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Jin F, Chang Z. Uncovering the membrane-integrated SecA N protein that plays a key role in translocating nascent outer membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140865. [PMID: 36272538 DOI: 10.1016/j.bbapap.2022.140865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/09/2022] [Accepted: 10/14/2022] [Indexed: 11/08/2022]
Abstract
A large number of nascent polypeptides have to get across a membrane in targeting to the proper subcellular locations. The SecYEG protein complex, a homolog of the Sec61 complex in eukaryotic cells, has been viewed as the common translocon at the inner membrane for targeting proteins to three extracytoplasmic locations in Gram-negative bacteria, despite the lack of direct verification in living cells. Here, via unnatural amino acid-mediated protein-protein interaction analyses in living cells, in combination with genetic studies, we unveiled a hitherto unreported SecAN protein that seems to be directly involved in translocationg nascent outer membrane proteins across the plasma membrane; it consists of the N-terminal 375 residues of the SecA protein and exists as a membrane-integrated homooligomer. Our new findings place multiple previous observations related to bacterial protein targeting in proper biochemical and evolutionary contexts.
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Affiliation(s)
- Feng Jin
- State key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Protein Science, Peking University, Beijing 100871, China
| | - Zengyi Chang
- State key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Protein Science, Peking University, Beijing 100871, China.
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2
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Potteth US, Upadhyay T, Saini S, Saraogi I. Novel Antibacterial Targets in Protein Biogenesis Pathways. Chembiochem 2021; 23:e202100459. [PMID: 34643994 DOI: 10.1002/cbic.202100459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/12/2021] [Indexed: 11/11/2022]
Abstract
Antibiotic resistance has emerged as a global threat due to the ability of bacteria to quickly evolve in response to the selection pressure induced by anti-infective drugs. Thus, there is an urgent need to develop new antibiotics against resistant bacteria. In this review, we discuss pathways involving bacterial protein biogenesis as attractive antibacterial targets since many of them are essential for bacterial survival and virulence. We discuss the structural understanding of various components associated with bacterial protein biogenesis, which in turn can be utilized for rational antibiotic design. We highlight efforts made towards developing inhibitors of these pathways with insights into future possibilities and challenges. We also briefly discuss other potential targets related to protein biogenesis.
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Affiliation(s)
- Upasana S Potteth
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Tulsi Upadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Snehlata Saini
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India
| | - Ishu Saraogi
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal, 462066, Madhya Pradesh, India.,Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal Bypass Road, Bhopal - 462066, Madhya Pradesh, India
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3
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Thiouracil SecA inhibitors: bypassing the effects of efflux pumps and attenuating virulence factor secretion in MRSA and Bacillus anthracis. Med Chem Res 2021. [DOI: 10.1007/s00044-021-02750-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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4
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5
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Bamba F, Jin J, Tai PC, Wang B. Synthesis and biological evaluation of novel 4-oxo-5-cyano thiouracil derivatives as SecA inhibitors. HETEROCYCL COMMUN 2020. [DOI: 10.1515/hc-2020-0100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractThe continuous emergence of drug-resistant strains of bacteria poses an urgent risk to human health and dictates the need for new antimicrobials. Along this line, we have been working on developing inhibitors of SecA, a key component of the bacterial Sec-dependent secretion machinery. Herein, we describe the synthesis and antimicrobial evaluation of 6-oxo-1,6-dihydropyrimidine-5-carbonitrile derivatives as potential SecA inhibitors.
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Affiliation(s)
- Fante Bamba
- Departments of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
- Laboratoire de Chimie Organique et des Substances Naturelles, Université Félix Houphouët-Boigny, 22 Bp 582 Abidjan 22, AbidjanCote d‘Ivoire
| | - Jinshan Jin
- Departments of Biology, Georgia State University, Atlanta, Georgia 30303, USA
| | - Phang C. Tai
- Departments of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, USA
| | - Binghe Wang
- Departments of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, USA
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6
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Substrate Proteins Take Shape at an Improved Bacterial Translocon. J Bacteriol 2018; 201:JB.00618-18. [PMID: 30322856 DOI: 10.1128/jb.00618-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 10/12/2018] [Indexed: 11/20/2022] Open
Abstract
Characterization of Sec-dependent bacterial protein transport has often relied on an in vitro protein translocation system comprised in part of Escherichia coli inverted inner membrane vesicles or, more recently, purified SecYEG translocons reconstituted into liposomes using mostly a single substrate (proOmpA). A paper published in this issue (P. Bariya and L. Randall, J Bacteriol 201:e00493-18, 2019, https://doi.org/10.1128/JB.00493-18) finds that inclusion of SecA protein during SecYEG proteoliposome reconstitution dramatically improves the number of active translocons. This experimentally useful and intriguing result that may arise from SecA membrane integration properties is discussed here. Furthermore, determination of the rate-limiting transport step for nine different substrates implicates the mature region distal to the signal peptide in the observed rate constant differences, indicating that more nuanced transport models that respond to differences in protein sequence and structure are needed.
