1
|
Complete Genome Sequences of
Microbacterium
Phages Clayda5 and Gshelby23 and
Gordonia
Phages Wrigley and Santhid. Microbiol Resour Announc 2022; 11:e0078922. [DOI: 10.1128/mra.00789-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacteriophages Clayda5, Gshelby23, Wrigley, and Santhid were isolated from soil samples collected in Iowa, with genomes typical of actinobacteriophages from clusters EB, EM, CY, and DY, respectively. Wrigley and Santhid were isolated on
Gordonia terrae
and are likely to be temperate. Clayda5 and Gshelby23 were isolated on
Microbacterium foliorum
.
Collapse
|
2
|
Jiang C, Wynne M, Huber D. How Quality Control Systems AID Sec-Dependent Protein Translocation. Front Mol Biosci 2021; 8:669376. [PMID: 33928127 PMCID: PMC8076867 DOI: 10.3389/fmolb.2021.669376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
The evolutionarily conserved Sec machinery is responsible for transporting proteins across the cytoplasmic membrane. Protein substrates of the Sec machinery must be in an unfolded conformation in order to be translocated across (or inserted into) the cytoplasmic membrane. In bacteria, the requirement for unfolded proteins is strict: substrate proteins that fold (or misfold) prematurely in the cytoplasm prior to translocation become irreversibly trapped in the cytoplasm. Partially folded Sec substrate proteins and stalled ribosomes containing nascent Sec substrates can also inhibit translocation by blocking (i.e., “jamming”) the membrane-embedded Sec machinery. To avoid these issues, bacteria have evolved a complex network of quality control systems to ensure that Sec substrate proteins do not fold in the cytoplasm. This quality control network can be broken into three branches, for which we have defined the acronym “AID”: (i) avoidance of cytoplasmic intermediates through cotranslationally channeling newly synthesized Sec substrates to the Sec machinery; (ii) inhibition of folding Sec substrate proteins that transiently reside in the cytoplasm by molecular chaperones and the requirement for posttranslational modifications; (iii) destruction of products that could potentially inhibit translocation. In addition, several stress response pathways help to restore protein-folding homeostasis when environmental conditions that inhibit translocation overcome the AID quality control systems.
Collapse
Affiliation(s)
- Chen Jiang
- School of Biosciences and the Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Max Wynne
- School of Biosciences and the Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Damon Huber
- School of Biosciences and the Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| |
Collapse
|
3
|
De Geyter J, Portaliou AG, Srinivasu B, Krishnamurthy S, Economou A, Karamanou S. Trigger factor is a bona fide secretory pathway chaperone that interacts with SecB and the translocase. EMBO Rep 2020; 21:e49054. [PMID: 32307852 DOI: 10.15252/embr.201949054] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 03/09/2020] [Accepted: 03/19/2020] [Indexed: 11/09/2022] Open
Abstract
Bacterial secretory preproteins are translocated across the inner membrane post-translationally by the SecYEG-SecA translocase. Mature domain features and signal peptides maintain preproteins in kinetically trapped, largely soluble, folding intermediates. Some aggregation-prone preproteins require chaperones, like trigger factor (TF) and SecB, for solubility and/or targeting. TF antagonizes the contribution of SecB to secretion by an unknown molecular mechanism. We reconstituted this interaction in vitro and studied targeting and secretion of the model preprotein pro-OmpA. TF and SecB display distinct, unsuspected roles in secretion. Tightly associating TF:pro-OmpA targets the translocase at SecA, but TF prevents pro-OmpA secretion. In solution, SecB binds TF:pro-OmpA with high affinity. At the membrane, when bound to the SecA C-tail, SecB increases TF and TF:pro-OmpA affinities for the translocase and allows pro-OmpA to resume translocation. Our data reveal that TF, a main cytoplasmic folding pathway chaperone, is also a bona fide post-translational secretory chaperone that directly interacts with both SecB and the translocase to mediate regulated protein secretion. Thus, TF links the cytoplasmic folding and secretion chaperone networks.
Collapse
Affiliation(s)
- Jozefien De Geyter
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Athina G Portaliou
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Bindu Srinivasu
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Srinath Krishnamurthy
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Anastassios Economou
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| |
Collapse
|
4
|
Jamshad M, Knowles TJ, White SA, Ward DG, Mohammed F, Rahman KF, Wynne M, Hughes GW, Kramer G, Bukau B, Huber D. The C-terminal tail of the bacterial translocation ATPase SecA modulates its activity. eLife 2019; 8:48385. [PMID: 31246174 PMCID: PMC6620043 DOI: 10.7554/elife.48385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 06/26/2019] [Indexed: 11/25/2022] Open
Abstract
In bacteria, the translocation of proteins across the cytoplasmic membrane by the Sec machinery requires the ATPase SecA. SecA binds ribosomes and recognises nascent substrate proteins, but the molecular mechanism of nascent substrate recognition is unknown. We investigated the role of the C-terminal tail (CTT) of SecA in nascent polypeptide recognition. The CTT consists of a flexible linker (FLD) and a small metal-binding domain (MBD). Phylogenetic analysis and ribosome binding experiments indicated that the MBD interacts with 70S ribosomes. Disruption of the MBD only or the entire CTT had opposing effects on ribosome binding, substrate-protein binding, ATPase activity and in vivo function, suggesting that the CTT influences the conformation of SecA. Site-specific crosslinking indicated that F399 in SecA contacts ribosomal protein uL29, and binding to nascent chains disrupts this interaction. Structural studies provided insight into the CTT-mediated conformational changes in SecA. Our results suggest a mechanism for nascent substrate protein recognition.
