germany
| | - Georg Hierl
- Institute of Botany, Center of Life and Food Sciences Weihenstephan, TU Munich, Emil-Ramann-Str. 4, 85350 Freising, Germany
| | - Erika Isono
- Department of Plant Systems Biology, Center of Life and Food Sciences Weihenstephan, TU Munich, 85350 Freising, Germany
| | - Ute C. Vothknecht
- Department of Biology, Center of Integrated Protein Science, LMU Munich, 82152 Martinsried, Germany
| | - Christine Gietl
- Institute of Botany, Center of Life and Food Sciences Weihenstephan, TU Munich, Emil-Ramann-Str. 4, 85350 Freising, Germany
| |
Collapse
|
36
|
López-Madrigal S, Latorre A, Porcar M, Moya A, Gil R. Mealybugs nested endosymbiosis: going into the 'matryoshka' system in Planococcus citri in depth. BMC Microbiol 2013; 13:74. [PMID: 23548081 PMCID: PMC3620526 DOI: 10.1186/1471-2180-13-74] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 03/25/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND In all branches of life there are plenty of symbiotic associations. Insects are particularly well suited to establishing intracellular symbiosis with bacteria, providing them with metabolic capabilities they lack. Essential primary endosymbionts can coexist with facultative secondary symbionts which can, eventually, establish metabolic complementation with the primary endosymbiont, becoming a co-primary. Usually, both endosymbionts maintain their cellular identity. An exception is the endosymbiosis found in mealybugs of the subfamily Pseudoccinae, such as Planococcus citri, with Moranella endobia located inside Tremblaya princeps. RESULTS We report the genome sequencing of M. endobia str. PCVAL and the comparative genomic analyses of the genomes of strains PCVAL and PCIT of both consortium partners. A comprehensive analysis of their functional capabilities and interactions reveals their functional coupling, with many cases of metabolic and informational complementation. Using comparative genomics, we confirm that both genomes have undergone a reductive evolution, although with some unusual genomic features as a consequence of coevolving in an exceptional compartmentalized organization. CONCLUSIONS M. endobia seems to be responsible for the biosynthesis of most cellular components and energy provision, and controls most informational processes for the consortium, while T. princeps appears to be a mere factory for amino acid synthesis, and translating proteins, using the precursors provided by M. endobia. In this scenario, we propose that both entities should be considered part of a composite organism whose compartmentalized scheme (somehow) resembles a eukaryotic cell.
Collapse
Affiliation(s)
- Sergio López-Madrigal
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartado Postal 22085, València, 46071, Spain
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartado Postal 22085, València, 46071, Spain
- Área de Genómica y Salud, Centro Superior de Investigación en Salud Pública (CSISP), Avenida de Cataluña 21, Valencia, 46020, Spain
| | - Manuel Porcar
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartado Postal 22085, València, 46071, Spain
- Fundació General de la Universitat de València, Apartado Postal 22085, València, 46071, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartado Postal 22085, València, 46071, Spain
- Área de Genómica y Salud, Centro Superior de Investigación en Salud Pública (CSISP), Avenida de Cataluña 21, Valencia, 46020, Spain
| | - Rosario Gil
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartado Postal 22085, València, 46071, Spain
| |
Collapse
|
37
|
Small JL, O'Donoghue AJ, Boritsch EC, Tsodikov OV, Knudsen GM, Vandal O, Craik CS, Ehrt S. Substrate specificity of MarP, a periplasmic protease required for resistance to acid and oxidative stress in Mycobacterium tuberculosis. J Biol Chem 2013; 288:12489-99. [PMID: 23504313 DOI: 10.1074/jbc.m113.456541] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The transmembrane serine protease MarP is important for pH homeostasis in Mycobacterium tuberculosis (Mtb). Previous structural studies revealed that MarP contains a chymotrypsin fold and a disulfide bond that stabilizes the protease active site in the substrate-bound conformation. Here, we determined that MarP is located in the Mtb periplasm and showed that this localization is essential for function. Using the recombinant protease domain of MarP, we identified its substrate specificity using two independent assays: positional-scanning synthetic combinatorial library profiling and multiplex substrate profiling by mass spectrometry. These methods revealed that MarP prefers bulky residues at P4, tryptophan or leucine at P2, arginine or hydrophobic residues at P1, and alanine or asparagine at P1'. Guided by these data, we designed fluorogenic peptide substrates and characterized the kinetic properties of MarP. Finally, we tested the impact of mutating MarP cysteine residues on the peptidolytic activity of recombinant MarP and its ability to complement phenotypes of Mtb ΔMarP. Taken together, our studies provide insight into the enzymatic properties of MarP, its substrate preference, and the importance of its transmembrane helices and disulfide bond.