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7
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Jin J, Hsieh YH, Chaudhary AS, Cui J, Houghton JE, Sui SF, Wang B, Tai PC. SecA inhibitors as potential antimicrobial agents: differential actions on SecA-only and SecA-SecYEG protein-conducting channels. FEMS Microbiol Lett 2018; 365:5037921. [PMID: 30007321 PMCID: PMC7190897 DOI: 10.1093/femsle/fny145] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/13/2018] [Indexed: 12/13/2022] Open
Abstract
Sec-dependent protein translocation is an essential process in bacteria. SecA is a key component of the translocation machinery and has multiple domains that interact with various ligands. SecA acts as an ATPase motor to drive the precursor protein/peptide through the SecYEG protein translocation channels. As SecA is unique to bacteria and there is no mammalian counterpart, it is an ideal target for the development of new antimicrobials. Several reviews detail the assays for ATPase and protein translocation, as well as the search for SecA inhibitors. Recent studies have shown that, in addition to the SecA-SecYEG translocation channels, there are SecA-only channels in the lipid bilayers, which function independently from the SecYEG machinery. This mini-review focuses on recent advances on the newly developed SecA inhibitors that allow the evaluation of their potential as antimicrobial agents, as well as a fundamental understanding of mechanisms of SecA function(s). These SecA inhibitors abrogate the effects of efflux pumps in both Gram-positive and Gram-negative bacteria. We also discuss recent findings that SecA binds to ribosomes and nascent peptides, which suggest other roles of SecA. A model for the multiple roles of SecA is presented.
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Affiliation(s)
- Jinshan Jin
- Department of Biology, Center for Biotechnology and Drug Design and Georgia State University, Atlanta, GA 30303, USA
| | - Ying-Hsin Hsieh
- Department of Biology, Center for Biotechnology and Drug Design and Georgia State University, Atlanta, GA 30303, USA
| | - Arpana S Chaudhary
- Department of Chemistry, Center for Biotechnology and Drug Design and Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA
| | - Jianmei Cui
- Department of Chemistry, Center for Biotechnology and Drug Design and Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA
| | - John E Houghton
- Department of Biology, Center for Biotechnology and Drug Design and Georgia State University, Atlanta, GA 30303, USA
| | - Sen-fang Sui
- State Key Laboratory of Membrane Biology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Binghe Wang
- Department of Chemistry, Center for Biotechnology and Drug Design and Georgia State University, P.O. Box 3965, Atlanta, GA 30303, USA
| | - Phang C Tai
- Department of Biology, Center for Biotechnology and Drug Design and Georgia State University, Atlanta, GA 30303, USA
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8
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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.
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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
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9
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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.
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Affiliation(s)
- Jennine M. Crane
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Linda L. Randall
- Department of Biochemistry, University of Missouri, Columbia, Missouri
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10
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Banerjee T, Zheng Z, Abolafia J, Harper S, Oliver D. The SecA protein deeply penetrates into the SecYEG channel during insertion, contacting most channel transmembrane helices and periplasmic regions. J Biol Chem 2017; 292:19693-19707. [PMID: 28986446 DOI: 10.1074/jbc.ra117.000130] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Indexed: 11/06/2022] Open
Abstract
The bacterial Sec-dependent system is the major protein-biogenic pathway for protein secretion across the cytoplasmic membrane or insertion of integral membrane proteins into the phospholipid bilayer. The mechanism of SecA-driven protein transport across the SecYEG channel complex has remained controversial with conflicting claims from biochemical and structural studies regarding the depth and extent of SecA insertion into SecYEG during ongoing protein transport. Here we utilized site-specific in vivo photo-crosslinking to thoroughly map SecY regions that are in contact with SecA during its insertion cycle. An arabinose-inducible, rapidly folding OmpA-GFP chimera was utilized to jam the SecYEG channels with an arrested substrate protein to "freeze" them in their SecA-inserted state. Examination of 117 sites distributed throughout SecY indicated that SecA not only interacts extensively with the cytosolic regions of SecY as shown previously, but it also interacts with most of the transmembrane helices and periplasmic regions of SecY, with a clustering of interaction sights around the lateral gate and pore ring regions. Our observations support previous reports of SecA membrane insertion during in vitro protein transport as well as those documenting the membrane penetration properties of this protein. They suggest that one or more SecA regions transiently integrate into the heart of the SecY channel complex to span the membrane to promote the protein transport cycle. These findings indicate that high-resolution structural information about the membrane-inserted state of SecA is still lacking and will be critical for elucidating the bacterial protein transport mechanism.