Collapse
Affiliation(s)
- Mohammed Jamshad
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Timothy J Knowles
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Scott A White
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Douglas G Ward
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Fiyaz Mohammed
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Kazi Fahmida Rahman
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Max Wynne
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Gareth W Hughes
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ), ZMBH-DKFZ Alliance, Heidelberg, Germany
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ), ZMBH-DKFZ Alliance, Heidelberg, Germany
| | - Damon Huber
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| |
Collapse
|
5
|
Structural insights into chaperone addiction of toxin-antitoxin systems. Nat Commun 2019; 10:782. [PMID: 30770830 PMCID: PMC6377645 DOI: 10.1038/s41467-019-08747-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 01/10/2019] [Indexed: 12/20/2022] Open
Abstract
SecB chaperones assist protein export by binding both unfolded proteins and the SecA motor. Certain SecB homologs can also control toxin-antitoxin (TA) systems known to modulate bacterial growth in response to stress. In such TA-chaperone (TAC) systems, SecB assists the folding and prevents degradation of the antitoxin, thus facilitating toxin inhibition. Chaperone dependency is conferred by a C-terminal extension in the antitoxin known as chaperone addiction (ChAD) sequence, which makes the antitoxin aggregation-prone and prevents toxin inhibition. Using TAC of Mycobacterium tuberculosis, we present the structure of a SecB-like chaperone bound to its ChAD peptide. We find differences in the binding interfaces when compared to SecB–SecA or SecB-preprotein complexes, and show that the antitoxin can reach a functional form while bound to the chaperone. This work reveals how chaperones can use discrete surface binding regions to accommodate different clients or partners and thereby expand their substrate repertoire and functions. SecB homologs can be associated with stress-responsive type II toxin–antitoxin (TA) systems and form tripartite toxin-antitoxin-chaperone systems (TAC). Here the authors provide structural insights into TACs by presenting the crystal structure of the M. tuberculosis TA-associated SecB chaperone in complex with the C-terminal ChAD (chaperone addiction) extension of the antitoxin HigA1.
Collapse
|
6
|
Findik BT, Smith VF, Randall LL. Penetration into membrane of amino-terminal region of SecA when associated with SecYEG in active complexes. Protein Sci 2018; 27:681-691. [PMID: 29247569 DOI: 10.1002/pro.3362] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 11/12/2022]
Abstract
The general secretory (Sec) system of Escherichia coli translocates both periplasmic and outer membrane proteins through the cytoplasmic membrane. The pathway through the membrane is provided by a highly conserved translocon, which in E. coli comprises two heterotrimeric integral membrane complexes, SecY, SecE, and SecG (SecYEG), and SecD, SecF, and YajC (SecDF/YajC). SecA is an associated ATPase that is essential to the function of the Sec system. SecA plays two roles, it targets precursors to the translocon with the help of SecB and it provides energy via hydrolysis of ATP. SecA exists both free in the cytoplasm and integrally membrane associated. Here we describe details of association of the amino-terminal region of SecA with membrane. We use site-directed spin labelling and electron paramagnetic resonance spectroscopy to show that when SecA is co-assembled into lipids with SecYEG to yield highly active translocons, the N-terminal region of SecA penetrates the membrane and lies at the interface between the polar and the hydrophobic regions, parallel to the plane of the membrane at a depth of approximately 5 Å. When SecA is bound to SecYEG, preassembled into proteoliposomes, or nonspecifically bound to lipids in the absence of SecYEG, the N-terminal region penetrates more deeply (8 Å). Implications of partitioning of the SecA N-terminal region into lipids on the complex between SecB carrying a precursor and SecA are discussed.
Collapse
Affiliation(s)
- Bahar T Findik
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, Missouri, 65211
| | - Virginia F Smith
- Chemistry Department, U.S. Naval Academy, Annapolis, Maryland, 21402
| | - Linda L Randall
- Department of Biochemistry, 117 Schweitzer Hall, University of Missouri, Columbia, Missouri, 65211
| |
Collapse
|
7
|
Crane JM, Randall LL. The Sec System: Protein Export in Escherichia coli. EcoSal Plus 2017; 7:10.1128/ecosalplus.ESP-0002-2017. [PMID: 29165233 PMCID: PMC5807066 DOI: 10.1128/ecosalplus.esp-0002-2017] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Indexed: 11/20/2022]
Abstract
In Escherichia coli, proteins found in the periplasm or the outer membrane are exported from the cytoplasm by the general secretory, Sec, system before they acquire stably folded structure. This dynamic process involves intricate interactions among cytoplasmic and membrane proteins, both peripheral and integral, as well as lipids. In vivo, both ATP hydrolysis and proton motive force are required. Here, we review the Sec system from the inception of the field through early 2016, including biochemical, genetic, and structural data.
Collapse
Affiliation(s)
- Jennine M. Crane
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Linda L. Randall
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| |
Collapse
|
8
|
Findik BT, Randall LL. Determination of the intracellular concentration of the export chaperone SecB in Escherichia coli. PLoS One 2017; 12:e0183231. [PMID: 28850586 PMCID: PMC5574556 DOI: 10.1371/journal.pone.0183231] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 08/01/2017] [Indexed: 11/18/2022] Open
Abstract
SecB, a small tetrameric chaperone in Escherichia coli, plays a crucial role during protein export via the general secretory pathway by binding precursor polypeptides in a nonnative conformation and passing them to SecA, the ATPase of the translocon. The dissociation constants for the interactions are known; however to relate studies in vitro to export in a living cell requires knowledge of the concentrations of the proteins in the cell. Presently in the literature there is no report of a rigorous determination of the intracellular concentration of SecB. The values available vary over 60 fold and the details of the techniques used are not given. Here we use quantitative immunoblotting to determine the level of SecB expressed from the chromosome in E.coli grown in two commonly used media. In rich medium SecB was present at 1.6 ± 0.2 μM and in minimal medium at 2.5 ± 0.6 μM. These values allow studies of SecB carried out in vitro to be applied to the situation in the cell as SecB interacts with its binding partners to move precursor polypeptides through the export pathway.