Collapse
Affiliation(s)
- Jennifer L Small
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Hansen G, Hilgenfeld R. Architecture and regulation of HtrA-family proteins involved in protein quality control and stress response. Cell Mol Life Sci 2013; 70:761-75. [PMID: 22806565 PMCID: PMC11113883 DOI: 10.1007/s00018-012-1076-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 06/24/2012] [Accepted: 06/26/2012] [Indexed: 12/22/2022]
Abstract
Protein quality control is vital for all living cells and sophisticated molecular mechanisms have evolved to prevent the excessive accumulation of unfolded proteins. High-temperature requirement A (HtrA) proteases have been identified as important ATP-independent quality-control factors in most species. HtrA proteins harbor a serine-protease domain and at least one peptide-binding PDZ domain to ensure efficient removal of misfolded or damaged proteins. One distinctive property of HtrAs is their ability to assemble into complex oligomers. Whereas all examined HtrAs are capable of forming pyramidal 3-mers, higher-order complexes consisting of up to 24 molecules have been reported. Tight control of chaperone and protease function is of pivotal importance in preventing deleterious HtrA-protease activity. In recent years, structural biology provided detailed insights into the molecular basis of the regulatory mechanisms, which include unique intramolecular allosteric signaling cascades and the dynamic switching of oligomeric states of HtrA proteins. Based on these results, functional models for many family members have been developed. The HtrA protein family represents a remarkable example of how structural and functional diversity is attained from the assembly of simple molecular building blocks.
Collapse
Affiliation(s)
- Guido Hansen
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, 23538, Lübeck, Germany.
| | | |
Collapse
|
39
|
Dutta A, Katarkar A, Chaudhuri K. In-silico structural and functional characterization of a V. cholerae O395 hypothetical protein containing a PDZ1 and an uncommon protease domain. PLoS One 2013; 8:e56725. [PMID: 23441214 PMCID: PMC3575494 DOI: 10.1371/journal.pone.0056725] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 01/14/2013] [Indexed: 11/18/2022] Open
Abstract
Vibrio cholerae, the causative agent of epidemic cholera, has been a constant source of concern for decades. It has constantly evolved itself in order to survive the changing environment. Acquisition of new genetic elements through genomic islands has played a major role in its evolutionary process. In this present study a hypothetical protein was identified which was present in one of the predicted genomic island regions of the large chromosome of V. cholerae O395 showing a strong homology with a conserved phage encoded protein. In-silico physicochemical analysis revealed that the hypothetical protein was a periplasmic protein. Homology modeling study indicated that the hypothetical protein was an unconventional and atypical serine protease belonging to HtrA protein family. The predicted 3D-model of the hypothetical protein revealed a catalytic centre serine utilizing a single catalytic residue for proteolysis. The predicted catalytic triad may help to deduce the active site for the recruitment of the substrate for proteolysis. The active site arrangements of this predicted serine protease homologue with atypical catalytic triad is expected to allow these proteases to work in different environments of the host.