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Affiliation(s)
- Tithi Banerjee
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Zeliang Zheng
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Jane Abolafia
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Shelby Harper
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Donald Oliver
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
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11
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Hsieh YH, Huang YJ, Zhang H, Liu Q, Lu Y, Yang H, Houghton J, Jiang C, Sui SF, Tai PC. Dissecting structures and functions of SecA-only protein-conducting channels: ATPase, pore structure, ion channel activity, protein translocation, and interaction with SecYEG/SecDF•YajC. PLoS One 2017; 12:e0178307. [PMID: 28575061 PMCID: PMC5456053 DOI: 10.1371/journal.pone.0178307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/10/2017] [Indexed: 11/30/2022] Open
Abstract
SecA is an essential protein in the major bacterial Sec-dependent translocation pathways. E. coli SecA has 901 aminoacyl residues which form multi-functional domains that interact with various ligands to impart function. In this study, we constructed and purified tethered C-terminal deletion fragments of SecA to determine the requirements for N-terminal domains interacting with lipids to provide ATPase activity, pore structure, ion channel activity, protein translocation and interactions with SecYEG-SecDF•YajC. We found that the N-terminal fragment SecAN493 (SecA1-493) has low, intrinsic ATPase activity. Larger fragments have greater activity, becoming highest around N619-N632. Lipids greatly stimulated the ATPase activities of the fragments N608-N798, reaching maximal activities around N619. Three helices in amino-acyl residues SecA619-831, which includes the "Helical Scaffold" Domain (SecA619-668) are critical for pore formation, ion channel activity, and for function with SecYEG-SecDF•YajC. In the presence of liposomes, N-terminal domain fragments of SecA form pore-ring structures at fragment-size N640, ion channel activity around N798, and protein translocation capability around N831. SecA domain fragments ranging in size between N643-N669 are critical for functional interactions with SecYEG-SecDF•YajC. In the presence of liposomes, inactive C-terminal fragments complement smaller non-functional N-terminal fragments to form SecA-only pore structures with ion channel activity and protein translocation ability. Thus, SecA domain fragment interactions with liposomes defined critical structures and functional aspects of SecA-only channels. These data provide the mechanistic basis for SecA to form primitive, low-efficiency, SecA-only protein-conducting channels, as well as the minimal parameters for SecA to interact functionally with SecYEG-SecDF•YajC to form high-efficiency channels.
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Affiliation(s)
- Ying-hsin Hsieh
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, United States of America
| | - Ying-ju Huang
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, United States of America
| | - Hao Zhang
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, United States of America
| | - Qian Liu
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, United States of America
| | - Yang Lu
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, United States of America
| | - Hsiuchin Yang
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, United States of America
| | - John Houghton
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, United States of America
| | - Chun Jiang
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, United States of America
| | - Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing China
| | - Phang C. Tai
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA, United States of America
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12
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Hsieh YH, Zhang H, Jin J, Dai C, Jiang C, Wang B, Tai PC. Biphasic actions of SecA inhibitors on Prl/Sec suppressors: Possible physiological roles of SecA-only channels. Biochem Biophys Res Commun 2017; 482:296-300. [PMID: 27856243 DOI: 10.1016/j.bbrc.2016.11.057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 11/11/2016] [Indexed: 11/30/2022]
Abstract
SecA is an essential component in the bacterial Sec-dependent protein translocation process. We previously showed that in addition to the ubiquitous, high-affinity SecYEG-SecDF·YajC protein translocation channel, there is a low-affinity SecA-only channel that elicits ion channel activity and promotes protein translocation. The SecA-only channels are less efficient, and like Prl suppressors, lack signal peptide specificity; they function in the absence of signal peptides. The presence of SecYEG-SecDF·YajC alters the sensitivity of ATPase inhibitor Rose Bengal. In this study, we found that the suppressor membranes are much more resistant to inhibition by Rose Bengal. Similar results have been found for a SecA-specific inhibitor. Moreover, biphasic responses of inhibition of ion current and protein translocation activities were observed for many PrlA/SecY and PrlG/SecE suppressor membranes, with a low IC50 value similar to that of the SecA-only channels and a very high IC50. However, the suppressor strains are as sensitive to the inhibitor as the parental strain, suggesting that SecA-only channels have some essential physiological function(s) in the cells that are inhibited by the specific SecA inhibitor.
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Affiliation(s)
- Ying-Hsin Hsieh
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Hao Zhang
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Jinshan Jin
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Chaofeng Dai
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Chun Jiang
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Binghe Wang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Phang C Tai
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA.
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13
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Jin J, Hsieh YH, Cui J, Damera K, Dai C, Chaudhary AS, Zhang H, Yang H, Cao N, Jiang C, Vaara M, Wang B, Tai PC. Using Chemical Probes to Assess the Feasibility of Targeting SecA for Developing Antimicrobial Agents against Gram-Negative Bacteria. ChemMedChem 2016; 11:2511-2521. [PMID: 27753464 PMCID: PMC5189635 DOI: 10.1002/cmdc.201600421] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 09/25/2016] [Indexed: 11/07/2022]
Abstract
With the widespread emergence of drug resistance, there is an urgent need to search for new antimicrobials, especially those against Gram-negative bacteria. Along this line, the identification of viable targets is a critical first step. The protein translocase SecA is commonly believed to be an excellent target for the development of broad-spectrum antimicrobials. In recent years, we developed three structural classes of SecA inhibitors that have proven to be very effective against Gram-positive bacteria. However, we have not achieved the same level of success against Gram-negative bacteria, despite the potent inhibition of SecA in enzyme assays by the same inhibitors. In this study, we use representative inhibitors as chemical probes to gain an understanding as to why these inhibitors were not effective against Gram-negative bacteria. The results validate our initial postulation that the major difference in effectiveness against Gram-positive and Gram-negative bacteria is in the additional permeability barrier posed by the outer membrane of Gram-negative bacteria. We also found that the expression of efflux pumps, which are responsible for multidrug resistance (MDR), have no effect on the effectiveness of these SecA inhibitors. Identification of an inhibitor-resistant mutant and complementation tests of the plasmids containing secA in a secAts mutant showed that a single secA-azi-9 mutation increased the resistance, providing genetic evidence that SecA is indeed the target of these inhibitors in bacteria. Such results strongly suggest SecA as an excellent target for developing effective antimicrobials against Gram-negative bacteria with the intrinsic ability to overcome MDR. A key future research direction should be the optimization of membrane permeability.