Collapse
Affiliation(s)
- Bahar T. Findik
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Linda L. Randall
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
- * E-mail:
| |
Collapse
|
9
|
Liu X, Zhang W, Zhao Z, Dai X, Yang Y, Bai Z. Protein secretion in Corynebacterium glutamicum. Crit Rev Biotechnol 2016; 37:541-551. [PMID: 27737570 DOI: 10.1080/07388551.2016.1206059] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Corynebacterium glutamicum, a Gram-positive bacterium, has been widely used for the industrial production of amino acids, such as glutamate and lysine, for decades. Due to several characteristics - its ability to secrete properly folded and functional target proteins into culture broth, its low levels of endogenous extracellular proteins and its lack of detectable extracellular hydrolytic enzyme activity - C. glutamicum is also a very favorable host cell for the secretory production of heterologous proteins, important enzymes, and pharmaceutical proteins. The target proteins are secreted into the culture medium, which has attractive advantages over the manufacturing process for inclusion of body expression - the simplified downstream purification process. The secretory process of proteins is complicated and energy consuming. There are two major secretory pathways in C. glutamicum, the Sec pathway and the Tat pathway, both have specific signal peptides that mediate the secretion of the target proteins. In the present review, we critically discuss recent progress in the secretory production of heterologous proteins and examine in depth the mechanisms of the protein translocation process in C. glutamicum. Some successful case studies of actual applications of this secretory expression host are also evaluated. Finally, the existing issues and solutions in using C. glutamicum as a host of secretory proteins are specifically addressed.
Collapse
Affiliation(s)
- Xiuxia Liu
- a National Engineering Laboratory for Cereal Fermentation Technology , Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China
| | - Wei Zhang
- a National Engineering Laboratory for Cereal Fermentation Technology , Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China
| | - Zihao Zhao
- a National Engineering Laboratory for Cereal Fermentation Technology , Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China
| | - Xiaofeng Dai
- a National Engineering Laboratory for Cereal Fermentation Technology , Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China
| | - Yankun Yang
- a National Engineering Laboratory for Cereal Fermentation Technology , Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China
| | - Zhonghu Bai
- a National Engineering Laboratory for Cereal Fermentation Technology , Jiangnan University , Wuxi , China.,b The Key Laboratory of Industrial Biotechnology, Ministry of Education , School of Biotechnology, Jiangnan University , Wuxi , China
| |
Collapse
|
10
|
Abstract
There is a consensus in the medical profession of the pressing need for novel antimicrobial agents due to issues related to drug resistance. In practice, solutions to this problem to a large degree lie with the identification of new and vital targets in bacteria and subsequently designing their inhibitors. We consider SecA a very promising antimicrobial target. In this review, we compile and analyze information available on SecA to show that inhibition of SecA has a multitude of consequences. Furthermore, we discuss issues critical to the design and evaluation of SecA inhibitors.
Collapse
|
11
|
Dewi KS, Retnoningrum DS, Riani C, Fuad AM. Construction and Periplasmic Expression of the Anti-EGFRvIII ScFv Antibody Gene in Escherichia coli. Sci Pharm 2016; 84:141-52. [PMID: 27110505 PMCID: PMC4839555 DOI: 10.3797/scipharm.isp.2015.06] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 12/15/2015] [Indexed: 12/13/2022] Open
Abstract
In the previous study, we constructed an expression vector carrying the anti-EGFRvIII scFv antibody gene with VH-linker-VL orientation. The proteins were successfully produced in the periplasmic space of Escherichia coli. In this study, we substituted the inserted DNA with VL-linker-VH orientation of the anti-EGFRvIII scFv gene and analyzed its expression in E. coli. The DNA fragment was amplified from its cloning vector (pTz-rscFv), subsequently cloned into a previous expression vector containing the pelB signal sequence and his-tag, and then transformed into E. coli TOP10. The recombinant plasmids were characterized by restriction, PCR, and DNA sequencing analyses. The new anti-EGFRvIII scFv antibody proteins have been successfully expressed in the periplasmic compartment of E. coli Nico21(DE3) using 0.1 mM final concentration of IPTG induction. Total proteins, soluble periplasmic and cytoplasmic proteins, solubilized inclusion bodies, and extracellular proteins were analyzed by SDS-PAGE and Western Blot analyses. The results showed that soluble scFv proteins were found in all fractions except from the cytoplasmic space.
Collapse
Affiliation(s)
- Kartika Sari Dewi
- Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jalan Raya Bogor Km. 46, 16911, Cibinong, Bogor, Indonesia
- School of Pharmacy, Bandung Institute of Technology, Jalan Ganesha 10, 40132, Bandung, Indonesia
| | | | - Catur Riani
- School of Pharmacy, Bandung Institute of Technology, Jalan Ganesha 10, 40132, Bandung, Indonesia
| | - Asrul Muhamad Fuad
- Research Center for Biotechnology, Indonesian Institute of Sciences (LIPI), Jalan Raya Bogor Km. 46, 16911, Cibinong, Bogor, Indonesia
| |
Collapse
|
12
|
Yan S, Wu G. Large-scale evolutionary analyses on SecB subunits of bacterial sec system. PLoS One 2015; 10:e0120417. [PMID: 25775430 PMCID: PMC4361572 DOI: 10.1371/journal.pone.0120417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 01/21/2015] [Indexed: 01/10/2023] Open
Abstract
Protein secretion systems are extremely important in bacteria because they are involved in many fundamental cellular processes. Of the various secretion systems, the Sec system is composed of seven different subunits in bacteria, and subunit SecB brings secreted preproteins to subunit SecA, which with SecYEG and SecDF forms a complex for the translocation of secreted preproteins through the inner membrane. Because of the wide existence of Sec system across bacteria, eukaryota, and archaea, each subunit of the Sec system has a complicated evolutionary relationship. Until very recently, 5,162 SecB sequences have been documented in UniProtKB, however no phylogenetic study has been conducted on a large sampling of SecBs from bacterial Sec secretion system, and no statistical study has been conducted on such size of SecBs in order to exhaustively investigate their variances of pairwise p-distance along taxonomic lineage from kingdom to phylum, to class, to order, to family, to genus and to organism. To fill in these knowledge gaps, 3,813 bacterial SecB sequences with full taxonomic lineage from kingdom to organism covering 4 phyla, 11 classes, 41 orders, 82 families, 269 genera, and 3,744 organisms were studied. Phylogenetic analysis revealed how the SecBs evolved without compromising their function with examples of 3-D structure comparison of two SecBs from Proteobacteria, and possible factors that affected the SecB evolution were considered. The average pairwise p-distances showed that the variance varied greatly in each taxonomic group. Finally, the variance was further partitioned into inter- and intra-clan variances, which could correspond to vertical and horizontal gene transfers, with relevance for Achromobacter, Brevundimonas, Ochrobactrum, and Pseudoxanthomonas.