Collapse
Affiliation(s)
- Avirup Dutta
- CSIR-SRF, Molecular and Human Genetics Division, CSIR - Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Atul Katarkar
- ICMR-SRF, Molecular and Human Genetics Division, CSIR - Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Keya Chaudhuri
- Chief Scientist, Molecular and Human Genetics Division, and Head Academic Affairs Division, CSIR - Indian Institute of Chemical Biology, Kolkata, West Bengal, India
- * E-mail:
| |
Collapse
|
40
|
Cassone M, Gagne AL, Spruce LA, Seeholzer SH, Sebert ME. The HtrA protease from Streptococcus pneumoniae digests both denatured proteins and the competence-stimulating peptide. J Biol Chem 2012; 287:38449-59. [PMID: 23012372 DOI: 10.1074/jbc.m112.391482] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The HtrA protease of Streptococcus pneumoniae functions both in a general stress response role and as an error sensor that specifically represses genetic competence when the overall level of biosynthetic errors in cellular proteins is low. However, the mechanism through which HtrA inhibits development of competence has been unknown. We found that HtrA digested the pneumococcal competence-stimulating peptide (CSP) and constituted the primary extracytoplasmic CSP-degrading activity in cultures of S. pneumoniae. Mass spectrometry demonstrated that cleavage predominantly followed residue Phe-8 of the CSP-1 isoform of the peptide within its central hydrophobic patch, and in competition assays, both CSP-1 and CSP-2 interacted with HtrA with similar efficiencies. More generally, analysis of β-casein digestion and of digestion within HtrA itself revealed a preference for substrates with non-polar residues at the P1 site. Consistent with a specificity for exposed hydrophobic residues, competition from native BSA only weakly inhibited digestion of CSP, but denaturation converted BSA into a strong competitive inhibitor of such proteolysis. Together these findings support a model in which digestion of CSP by HtrA is reduced in the presence of other unfolded proteins that serve as alternative targets for degradation. Such competition may provide a mechanism by which HtrA functions in a quality control capacity to monitor the frequency of biosynthetic errors that result in protein misfolding.
Collapse
Affiliation(s)
- Marco Cassone
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | | | | | | | | |
Collapse
|
41
|
Sun R, Fan H, Gao F, Lin Y, Zhang L, Gong W, Liu L. Crystal structure of Arabidopsis Deg2 protein reveals an internal PDZ ligand locking the hexameric resting state. J Biol Chem 2012; 287:37564-9. [PMID: 22961982 PMCID: PMC3481350 DOI: 10.1074/jbc.m112.394585] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Eukaryotic organelles have developed elaborate protein quality control systems to ensure their normal activity, among which Deg/HtrA proteases play an essential role. Plant Deg2 protease is a homologue of prokaryotic DegQ/DegP proteases and is located in the chloroplast stroma, where its proteolytic activity is required to maintain the efficiency of photosynthetic machinery during stress. Here, we demonstrate that Deg2 exhibits dual protease-chaperone activities, and we present the hexameric structure of Deg2 complexed with co-purified peptides. The structure shows that Deg2 contains a unique second PDZ domain (PDZ2) following a conventional PDZ domain (PDZ1), with PDZ2 orchestrating the cage assembly of Deg2. We discovered a conserved internal ligand for PDZ2 that mediates hexamer formation and thus locks the protease in the resting state. These findings provide insight into the diverse modes of PDZ domain-mediated regulation of Deg proteases.
Collapse
Affiliation(s)
- Renhua Sun
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | | | | | | | | | | | | |
Collapse
|
42
|
Hoy B, Brandstetter H, Wessler S. The stability and activity of recombinant Helicobacter pylori HtrA under stress conditions. J Basic Microbiol 2012; 53:402-9. [PMID: 22736569 DOI: 10.1002/jobm.201200074] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 02/21/2012] [Indexed: 01/26/2023]
Abstract
The bifunctional protein HtrA displays chaperone and protease activities, enabling bacteria to cope with environmental stress conditions such as heat shock or extreme pH by orchestrating protein folding or degradation. Recently, we added a novel aspect to HtrA functions by identifying HtrA of the human pathogen and class I carcinogen Helicobacter pylori (Hp) as a secreted virulence factor that cleaves the cell adhesion molecule and tumor suppressor E-cadherin. In this study, we analyzed the structural integrity and activity of oligomeric HtrA from Hp under stress conditions. Examining different parameters, HtrA oligomers were investigated by casein zymography and HtrA activity was further analyzed in in vitro cleavage assays using E-cadherin as a substrate. HtrA showed temperature-dependent disintegration of oligomers. Denaturing agents targeting hydrogen bonds within HtrA destabilized HtrA oligomers while reducing agents disrupting disulfide bonds had no effect. Optimal proteolytic activity was dependent on a neutral pH; however, addition of mono- and divalent salts or reducing agents did not interfere with proteolytic activity. These data indicate the HtrA is active under stress conditions which might support Hp colonizing in the gastric environment.