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Affiliation(s)
- Jinshan Jin
- Department of Biology, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Ying-Hsin Hsieh
- Department of Biology, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Jianmei Cui
- Department of Chemistry, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Krishna Damera
- Department of Chemistry, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Chaofeng Dai
- Department of Chemistry, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Arpana S. Chaudhary
- Department of Chemistry, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Hao Zhang
- Department of Biology, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Hsiuchin Yang
- Department of Biology, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Nannan Cao
- Department of Biology, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Chun Jiang
- Department of Biology, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Martti Vaara
- Division of Clinical Microbiology, Helsinki University Hospital, FI-00029 HUSLAB, Helsinki, Finland, and Northern Antibiotics Ltd, FI-00720, Helsinki, Finland
| | - Binghe Wang
- Department of Chemistry, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
| | - Phang C. Tai
- Department of Biology, Center for Biotechnology and Drug Design, and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303
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14
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Kuppast B, Fahmy H. Thiazolo[4,5-d]pyrimidines as a privileged scaffold in drug discovery. Eur J Med Chem 2016; 113:198-213. [DOI: 10.1016/j.ejmech.2016.02.031] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/11/2016] [Accepted: 02/11/2016] [Indexed: 01/01/2023]
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15
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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.
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16
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Cui J, Jin J, Chaudhary AS, Hsieh YH, Zhang H, Dai C, Damera K, Chen W, Tai PC, Wang B. Design, Synthesis and Evaluation of Triazole-Pyrimidine Analogues as SecA Inhibitors. ChemMedChem 2016; 11:43-56. [PMID: 26607404 PMCID: PMC4778717 DOI: 10.1002/cmdc.201500447] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Indexed: 01/15/2023]
Abstract
SecA, a key component of the bacterial Sec-dependent secretion pathway, is an attractive target for the development of new antimicrobial agents. Through a combination of virtual screening and experimental exploration of the surrounding chemical space, we identified a hit bistriazole SecA inhibitor, SCA-21, and studied a series of analogues by systematic dissections of the core scaffold. Evaluation of these analogues allowed us to establish an initial structure-activity relationship in SecA inhibition. The best compounds in this group are potent inhibitors of SecA-dependent protein-conducting channel activity and protein translocation activity at low- to sub-micromolar concentrations. They also have minimal inhibitory concentration (MIC) values against various strains of bacteria that correlate well with the SecA and protein translocation inhibition data. These compounds are effective against methicillin-resistant Staphylococcus aureus strains with various levels of efflux pump activity, indicating the capacity of SecA inhibitors to null the effect of multidrug resistance. Results from studies of drug-affinity-responsive target stability and protein pull-down assays are consistent with SecA as a target for these compounds.
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Affiliation(s)
- Jianmei Cui
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Jinshan Jin
- Department of Biology, Center for Biotechnology and Drug Design, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303, USA
| | | | - Ying-hsin Hsieh
- Department of Biology, Center for Biotechnology and Drug Design, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303, USA
| | - Hao Zhang
- Department of Biology, Center for Biotechnology and Drug Design, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303, USA
| | - Chaofeng Dai
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Krishna Damera
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Weixuan Chen
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Phang C Tai
- Department of Biology, Center for Biotechnology and Drug Design, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303, USA.
| | - Binghe Wang
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA.
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17
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Jin J, Cui J, Chaudhary AS, Hsieh YH, Damera K, Zhang H, Yang H, Wang B, Tai PC. Evaluation of small molecule SecA inhibitors against methicillin-resistant Staphylococcus aureus. Bioorg Med Chem 2015; 23:7061-8. [PMID: 26432604 PMCID: PMC4661110 DOI: 10.1016/j.bmc.2015.09.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 09/09/2015] [Accepted: 09/16/2015] [Indexed: 12/11/2022]
Abstract
Due to the emergence and rapid spread of drug resistance in bacteria, there is an urgent need for the development of novel antimicrobials. SecA, a key component of the general bacterial secretion system required for viability and virulence, is an attractive antimicrobial target. Earlier we reported that systematical dissection of a SecA inhibitor, Rose Bengal (RB), led to the development of novel small molecule SecA inhibitors active against Escherichia coli and Bacillus subtilis. In this study, two potent RB analogs were further evaluated for activities against methicillin-resistant Staphylococcus aureus (MRSA) strains and for their mechanism of actions. These analogs showed inhibition on the ATPase activities of S. aureus SecA1 (SaSecA1) and SecA2 (SaSecA2), and inhibition of SaSecA1-dependent protein-conducting channel. Moreover, these inhibitors reduce the secretion of three toxins from S. aureus and exert potent bacteriostatic effects against three MRSA strains. Our best inhibitor SCA-50 showed potent concentration-dependent bactericidal activity against MRSA Mu50 strain and very importantly, 2-60 fold more potent inhibitory effect on MRSA Mu50 than all the commonly used antibiotics including vancomycin, which is considered the last resort option in treating MRSA-related infections. Protein pull down experiments further confirmed SaSecA1 as a target. Deletion or overexpression of NorA and MepA efflux pumps had minimal effect on the antimicrobial activities against S. aureus, indicating that the effects of SecA inhibitors were not affected by the presence of these efflux pumps. Our studies show that these small molecule analogs target SecA functions, have potent antimicrobial activities, reduce the secretion of toxins, and have the ability to overcome the effect efflux pumps, which are responsible for multi-drug resistance. Thus, targeting SecA is an attractive antimicrobial strategy against MRSA.