Collapse
Affiliation(s)
- Shaomin Yan
- State Key Laboratory of Non-food Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Biomass Industrialization Engineering Institute, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
| | - Guang Wu
- State Key Laboratory of Non-food Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Biomass Industrialization Engineering Institute, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
- * E-mail:
| |
Collapse
|
13
|
Suo Y, Hardy SJS, Randall LL. The basis of asymmetry in the SecA:SecB complex. J Mol Biol 2014; 427:887-900. [PMID: 25534082 DOI: 10.1016/j.jmb.2014.12.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 12/12/2014] [Accepted: 12/15/2014] [Indexed: 11/18/2022]
Abstract
During export in Escherichia coli, SecB, a homotetramer structurally organized as a dimer of dimers, forms a complex with two protomers of SecA, which is the ATPase that provides energy to transfer a precursor polypeptide through the membrane via the SecYEG translocon. There are two areas of contact on SecB that stabilize the SecA:SecB complex: the flat sides of the SecB tetramer and the C-terminal 13 residues of SecB. These contacts within the complex are distributed asymmetrically. Breaking contact between SecA and the sides of SecB results in release of only one protomer of SecA yielding a complex of stoichiometry SecA1:SecB4. This complex mediates export; however, the coupling of ATP hydrolysis to movements of the precursor through the translocon is much less efficient than the coupling by the SecA2:SecB4 complex. Here we used heterotetrameric species of SecB to understand the source of the asymmetry in the contacts and its role in the functioning of the complex. The model of interactions presented suggests a way that binding between SecA and SecB might decrease the affinity of precursor polypeptides for SecB and facilitate the transfer to SecA.
Collapse
Affiliation(s)
- Yuying Suo
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Simon J S Hardy
- Department of Biology, University of York, York YO10 5DD, UK
| | - Linda L Randall
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
| |
Collapse
|
14
|
Sala A, Bordes P, Genevaux P. Multitasking SecB chaperones in bacteria. Front Microbiol 2014; 5:666. [PMID: 25538690 PMCID: PMC4257090 DOI: 10.3389/fmicb.2014.00666] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/17/2014] [Indexed: 12/17/2022] Open
Abstract
Protein export in bacteria is facilitated by the canonical SecB chaperone, which binds to unfolded precursor proteins, maintains them in a translocation competent state and specifically cooperates with the translocase motor SecA to ensure their proper targeting to the Sec translocon at the cytoplasmic membrane. Besides its key contribution to the Sec pathway, SecB chaperone tasking is critical for the secretion of the Sec-independent heme-binding protein HasA and actively contributes to the cellular network of chaperones that control general proteostasis in Escherichia coli, as judged by the significant interplay found between SecB and the trigger factor, DnaK and GroEL chaperones. Although SecB is mainly a proteobacterial chaperone associated with the presence of an outer membrane and outer membrane proteins, secB-like genes are also found in Gram-positive bacteria as well as in certain phages and plasmids, thus suggesting alternative functions. In addition, a SecB-like protein is also present in the major human pathogen Mycobacterium tuberculosis where it specifically controls a stress-responsive toxin–antitoxin system. This review focuses on such very diverse chaperone functions of SecB, both in E. coli and in other unrelated bacteria.
Collapse
Affiliation(s)
- Ambre Sala
- Laboratoire de Microbiologie et Génétique Moléculaire, Centre National de la Recherche Scientifique, Université Paul Sabatier, Toulouse, France
| | - Patricia Bordes
- Laboratoire de Microbiologie et Génétique Moléculaire, Centre National de la Recherche Scientifique, Université Paul Sabatier, Toulouse, France
| | - Pierre Genevaux
- Laboratoire de Microbiologie et Génétique Moléculaire, Centre National de la Recherche Scientifique, Université Paul Sabatier, Toulouse, France
| |
Collapse
|
15
|
Chatzi KE, Sardis MF, Economou A, Karamanou S. SecA-mediated targeting and translocation of secretory proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1466-74. [PMID: 24583121 DOI: 10.1016/j.bbamcr.2014.02.014] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 02/12/2014] [Accepted: 02/15/2014] [Indexed: 11/26/2022]
Abstract
More than 30 years of research have revealed that the dynamic nanomotor SecA is a central player in bacterial protein secretion. SecA associates with the SecYEG channel and transports polypeptides post-translationally to the trans side of the cytoplasmic membrane. It comprises a helicase-like ATPase core coupled to two domains that provide specificity for preprotein translocation. Apart from SecYEG, SecA associates with multiple ligands like ribosomes, nucleotides, lipids, chaperones and preproteins. It exerts its essential contribution in two phases. First, SecA, alone or in concert with chaperones, helps mediate the targeting of the secretory proteins from the ribosome to the membrane. Next, at the membrane it converts chemical energy to mechanical work and translocates preproteins through the SecYEG channel. SecA is a highly dynamic enzyme, it exploits disorder-order kinetics, swiveling and dissociation of domains and dimer to monomer transformations that are tightly coupled with its catalytic function. Preprotein signal sequences and mature domains exploit these dynamics to manipulate the nanomotor and thus achieve their export at the expense of metabolic energy. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
Collapse
Affiliation(s)
- Katerina E Chatzi
- Institute of Molecular Biology and Biotechnology, FORTH, University of Crete, PO Box 1385, GR-711 10 Iraklio, Crete, Greece; KU Leuven, Rega Institute for Medical Research, Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
| | - Marios Frantzeskos Sardis
- KU Leuven, Rega Institute for Medical Research, Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium
| | - Anastassios Economou
- Institute of Molecular Biology and Biotechnology, FORTH, University of Crete, PO Box 1385, GR-711 10 Iraklio, Crete, Greece; Department of Biology, University of Crete, PO Box 1385, GR-711 10 Iraklio, Crete, Greece; KU Leuven, Rega Institute for Medical Research, Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium.