Collapse
Affiliation(s)
- Benjamin Hoy
- Division of Microbiology, Paris-Lodron University, Salzburg, Austria
| | | | | |
Collapse
|
43
|
Tennstaedt A, Pöpsel S, Truebestein L, Hauske P, Brockmann A, Schmidt N, Irle I, Sacca B, Niemeyer CM, Brandt R, Ksiezak-Reding H, Tirniceriu AL, Egensperger R, Baldi A, Dehmelt L, Kaiser M, Huber R, Clausen T, Ehrmann M. Human high temperature requirement serine protease A1 (HTRA1) degrades tau protein aggregates. J Biol Chem 2012; 287:20931-41. [PMID: 22535953 PMCID: PMC3375517 DOI: 10.1074/jbc.m111.316232] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 04/24/2012] [Indexed: 11/06/2022] Open
Abstract
Protective proteases are key elements of protein quality control pathways that are up-regulated, for example, under various protein folding stresses. These proteases are employed to prevent the accumulation and aggregation of misfolded proteins that can impose severe damage to cells. The high temperature requirement A (HtrA) family of serine proteases has evolved to perform important aspects of ATP-independent protein quality control. So far, however, no HtrA protease is known that degrades protein aggregates. We show here that human HTRA1 degrades aggregated and fibrillar tau, a protein that is critically involved in various neurological disorders. Neuronal cells and patient brains accumulate less tau, neurofibrillary tangles, and neuritic plaques, respectively, when HTRA1 is expressed at elevated levels. Furthermore, HTRA1 mRNA and HTRA1 activity are up-regulated in response to elevated tau concentrations. These data suggest that HTRA1 is performing regulated proteolysis during protein quality control, the implications of which are discussed.
Collapse
Affiliation(s)
- Annette Tennstaedt
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
| | - Simon Pöpsel
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
| | - Linda Truebestein
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
| | - Patrick Hauske
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
| | - Anke Brockmann
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
| | - Nina Schmidt
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
| | - Inga Irle
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
| | - Barbara Sacca
- the Fakultät Chemie, Biologisch-Chemische Mikrostrukturtechnik, Technische Universität Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Christof M. Niemeyer
- the Fakultät Chemie, Biologisch-Chemische Mikrostrukturtechnik, Technische Universität Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Roland Brandt
- the Fachbereich Biologie/Chemie, University Osnabrueck, D-49076 Osnabrueck, Germany
| | - Hanna Ksiezak-Reding
- the Department of Neurology, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, New York 10029
| | - Anca Laura Tirniceriu
- the Center for Neuropathology and Prion Research, Ludwig Maximilians University of Munich, Feodor-Lynen-Strasse 23, 81377 Munich, Germany
| | - Rupert Egensperger
- the Center for Neuropathology and Prion Research, Ludwig Maximilians University of Munich, Feodor-Lynen-Strasse 23, 81377 Munich, Germany
| | - Alfonso Baldi
- the Department of Biochemistry and Biophysics, Section of Pathology, the Second University of Naples, 80100 Naples, Italy
| | - Leif Dehmelt
- the Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Markus Kaiser
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
| | - Robert Huber
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
- the Department for Chemical Biology, Technische Universität Dortmund University, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
- the Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, 82152 Martinsried, Germany
- the School of Biosciences, Cardiff University, Cardiff CF10 3US, United Kingdom, and
| | - Tim Clausen
- the Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, A-1030 Vienna, Austria
| | - Michael Ehrmann
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
- the School of Biosciences, Cardiff University, Cardiff CF10 3US, United Kingdom, and
| |
Collapse
|
44
|