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Affiliation(s)
- Jinshan Jin
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA.
| | - Jianmei Cui
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
| | - Arpana Sagwal Chaudhary
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
| | - Ying-Hsin Hsieh
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA.
| | - Krishna Damera
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
| | - Hao Zhang
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA.
| | - Hsiuchin Yang
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA.
| | - Binghe Wang
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
| | - Phang C Tai
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA.
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18
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Hsieh YH, Zou J, Jin JS, Yang H, Chen Y, Jiang C, Yang J, Tai PC. Monitoring channel activities of proteoliposomes with SecA and Cx26 gap junction in single oocytes. Anal Biochem 2015; 480:58-66. [PMID: 25862083 DOI: 10.1016/j.ab.2015.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 04/01/2015] [Accepted: 04/03/2015] [Indexed: 10/23/2022]
Abstract
Establishing recordable channels in membranes of oocytes formed by expressing exogenous complementary DNA (cDNA) or messenger RNA (mRNA) has contributed greatly to understanding the molecular mechanisms of channel functions. Here, we report the extension of this semi-physiological system for monitoring the channel activity of preassembled membrane proteins in single cell oocytes by injecting reconstituted proteoliposomes along with substrates or regulatory molecules. We build on the observation that SecA from various bacteria forms active protein-conducting channels with injection of proteoliposomes, protein precursors, and ATP-Mg(2+). Such activity was enhanced by reconstituted SecYEG-SecDF•YajC liposome complexes that could be monitored easily and efficiently, providing correlation of in vitro and intact cell functionality. In addition, inserting reconstituted gap junction Cx26 liposomes into the oocytes allowed the demonstration of intracellular/extracellular Ca(2+)-regulated hemi-channel activities. The channel activities can be detected rapidly after injection, can be monitored for various effectors, and are dependent on specific exogenous lipid compositions. This simple and effective functional system with low endogenous channel activity should have broad applications for monitoring the specific channel activities of complex interactions of purified membrane proteins with their effectors and regulatory molecules.
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Affiliation(s)
- Ying-Hsin Hsieh
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA
| | - Juan Zou
- Department of Chemistry, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA
| | - Jin-Shan Jin
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA
| | - Hsiuchin Yang
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA
| | - Yanyi Chen
- Department of Chemistry, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA
| | - Chun Jiang
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA
| | - Jenny Yang
- Department of Chemistry, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA.
| | - Phang C Tai
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA.
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19
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Chaudhary AS, Jin J, Chen W, Tai PC, Wang B. Design, syntheses and evaluation of 4-oxo-5-cyano thiouracils as SecA inhibitors. Bioorg Med Chem 2014; 23:105-17. [PMID: 25498235 DOI: 10.1016/j.bmc.2014.11.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 11/02/2014] [Accepted: 11/14/2014] [Indexed: 11/26/2022]
Abstract
Protein translocation is essential for bacterial survival and the most important translocation mechanism is the secretion (Sec) pathway in which SecA is a central core driving force. Thus targeting SecA is a promising strategy for developing novel antibacterial therapeutics. Herein, we report the syntheses and evaluation of a series of nearly 60 4-oxo-5-cyano thiouracil derivatives based upon our previously reported core pyrimidine structure. Introduction of polar group such as -N3 and linker groups such as -CH2-O- enhanced the potency several fold. Apart from being potential antibacterial agents, these inhibitors can be indispensable tools for biologists to probe the mechanism of protein translocation via the SecA machinery in bacteria.
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Affiliation(s)
- Arpana S Chaudhary
- College of Arts and Sciences, Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Jinshan Jin
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA
| | - Weixuan Chen
- College of Arts and Sciences, Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Phang C Tai
- Department of Biology, Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA.
| | - Binghe Wang
- College of Arts and Sciences, Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
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20
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Hsieh YH, Huang YJ, Jin JS, Yu L, Yang H, Jiang C, Wang B, Tai PC. Mechanisms of Rose Bengal inhibition on SecA ATPase and ion channel activities. Biochem Biophys Res Commun 2014; 454:308-12. [PMID: 25450394 DOI: 10.1016/j.bbrc.2014.10.070] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
Abstract
SecA is an essential protein possessing ATPase activity in bacterial protein translocation for which Rose Bengal (RB) is the first reported sub-micromolar inhibitor in ATPase activity and protein translocation. Here, we examined the mechanisms of inhibition on various forms of SecA ATPase by conventional enzymatic assays, and by monitoring the SecA-dependent channel activity in the semi-physiological system in cells. We build on the previous observation that SecA with liposomes form active protein-conducting channels in the oocytes. Such ion channel activity is enhanced by purified Escherichia coli SecYEG-SecDF·YajC liposome complexes. Inhibition by RB could be monitored, providing correlation of in vitro activity and intact cell functionality. In this work, we found the intrinsic SecA ATPase is inhibited by RB competitively at low ATP concentration, and non-competitively at high ATP concentrations while the translocation ATPase with precursors and SecYEG is inhibited non-competitively by RB. The Inhibition by RB on SecA channel activity in the oocytes with exogenous ATP-Mg(2+), mimicking translocation ATPase activity, is also non-competitive. The non-competitive inhibition on channel activity has also been observed with SecA from other bacteria which otherwise would be difficult to examine without the cognate precursors and membranes.