| | - Spyridoula Karamanou
- Institute of Molecular Biology and Biotechnology, FORTH, University of Crete, PO Box 1385, GR-711 10 Iraklio, Crete, Greece; KU Leuven, Rega Institute for Medical Research, Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium.
| |
Collapse
|
16
|
Rao C V S, De Waelheyns E, Economou A, Anné J. Antibiotic targeting of the bacterial secretory pathway. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1762-83. [PMID: 24534745 DOI: 10.1016/j.bbamcr.2014.02.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 01/27/2014] [Accepted: 02/06/2014] [Indexed: 02/06/2023]
Abstract
Finding new, effective antibiotics is a challenging research area driven by novel approaches required to tackle unconventional targets. In this review we focus on the bacterial protein secretion pathway as a target for eliminating or disarming pathogens. We discuss the latest developments in targeting the Sec-pathway for novel antibiotics focusing on two key components: SecA, the ATP-driven motor protein responsible for driving preproteins across the cytoplasmic membrane and the Type I signal peptidase that is responsible for the removal of the signal peptide allowing the release of the mature protein from the membrane. We take a bird's-eye view of other potential targets in the Sec-pathway as well as other Sec-dependent or Sec-independent protein secretion pathways as targets for the development of novel antibiotics. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
Collapse
Affiliation(s)
- Smitha Rao C V
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium.
| | - Evelien De Waelheyns
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium.
| | - Anastassios Economou
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium; Institute of Molecular Biology and Biotechnology, FORTH, University of Crete, P.O. Box 1385, GR-711 10 Iraklio, Crete, Greece; Department of Biology, University of Crete, P.O. Box 1385, GR-71110 Iraklio, Crete, Greece.
| | - Jozef Anné
- Laboratory of Molecular Bacteriology, Rega Institute, Department of Microbiology and Immunology, KU Leuven, O&N1, 6th floor, Herestraat 49, P.O. Box 1037, B-3000 Leuven, Belgium.
| |
Collapse
|
17
|
Breaking on through to the other side: protein export through the bacterial Sec system. Biochem J 2013; 449:25-37. [PMID: 23216251 DOI: 10.1042/bj20121227] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
More than one-third of cellular proteomes traffic into and across membranes. Bacteria have invented several sophisticated secretion systems that guide various proteins to extracytoplasmic locations and in some cases inject them directly into hosts. Of these, the Sec system is ubiquitous, essential and by far the best understood. Secretory polypeptides are sorted from cytoplasmic ones initially due to characteristic signal peptides. Then they are targeted to the plasma membrane by chaperones/pilots. The translocase, a dynamic nanomachine, lies at the centre of this process and acts as a protein-conducting channel with a unique property; allowing both forward transfer of secretory proteins but also lateral release into the lipid bilayer with high fidelity and efficiency. This process, tightly orchestrated at the expense of energy, ensures fundamental cell processes such as membrane biogenesis, cell division, motility, nutrient uptake and environmental sensing. In the present review, we examine this fascinating process, summarizing current knowledge on the structure, function and mechanics of the Sec pathway.
Collapse
|
18
|
Lycklama A Nijeholt JA, Driessen AJM. The bacterial Sec-translocase: structure and mechanism. Philos Trans R Soc Lond B Biol Sci 2012; 367:1016-28. [PMID: 22411975 DOI: 10.1098/rstb.2011.0201] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most bacterial secretory proteins pass across the cytoplasmic membrane via the translocase, which consists of a protein-conducting channel SecYEG and an ATP-dependent motor protein SecA. The ancillary SecDF membrane protein complex promotes the final stages of translocation. Recent years have seen a major advance in our understanding of the structural and biochemical basis of protein translocation, and this has led to a detailed model of the translocation mechanism.
Collapse
Affiliation(s)
- Jelger A Lycklama A Nijeholt
- Department of Molecular Microbiology, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands.
| | | |
Collapse
|
19
|
SecA, a remarkable nanomachine. Cell Mol Life Sci 2011; 68:2053-66. [PMID: 21479870 PMCID: PMC3101351 DOI: 10.1007/s00018-011-0681-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Revised: 03/22/2011] [Accepted: 03/28/2011] [Indexed: 01/03/2023]
Abstract
Biological cells harbor a variety of molecular machines that carry out mechanical work at the nanoscale. One of these nanomachines is the bacterial motor protein SecA which translocates secretory proteins through the protein-conducting membrane channel SecYEG. SecA converts chemically stored energy in the form of ATP into a mechanical force to drive polypeptide transport through SecYEG and across the cytoplasmic membrane. In order to accommodate a translocating polypeptide chain and to release transmembrane segments of membrane proteins into the lipid bilayer, SecYEG needs to open its central channel and the lateral gate. Recent crystal structures provide a detailed insight into the rearrangements required for channel opening. Here, we review our current understanding of the mode of operation of the SecA motor protein in concert with the dynamic SecYEG channel. We conclude with a new model for SecA-mediated protein translocation that unifies previous conflicting data.