Genetic analysis of 15 protein folding factors and proteases of the Escherichia coli cell envelope. J Bacteriol 2012; 194:3225-33. [PMID: 22505681 DOI: 10.1128/jb.00221-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Each cell hosts thousands of proteins that vary greatly in abundance, structure, and chemical properties. To ensure that all proteins are biologically active and properly localized, efficient quality control systems have evolved. While the structure, function, and regulation of some individual protein folding factors and proteases were resolved up to atomic resolution, others remain poorly characterized. In addition, little is known about which factors are required for viability under specific stress conditions. We therefore determined the physiological implications of 15 factors of the E. coli cell envelope by an integrated genetic approach comprising phenotypic analyses. Our data indicate that surA and tsp null mutations are a lethal combination in rich medium, that surA dsbA and surA dsbC double mutants are temperature sensitive, and that surA ptrA, surA yfgC, dsbA fkpA, degP tsp, degP ppiD, tsp ppiD, and degP dsbA double mutants are temperature sensitive in rich medium containing 0.5 M NaCl, while degP dsbA, degP yfgC, tsp ydgD, and degP tsp double mutants do not grow in the presence of SDS/EDTA. Furthermore, we show that in degP dsbA, degP tsp, and degP yfgC double mutants a subpopulation of LamB exists as unfolded monomers. In addition, dsbA null mutants expressed lower levels of the outer membrane proteins LptD, LamB, FhuA, and OmpW while FhuA levels were reduced in surA single and degP ppiD double mutants. Lower FhuA levels in degP ppiD strains depend on Tsp, since in a tsp degP ppiD triple mutant FhuA levels are restored.
Collapse
|
45
|
Malet H, Canellas F, Sawa J, Yan J, Thalassinos K, Ehrmann M, Clausen T, Saibil HR. Newly folded substrates inside the molecular cage of the HtrA chaperone DegQ. Nat Struct Mol Biol 2012; 19:152-7. [PMID: 22245966 PMCID: PMC3272482 DOI: 10.1038/nsmb.2210] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 11/14/2011] [Indexed: 11/08/2022]
Abstract
The HtrA protein family combines chaperone and protease activities and is essential for protein quality control in many organisms. Whereas the mechanisms underlying the proteolytic function of HtrA proteins are well characterized, their chaperone activity remains poorly understood. Here we describe cryo-EM structures of Escherichia coli DegQ in its 12- and 24-mer states in complex with model substrates, providing a structural model of HtrA chaperone action. Up to six lysozyme substrates bind inside the DegQ 12-mer cage and are visualized in a close-to-native state. An asymmetric reconstruction reveals the binding of a well-ordered lysozyme to four DegQ protomers. DegQ PDZ domains are located adjacent to substrate density and their presence is required for chaperone activity. The substrate-interacting regions appear conserved in 12- and 24-mer cages, suggesting a common mechanism of chaperone function.
Collapse
Affiliation(s)
- Hélène Malet
- Institute of Structural and Molecular Biology, Crystallography, Birkbeck College, London, UK
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Singh N, Kuppili RR, Bose K. The structural basis of mode of activation and functional diversity: a case study with HtrA family of serine proteases. Arch Biochem Biophys 2011; 516:85-96. [PMID: 22027029 DOI: 10.1016/j.abb.2011.10.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 10/03/2011] [Indexed: 12/15/2022]
Abstract
HtrA (High temperature requirement protease A) proteins that are primarily involved in protein quality control belong to a family of serine proteases conserved from bacteria to humans. HtrAs are oligomeric proteins that share a common trimeric pyramidal architecture where each monomer comprises a serine protease domain and one or two PDZ domains. Although the overall structural integrity is well maintained and they exhibit similar mechanism of activation, subtle conformational changes and structural plasticity especially in the flexible loop regions and domain interfaces lead to differences in their active site conformation and hence in their specificity and functions.