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Affiliation(s)
- Ying-Hsin Hsieh
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Ying-Ju Huang
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Jin-Shan Jin
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Liyan Yu
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Hsiuchin Yang
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Chun Jiang
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Binghe Wang
- Department of Chemistry, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Phang C Tai
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States.
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21
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Floyd JH, You Z, Hsieh YH, Ma Y, Yang H, Tai PC. The dispensability and requirement of SecA N-terminal aminoacyl residues for complementation, membrane binding, lipid-specific domains and channel activities. Biochem Biophys Res Commun 2014; 453:138-42. [PMID: 25264203 DOI: 10.1016/j.bbrc.2014.09.080] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 09/18/2014] [Indexed: 11/24/2022]
Abstract
SecA is an essential multifunctional protein for the translocation of proteins across bacterial membranes. Though SecA is known to function in the membrane, the detailed mechanism for this process remains unclear. In this study we constructed a series of SecA N-terminal deletions and identified two specific domains crucial for initial SecA/membrane interactions. The first small helix, the linker and part of the second helix (Δ2-22) were found to be dispensable for SecA activity in complementing the growth of a SecA ts mutant. However, deletions of N-terminal aminoacyl residues 23-25 resulted in severe progressive retardation of growth. Moreover, a decrease of SecA activity caused by N-terminal deletions correlated to the loss of SecA membrane binding, formation of lipid-specific domains and channel activity. All together, the results indicate that the N-terminal aminoacyl residues 23-25 play a critical role for SecA binding to membranes and that the N-terminal limit of SecA for activity is at the 25th amino acid.
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Affiliation(s)
- Jeanetta Holley Floyd
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Zhipeng You
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Ying-Hsin Hsieh
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Yamin Ma
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Hsuichin Yang
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Phang C Tai
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States.
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22
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Wang H, Ma Y, Hsieh YH, Yang H, Li M, Wang B, Tai PC. SecAAA trimer is fully functional as SecAA dimer in the membrane: existence of higher oligomers? Biochem Biophys Res Commun 2014; 447:250-4. [PMID: 24704204 DOI: 10.1016/j.bbrc.2014.03.116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 03/24/2014] [Indexed: 11/17/2022]
Abstract
SecA is an essential ATPase in bacterial Sec-dependent protein translocation pathway, and equilibrates between monomers and dimers in solution. The question of whether SecA functions as monomers or dimers in membranes during the protein translocation is controversial. We previously constructed a tail-to-head SecAA tandem dimer, and showed it is fully functional by complementation in vivo and protein translocation in vitro, indicating that SecA can function at least as a dimer in the membrane without dissociating into monomers. In this study, we further constructed genetically a tail-to-head SecAAA trimer, which is functional in complementing a temperature-sensitive secA mutant. The purified SecAAA trimer per protomer is fully active as SecAA tandem dimers in ATPase activity, in protein translocation in vitro and in ion channel activities in the oocytes. With these functional tail-to-head trimer SecAAA and tandem SecAA, we examined their surface topology in the presence of liposomes using AFM. As expected, the soluble SecAAA without lipids are larger than SecAA. However, the ring/pore structures of SecAAA trimers were, surprisingly, almost identical to the SecA 2-monomers and SecAA dimers, raising the intriguing possibility that the SecA may exist and function as hexamer ring-structures in membranes. Cross-linking with formaldehyde showed that SecA, SecAA and SecAAA could form larger oligomers, including the hexamers. The molecular modeling simulation shows that both tail-to-head and tail-to-tail hexamers in the membranes are possible.
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Affiliation(s)
- Hongyun Wang
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States
| | - Yamin Ma
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States
| | - Ying-Hsin Hsieh
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States
| | - Hsiuchin Yang
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States
| | - Minyong Li
- Department of Chemistry, and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States; Key Laboratory of Chemical Biology, School of Pharmacy, Shandong University, Jinan, Shandong 250012, China
| | - Binghe Wang
- Department of Chemistry, and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, United States
| | - Phang C Tai
- Department of Biology, Georgia State University, Atlanta, GA 30303, United States.
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23
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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.
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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.
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24
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Singh R, Kraft C, Jaiswal R, Sejwal K, Kasaragod VB, Kuper J, Bürger J, Mielke T, Luirink J, Bhushan S. Cryo-electron microscopic structure of SecA protein bound to the 70S ribosome. J Biol Chem 2014; 289:7190-7199. [PMID: 24443566 DOI: 10.1074/jbc.m113.506634] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SecA is an ATP-dependent molecular motor pumping secretory and outer membrane proteins across the cytoplasmic membrane in bacteria. SecA associates with the protein-conducting channel, the heterotrimeric SecYEG complex, in a so-called posttranslational manner. A recent study further showed binding of a monomeric state of SecA to the ribosome. However, the true oligomeric state of SecA remains controversial because SecA can also form functional dimers, and high-resolution crystal structures exist for both the monomer and the dimer. Here we present the cryo-electron microscopy structures of Escherichia coli SecA bound to the ribosome. We show that not only a monomeric SecA binds to the ribosome but also that two copies of SecA can be observed that form an elongated dimer. Two copies of SecA completely surround the tunnel exit, providing a unique environment to the nascent polypeptides emerging from the ribosome. We identified the N-terminal helix of SecA required for a stable association with the ribosome. The structures indicate a possible function of the dimeric form of SecA at the ribosome.