Collapse
|
20
|
Randall LL, Henzl MT. Direct identification of the site of binding on the chaperone SecB for the amino terminus of the translocon motor SecA. Protein Sci 2010; 19:1173-9. [PMID: 20512970 DOI: 10.1002/pro.392] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein export mediated by the general secretory Sec system in Escherichia coli proceeds by a dynamic transfer of a precursor polypeptide from the chaperone SecB to the SecA ATPase motor of the translocon and subsequently into and through the channel of the membrane-embedded SecYEG heterotrimer. The complex between SecA and SecB is stabilized by several separate sites of contact. Here we have demonstrated directly an interaction between the N-terminal residues 2 through 11 of SecA and the C-terminal 13 residues of SecB by isothermal titration calorimetry and analytical sedimentation velocity centrifugation. We discuss the unusual binding properties of SecA and SecB in context of a model for transfer of the precursor along the pathway of export.
Collapse
Affiliation(s)
- Linda L Randall
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA.
| | | |
Collapse
|
21
|
|
22
|
Characterization of interactions between proteins using site-directed spin labeling and electron paramagnetic resonance spectroscopy. Methods Mol Biol 2010; 619:173-90. [PMID: 20419411 PMCID: PMC5814136 DOI: 10.1007/978-1-60327-412-8_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Site-directed spin-labeling and the analysis of proteins by electron paramagnetic resonance spectroscopy provides a powerful tool for identifying sites of contact within protein complexes at the resolution of aminoacyl side chains. Here we describe the method as we have used it to study interactions of proteins involved in export via the Sec secretory system in Escherichia coli. The method is amendable to the study of most protein interactions.
Collapse
|
23
|
Bechtluft P, Nouwen N, Tans SJ, Driessen AJM. SecB--a chaperone dedicated to protein translocation. MOLECULAR BIOSYSTEMS 2009; 6:620-7. [PMID: 20237639 DOI: 10.1039/b915435c] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SecB is a molecular chaperone in Gram-negative bacteria dedicated to the post-translational translocation of proteins across the cytoplasmic membrane. The entire surface of this chaperone is used for both of its native functions in protein targeting and unfolding. Single molecule studies revealed how SecB affects the folding pathway of proteins and how it prevents the tertiary structure formation and aggregation to support protein translocation.
Collapse
Affiliation(s)
- Philipp Bechtluft
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands.
| | | | | | | |
Collapse
|
24
|
Abstract
Abstract
The key enzymes that catalyze the insertion of proteins into membranes are the Sec translocase and the YidC membrane insertase. Recent insights into the structure and functional intermediates of these enzymes have provided a first molecular glimpse of how they help the newly synthesized proteins to enter the membrane bilayer. In this process, the new proteins undergo a number of specific interactions in the cytoplasm and at the membrane surface before they insert into the bilayer and translocate their external domains across the membrane. The components involved in this pathway recognize each other at the molecular level, forming a route the membrane protein can move along.
Collapse
|
25
|
Stephenson K. Sec-dependent protein translocation across biological membranes: evolutionary conservation of an essential protein transport pathway (Review). Mol Membr Biol 2009; 22:17-28. [PMID: 16092521 DOI: 10.1080/09687860500063308] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
All living organisms, no matter how simple or complex, possess the ability to translocate proteins across biological membranes and into different cellular compartments. Although a range of membrane transport processes exist, the major pathway used to translocate proteins across the bacterial cytoplasmic membrane or the eukaryotic endoplasmic reticulum membrane is conserved and is known as the Sec or Sec61 pathway, respectively. Over the past two decades the Sec and Sec61 pathways have been studied extensively and are well characterised at the genetic and biochemical levels. However, it is only now with the recent structural determination of a number of the key elements of the pathways that the translocation complex is beginning to give up its secrets in exquisite molecular detail. This article will focus on the routes of Sec- and Sec61-dependent membrane targeting and the nature of the translocation channel in bacteria and eukaryotes.
Collapse
Affiliation(s)
- Keith Stephenson
- School of Biochemistry and Microbiology, Leeds University, Leeds, UK.
| |
Collapse
|
26
|
Maximal efficiency of coupling between ATP hydrolysis and translocation of polypeptides mediated by SecB requires two protomers of SecA. J Bacteriol 2008; 191:978-84. [PMID: 18978043 DOI: 10.1128/jb.01321-08] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
SecA is the ATPase that provides energy for translocation of precursor polypeptides through the SecYEG translocon in Escherichia coli during protein export. We showed previously that when SecA receives the precursor from SecB, the ternary complex is fully active only when two protomers of SecA are bound. Here we used variants of SecA and of SecB that populate complexes containing two protomers of SecA to different degrees to examine both the hydrolysis of ATP and the translocation of polypeptides. We conclude that the low activity of the complexes with only one protomer is the result of a low efficiency of coupling between ATP hydrolysis and translocation.
Collapse
|
27
|
Affiliation(s)
- Arnold J.M. Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, 9751 NN, Haren, The Netherlands; ,
| | - Nico Nouwen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, 9751 NN, Haren, The Netherlands; ,
| |
Collapse
|
28
|
Ribnicky B, Van Blarcom T, Georgiou G. A scFv antibody mutant isolated in a genetic screen for improved export via the twin arginine transporter pathway exhibits faster folding. J Mol Biol 2007; 369:631-9. [PMID: 17462668 PMCID: PMC1995598 DOI: 10.1016/j.jmb.2007.03.068] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Revised: 03/16/2007] [Accepted: 03/27/2007] [Indexed: 11/15/2022]
Abstract
Proteins destined for export across the cytoplasmic membrane via the post-translational Sec-dependent route have to be maintained in a largely unfolded state within the cytoplasm. In sharp contrast, only proteins that have folded into a native-like state within the cytoplasm are competent for export via the twin arginine translocation (Tat) pathway. Proteins that contain disulfide bonds, such as scFv antibody fragments, can be translocated via Tat only when expressed in Escherichia coli trxB gor mutant strains having an oxidizing cytoplasm. However, export is poor with the majority of the protein accumulating in the cytoplasm and only a fraction exported to the periplasmic space. Using a high throughput fluorescence screen, we isolated a mutant of the anti-digoxin 26-10 scFv from a large library of random mutants that is exported with a higher yield into the periplasm. In vitro refolding experiments revealed that the mutant scFv exhibits a 250% increase in the rate constant of the critical second phase of folding. This result suggests that Tat export competence is related to the protein folding rate and could be exploited for the isolation of faster folding protein mutants.