Collapse
Affiliation(s)
- Nitu Singh
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India
| | | | | |
Collapse
|
47
|
Wang W, Rasmussen T, Harding AJ, Booth NA, Booth IR, Naismith JH. Salt bridges regulate both dimer formation and monomeric flexibility in HdeB and may have a role in periplasmic chaperone function. J Mol Biol 2011; 415:538-46. [PMID: 22138344 PMCID: PMC3299563 DOI: 10.1016/j.jmb.2011.11.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 11/14/2011] [Accepted: 11/15/2011] [Indexed: 12/20/2022]
Abstract
Escherichia coli and Gram-negative bacteria that live in the human gut must be able to tolerate rapid and large changes in environmental pH. Low pH irreversibly denatures and precipitates many bacterial proteins. While cytoplasmic proteins are well buffered against such swings, periplasmic proteins are not. Instead, it appears that some bacteria utilize chaperone proteins that stabilize periplasmic proteins, preventing their precipitation. Two highly expressed and related proteins, HdeA and HdeB, have been identified as acid-activated chaperones. The structure of HdeA is known and a mechanism for activation has been proposed. In this model, dimeric HdeA dissociates at low pH, and the exposed dimeric interface binds exposed hydrophobic surfaces of acid-denatured proteins, preventing their irreversible aggregation. We now report the structure and biophysical characterization of the HdeB protein. The monomer of HdeB shares a similar structure with HdeA, but its dimeric interface is different in composition and spatial location. We have used fluorescence to study the behavior of HdeB as pH is lowered, and like HdeA, it dissociates to monomers. We have identified one of the key intersubunit interactions that controls pH-induced monomerization. Our analysis identifies a structural interaction within the HdeB monomer that is disrupted as pH is lowered, leading to enhanced structural flexibility.
Collapse
Affiliation(s)
- Wenjian Wang
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | | | | | | | | | | |
Collapse
|
48
|
Abstract
UNLABELLED Competence for genetic transformation in Streptococcus pneumoniae develops in response to accumulation of a secreted peptide pheromone and was one of the initial examples of bacterial quorum sensing. Activation of this signaling system induces not only expression of the proteins required for transformation but also the production of cellular chaperones and proteases. We have shown here that activity of this pathway is sensitively responsive to changes in the accuracy of protein synthesis that are triggered by either mutations in ribosomal proteins or exposure to antibiotics. Increasing the error rate during ribosomal decoding promoted competence, while reducing the error rate below the baseline level repressed the development of both spontaneous and antibiotic-induced competence. This pattern of regulation was promoted by the bacterial HtrA serine protease. Analysis of strains with the htrA (S234A) catalytic site mutation showed that the proteolytic activity of HtrA selectively repressed competence when translational fidelity was high but not when accuracy was low. These findings redefine the pneumococcal competence pathway as a response to errors during protein synthesis. This response has the capacity to address the immediate challenge of misfolded proteins through production of chaperones and proteases and may also be able to address, through genetic exchange, upstream coding errors that cause intrinsic protein folding defects. The competence pathway may thereby represent a strategy for dealing with lesions that impair proper protein coding and for maintaining the coding integrity of the genome. IMPORTANCE The signaling pathway that governs competence in the human respiratory tract pathogen Streptococcus pneumoniae regulates both genetic transformation and the production of cellular chaperones and proteases. The current study shows that this pathway is sensitively controlled in response to changes in the accuracy of protein synthesis. Increasing the error rate during ribosomal decoding induced competence, while decreasing the error rate repressed competence. This pattern of regulation was promoted by the HtrA protease, which selectively repressed competence when translational fidelity was high but not when accuracy was low. Our findings demonstrate that this organism is able to monitor the accuracy of information used for protein biosynthesis and suggest that errors trigger a response addressing both the immediate challenge of misfolded proteins and, through genetic exchange, upstream coding errors that may underlie protein folding defects. This pathway may represent an evolutionary strategy for maintaining the coding integrity of the genome.
Collapse
|