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Affiliation(s)
- Rajkumar Singh
- Rudolf Virchow Center/DFG Research Center for Experimental Biomedicine, University of Würzburg, Josef Schneider Str. 2, 97078 Würzburg, Germany
| | - Christian Kraft
- Rudolf Virchow Center/DFG Research Center for Experimental Biomedicine, University of Würzburg, Josef Schneider Str. 2, 97078 Würzburg, Germany
| | - Rahul Jaiswal
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Kushal Sejwal
- Rudolf Virchow Center/DFG Research Center for Experimental Biomedicine, University of Würzburg, Josef Schneider Str. 2, 97078 Würzburg, Germany
| | - Vikram Babu Kasaragod
- Rudolf Virchow Center/DFG Research Center for Experimental Biomedicine, University of Würzburg, Josef Schneider Str. 2, 97078 Würzburg, Germany
| | - Jochen Kuper
- Rudolf Virchow Center/DFG Research Center for Experimental Biomedicine, University of Würzburg, Josef Schneider Str. 2, 97078 Würzburg, Germany
| | - Jörg Bürger
- UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany; Institut für Medizinische Physik und Biophysik, Charité, Ziegelstrasse 5-8, 10117 Berlin, Germany
| | - Thorsten Mielke
- UltraStrukturNetzwerk, Max Planck Institute for Molecular Genetics, Ihnestr. 73, 14195 Berlin, Germany; Institut für Medizinische Physik und Biophysik, Charité, Ziegelstrasse 5-8, 10117 Berlin, Germany
| | - Joen Luirink
- Department of Molecular Microbiology, Institute of Molecular Cell Biology, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Shashi Bhushan
- Rudolf Virchow Center/DFG Research Center for Experimental Biomedicine, University of Würzburg, Josef Schneider Str. 2, 97078 Würzburg, Germany; Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore 637551.
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25
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Kedrov A, Kusters I, Driessen AJM. Single-Molecule Studies of Bacterial Protein Translocation. Biochemistry 2013; 52:6740-54. [DOI: 10.1021/bi400913x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Alexej Kedrov
- Department of Molecular Microbiology, Groningen
Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Ilja Kusters
- Department of Molecular Microbiology, Groningen
Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Arnold J. M. Driessen
- Department of Molecular Microbiology, Groningen
Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
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26
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You Z, Liao M, Zhang H, Yang H, Pan X, Houghton JE, Sui SF, Tai PC. Phospholipids induce conformational changes of SecA to form membrane-specific domains: AFM structures and implication on protein-conducting channels. PLoS One 2013; 8:e72560. [PMID: 23977317 PMCID: PMC3745498 DOI: 10.1371/journal.pone.0072560] [Citation(s) in RCA: 10] [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: 03/12/2013] [Accepted: 07/12/2013] [Indexed: 11/23/2022] Open
Abstract
SecA, an essential component of the Sec machinery, exists in a soluble and a membrane form in Escherichia coli. Previous studies have shown that the soluble SecA transforms into pore structures when it interacts with liposomes, and integrates into membranes containing SecYEG in two forms: SecAS and SecAM; the latter exemplified by two tryptic membrane-specific domains, an N-terminal domain (N39) and a middle M48 domain (M48). The formation of these lipid-specific domains was further investigated. The N39 and M48 domains are induced only when SecA interacts with anionic liposomes. Additionally, the N-terminus, not the C-terminus of SecA is required for inducing such conformational changes. Proteolytic treatment and sequence analyses showed that liposome-embedded SecA yields the same M48 and N39 domains as does the membrane-embedded SecA. Studies with chemical extraction and resistance to trypsin have also shown that these proteoliposome-embedded SecA fragments exhibit the same stability and characteristics as their membrane-embedded SecA equivalents. Furthermore, the cloned lipid-specific domains N39 and M48, but not N68 or C34, are able to form partial, but imperfect ring-like structures when they interact with phospholipids. These ring-like structures are characteristic of a SecA pore-structure, suggesting that these domains contribute part of the SecA-dependent protein-conducting channel. We, therefore, propose a model in which SecA alone is capable of forming a lipid-specific, asymmetric dimer that is able to function as a viable protein-conducting channel in the membrane, without any requirement for SecYEG.