Collapse
Affiliation(s)
- Brian Ribnicky
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
| | - Thomas Van Blarcom
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
- Department of Biomedical Engineering, University of Texas, Austin, TX 78712, USA
- *Corresponding author: , Department of Chemical Engineering, CPE 4.410, University of Texas at Austin, Austin, TX 78712, Phone 512-471-6975, Fax 512-471-7963
| |
Collapse
|
29
|
Patel CN, Smith VF, Randall LL. Characterization of three areas of interactions stabilizing complexes between SecA and SecB, two proteins involved in protein export. Protein Sci 2006; 15:1379-86. [PMID: 16731972 PMCID: PMC2265093 DOI: 10.1110/ps.062141006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The general secretory, Sec, system translocates precursor polypeptides from the cytosol across the cytoplasmic membrane in Escherichia coli. SecB, a small cytosolic chaperone, captures the precursor polypeptides before they fold and delivers them to the membrane translocon through interactions with SecA. Both SecB and SecA display twofold symmetry and yet the complex between the two is stabilized by contacts that are distributed asymmetrically. Two distinct regions of interaction have been defined previously and here we identify a third. Calorimetric studies of complexes stabilized by different subsets of these interactions were carried out to determine the binding affinities and the thermodynamic parameters that underlie them. We show here that there is no change in affinity when either one of two contact areas out of the three is lacking. This fact and the asymmetry of the binding contacts may be important to the function of the complex in protein export.
Collapse
Affiliation(s)
- Chetan N Patel
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
| | | | | |
Collapse
|
30
|
Hoefer MM, Boneberg EM, Grotegut S, Kusch J, Illges H. Possible tetramerisation of the proteasome maturation factor POMP/proteassemblin/hUmp1 and its subcellular localisation. Int J Biol Macromol 2006; 38:259-67. [PMID: 16624403 DOI: 10.1016/j.ijbiomac.2006.03.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Revised: 02/22/2006] [Accepted: 03/06/2006] [Indexed: 11/24/2022]
Abstract
The proteasome is a multisubunit complex with a central role in non-lysosomal proteolysis and the processing of proteins for presentation by the MHC class I pathway. The 16kDa proteasome maturation protein POMP (also named proteassemblin or hUmp1) acts as a chaperone and is essential for the maturation of the 20S proteasome proteolytic core complex. However, the exact mechanism, timing and localisation of mammalian proteasome assembly remains elusive. We sought to investigate the localisation of POMP within the cell and therefore purified the protein and produced a polyclonal antibody. For immunisation, POMP was overexpressed and purified from a bacterial GST-system. Interestingly, after removal of the GST-tag, POMP was hardly detectable by Coomassie blue- and Ponceau red-staining. However, with a reverse zinc-staining, the protein could easily be visualised. POMP was gel-filtrated and eluted from a calibrated chromatography column with an apparent molecular weight of approximately 64kDa, suggesting that it forms tetramers. Moreover, localisation studies by immunofluorescence stainings and confocal microscopy revealed that POMP is present in the cytoplasm as well as in the nucleus.
Collapse
|
31
|
Papanikou E, Karamanou S, Baud C, Frank M, Sianidis G, Keramisanou D, Kalodimos CG, Kuhn A, Economou A. Identification of the Preprotein Binding Domain of SecA. J Biol Chem 2005; 280:43209-17. [PMID: 16243836 DOI: 10.1074/jbc.m509990200] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SecA, the preprotein translocase ATPase, has a helicase DEAD motor. To catalyze protein translocation, SecA possesses two additional flexible domains absent from other helicases. Here we demonstrate that one of these "specificity domains" is a preprotein binding domain (PBD). PBD is essential for viability and protein translocation. PBD mutations do not abrogate the basal enzymatic properties of SecA (nucleotide binding and hydrolysis), nor do they prevent SecA binding to the SecYEG protein conducting channel. However, SecA PBD mutants fail to load preproteins onto SecYEG, and their translocation ATPase activity does not become stimulated by preproteins. Bulb and Stem, the two sterically proximal PBD substructures, are physically separable and have distinct roles. Stem binds signal peptides, whereas the Bulb binds mature preprotein regions as short as 25 amino acids. Binding of signal or mature region peptides or full-length preproteins causes distinct conformational changes to PBD and to the DEAD motor. We propose that (a) PBD is a preprotein receptor and a physical bridge connecting bound preproteins to the DEAD motor, and (b) preproteins control the ATPase cycle via PBD.
Collapse
Affiliation(s)
- Efrosyni Papanikou
- Institute of Molecular Biology and Biotechnology, F.O.R.T.H., University of Crete, P.O. Box 1527, GR-711 10 Iraklio, Crete, Greece
| | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Crane JM, Mao C, Lilly AA, Smith VF, Suo Y, Hubbell WL, Randall LL. Mapping of the docking of SecA onto the chaperone SecB by site-directed spin labeling: insight into the mechanism of ligand transfer during protein export. J Mol Biol 2005; 353:295-307. [PMID: 16169560 DOI: 10.1016/j.jmb.2005.08.022] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2005] [Revised: 08/11/2005] [Accepted: 08/15/2005] [Indexed: 10/25/2022]
Abstract
Export of protein into the periplasm of Escherichia coli via the general secretory system is achieved by action of a ternary complex comprising the polypeptide ligand, the chaperone SecB and SecA, a peripheral component of the membrane translocon, which is itself an ATPase. The unfolded ligand is captured initially by SecB and must be transferred to SecA and subsequently through the membrane translocon into the periplasm. We have taken the first steps in the elucidation of the mechanism of this dynamic transfer by determining the interface of interaction between SecB and SecA. Site-directed spin labeling and electron paramagnetic resonance spectroscopy were combined to identify which of the residues on SecB showed changes in spectral line shape upon addition of SecA. In all, 43% of the surface of SecB was covered by the 41 positions examined. A model of docking between SecB and SecA is proposed based on the pattern of amino acid residues on SecB shown to make contacts when in complex with SecA. This model in combination with previously published biochemical data provides insight into the transfer of the unfolded polypeptide from the chaperone SecB to SecA.
Collapse
Affiliation(s)
- Jennine M Crane
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | | | | | | | | | | | | |
Collapse
|
33
|
Zhou J, Xu Z. The structural view of bacterial translocation-specific chaperone SecB: implications for function. Mol Microbiol 2005; 58:349-57. [PMID: 16194224 DOI: 10.1111/j.1365-2958.2005.04842.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
SecB is a molecular chaperone that functions in bacterial post-translational protein translocation pathway. It maintains newly synthesized precursor polypeptide chains in a translocation-competent state and guides them to the translocon via its high-affinity binding to the ligand as well as to the membrane-embedded ATPase SecA. Recent advances in elucidating the structures of SecB have enabled the examination of protein function in the structural context. Structures of SecB from both Haemophilus influenzae and Escherichia coli support the early two-subsite polypeptide-binding model. In addition, the detailed molecular interaction between SecB and SecA was revealed by a structure of SecB in complex with the C-terminal zinc-containing domain of SecA. These observations explain the dual role of SecB plays in the translocation pathway, as a molecular chaperone and a specific targeting factor. A model of SecB-SecA complex suggests that the binding of SecA to SecB changes the conformation of the polypeptide binding sites in the chaperone, enabling transfer of precursor polypeptides from SecB to SecA. Recent studies also show the presence of a second zinc-independent SecB binding site in SecA and the new interaction might contribute to the function of SecB.
Collapse
Affiliation(s)
- Jiahai Zhou
- Department of Biological Chemistry, Medical School and Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216, USA
| | | |
Collapse
|
34
|
Randall LL, Crane JM, Lilly AA, Liu G, Mao C, Patel CN, Hardy SJS. Asymmetric Binding Between SecA and SecB Two Symmetric Proteins: Implications for Function in Export. J Mol Biol 2005; 348:479-89. [PMID: 15811382 DOI: 10.1016/j.jmb.2005.02.036] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2004] [Revised: 02/15/2005] [Accepted: 02/18/2005] [Indexed: 10/25/2022]
Abstract
SecB, a small tetrameric chaperone in Escherichia coli, facilitates export of precursor polypeptides from the cytoplasm to the periplasmic space. During this process, SecB displays two modes of binding. As a chaperone, it binds promiscuously to precursors to maintain them in a non-native conformation. SecB also demonstrates specific recognition of, and binding to, SecA. SecB with the precursor tightly bound enters an export-active complex with SecA and must pass the ligand to SecA at the translocon in the membrane. Here we use variants of SecA and SecB to further probe these interactions. We show that, unexpectedly, the binding between the two symmetric molecules is asymmetric and that the C-terminal alpha-helices of SecB bind in the interfacial region of the SecA dimer. We suggest that disruption of this interface by SecB facilitates conformational changes of SecA that are crucial to the transfer of the precursor from SecB to SecA.
Collapse
Affiliation(s)
- Linda L Randall
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
| | | | | | | | | | | | | |
Collapse
|
35
|
Vrontou E, Economou A. Structure and function of SecA, the preprotein translocase nanomotor. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1694:67-80. [PMID: 15546658 DOI: 10.1016/j.bbamcr.2004.06.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2003] [Revised: 06/03/2004] [Accepted: 06/17/2004] [Indexed: 11/22/2022]
Abstract
Most secretory proteins that are destined for the periplasm or the outer membrane are exported through the bacterial plasma membrane by the Sec translocase. Translocase is a complex nanomachine that moves processively along its aminoacyl polymeric substrates effectively pumping them to the periplasmic space. The salient features of this process are: (a) a membrane-embedded "clamp" formed by the trimeric SecYEG protein, (b) a "motor" provided by the dimeric SecA ATPase, (c) regulatory subunits that optimize catalysis and (d) both chemical and electrochemical metabolic energy. Significant recent strides have allowed structural, biochemical and biophysical dissection of the export reaction. A model incorporating stepwise strokes of the translocase nanomachine at work is discussed.
Collapse
Affiliation(s)
- Eleftheria Vrontou
- Laboratory Unicellular, Organisms Group, Institute of Molecular Biology and Biotechnology, FO.R.T.H. and Department of Biology, University of Crete, Vassilika Vouton, P.O. Box 1527, GR-711 10 Iraklio, Crete, Greece
| | | |
Collapse
|
36
|
Matousek WM, Alexandrescu AT. NMR structure of the C-terminal domain of SecA in the free state. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1702:163-71. [PMID: 15488768 DOI: 10.1016/j.bbapap.2004.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2004] [Revised: 08/14/2004] [Accepted: 08/17/2004] [Indexed: 11/18/2022]
Abstract
SecA is an integral component of the prokaryotic Sec preprotein secretory translocase system. We report here the solution NMR structure of a fragment corresponding to the C-terminal domain of Escherichia coli SecA. In the presence of Zn2+, the fragment adopts a shortened version of the classic betabetaalpha zinc finger fold. The isolated C-terminal domain shows substantial differences from the X-ray structure of a homologous SecA domain bound to the chaperone-like cofactor SecB. The differences between the structures of the free and bound forms suggest that binding to SecB causes a perturbation of the C-terminal domain's intrinsically favored betabetaalpha fold.
Collapse
Affiliation(s)
- William M Matousek
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, U-3125, Storrs, CT 06269-3125, USA
| | | |
Collapse
|