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Affiliation(s)
- Zhipeng You
- Department of Biology and Center of Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia, United States of America
| | - Meijiang Liao
- Department of Biology and Center of Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia, United States of America
| | - Hao Zhang
- Department of Biology and Center of Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia, United States of America
| | - Hsiuchin Yang
- Department of Biology and Center of Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia, United States of America
| | - Xijian Pan
- School of Life Sciences, Center for Structural Biology, Tsinghua University, Beijing, China
| | - John E. Houghton
- Department of Biology and Center of Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia, United States of America
| | - Sen-fang Sui
- School of Life Sciences, Center for Structural Biology, Tsinghua University, Beijing, China
| | - Phang C. Tai
- Department of Biology and Center of Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia, United States of America
- * E-mail:
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27
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Zhang H, Hsieh YH, Lin BR, Yu L, Yang H, Jiang C, Sui SF, Tai PC. Specificity of SecYEG for PhoA precursors and SecA homologs on SecA protein-conducting channels. Biochem Biophys Res Commun 2013; 437:212-216. [PMID: 23791875 DOI: 10.1016/j.bbrc.2013.06.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 06/12/2013] [Indexed: 11/18/2022]
Abstract
Previous studies showed that Escherichia coli membranes depleted of SecYEG are capable of translocating certain precursor proteins, but not other precursors such as pPhoA, indicating a differential requirement for SecYEG. In this study, we examined the role of SecYEG in pPhoA translocation using a purified reconstituted SecA-liposomes system. We found that translocation of pPhoA, in contrast to that of pOmpA, requires the presence of purified SecYEG. A differential specificity of the SecYEG was also revealed in its interaction with SecA: EcSecYEG did not enhance SecA-mediated pOmpA translocation by purified SecA either from Pseudomonas aeruginosa or Bacillus subtilis. Neither was SecYEG required for eliciting ion channel activity, which could be opened by unfolded pPhoA or unfolded PhoA. Addition of the SecYEG complex did restore the specificity of signal peptide recognition in the ion-channel activity. We concluded that SecYEG confers specificity in interacting with protein precursors and SecAs.
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Affiliation(s)
- Hao Zhang
- Department of Biology and Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303
| | - Ying-Hsin Hsieh
- Department of Biology and Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303
| | - Bor-Ruei Lin
- Department of Biology and Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303
| | - Liyan Yu
- Department of Biology and Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303
| | - Hsiuchin Yang
- Department of Biology and Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303
| | - Chun Jiang
- Department of Biology and Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303
| | - Sen-Fang Sui
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China 100084
| | - Phang C Tai
- Department of Biology and Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303
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Yang CK, Lu CD, Tai PC. Differential expression of secretion machinery during bacterial growth: SecY and SecF decrease while SecA increases during transition from exponential phase to stationary phase. Curr Microbiol 2013; 67:682-7. [PMID: 23852076 DOI: 10.1007/s00284-013-0421-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 05/30/2013] [Indexed: 11/25/2022]
Abstract
Transcription of many house-keeping genes, including secY and some other sec genes, decreases in the transition from the exponential phase to the stationary phase (feast to famine) in Bacillus subtilis. Unexpectedly and in contradiction to earlier reports, enhanced transcription was observed for another group of sec genes, including secA which codes for an essential ATPase for protein secretion. Consistent with the transcription data, the SecA protein of B. subtilis increases significantly in the stationary phase. Immunoblot analyses of Sec proteins during the transition in Escherichia coli also revealed the pronounced decreases of SecY and SecF and the increase of SecA, resulting in drastic increases of SecA/SecY and SecA/SecF ratios from exponential to stationary phases. The differential expression of Sec proteins in the stationary phase suggests the possibility of specific physiological functions.
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Affiliation(s)
- Chun-Kai Yang
- Department of Biology, Center of Biotechnology and Drug Design, Georgia State University, 592 PSC, 161 Jesse Hill Jr. Road, Atlanta, GA, 30303, USA
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Cui J, Jin J, Hsieh YH, Yang H, Ke B, Damera K, Tai PC, Wang B. Design, Synthesis and Biological Evaluation of Rose Bengal Analogues as SecA Inhibitors. ChemMedChem 2013; 8:1384-93. [DOI: 10.1002/cmdc.201300216] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Indexed: 11/06/2022]
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Hsieh YH, Zhang H, Wang H, Yang H, Jiang C, Sui SF, Tai PC. Reconstitution of functionally efficient SecA-dependent protein-conducting channels: transformation of low-affinity SecA-liposome channels to high-affinity SecA-SecYEG-SecDF·YajC channels. Biochem Biophys Res Commun 2013; 431:388-92. [PMID: 23337498 DOI: 10.1016/j.bbrc.2013.01.042] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Accepted: 01/10/2013] [Indexed: 11/20/2022]
Abstract
Previous work showed that SecA alone can promote protein translocation and ion-channel activity in liposomes, and that SecYEG increases efficiency as well as signal peptide specificity. We now report that SecDF·YajC further increases translocation and ion-channel activity. These activities of reconstituted SecA-SecYEG-SecDF·YajC-liposome are almost the same as those of native membranes, indicating the transformation of reconstituted functional high-affinity protein-conducting channels from the low-affinity SecA-channels.
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Affiliation(s)
- Ying-hsin Hsieh
- Department of Biology and Center of Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30303, USA
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Prediction of Lipid-Binding Regions in Cytoplasmic and Extracellular Loops of Membrane Proteins as Exemplified by Protein Translocation Membrane Proteins. J Membr Biol 2012; 246:21-9. [DOI: 10.1007/s00232-012-9498-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 08/18/2012] [Indexed: 02/07/2023]
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Lin BR, Hsieh YH, Jiang C, Tai PC. Escherichia coli Membranes Depleted of SecYEG Elicit SecA-Dependent Ion-Channel Activity but Lose Signal Peptide Specificity. J Membr Biol 2012; 245:747-57. [DOI: 10.1007/s00232-012-9477-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 06/30/2012] [Indexed: 11/29/2022]
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