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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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Molecular movie of nucleotide binding to a motor protein. Biochim Biophys Acta Gen Subj 2020; 1864:129654. [PMID: 32512170 DOI: 10.1016/j.bbagen.2020.129654] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/13/2020] [Accepted: 05/28/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND The SecA DEAD (Asp-Glu-Ala-Asp) motor protein uses binding and hydrolysis of adenosine triphosphate (ATP) to push secretory proteins across the plasma membrane of bacteria. The reaction coordinate of nucleotide exchange is unclear at the atomic level of detail. METHODS We performed multiple atomistic computations of the DEAD motor domain of SecA with different occupancies of the nucleotide and magnesium ion sites, for a total of ~1.7 μs simulation time. To characterize dynamics at the active site we analyzed hydrogen-bond networks. RESULTS ATP and ADP can bind spontaneously at the interface between the nucleotide binding domains, albeit at an intermediate binding site distinct from the native site. Binding of the nucleotide is facilitated by the presence of a magnesium ion close to the glutamic group of the conserved DEAD motif. In the absence of the magnesium ion, protein interactions of the ADP molecule are perturbed. CONCLUSIONS A protein hydrogen-bond network whose dynamics couples to the occupancy of the magnesium ion site helps guide the nucleotide along the nucleotide exchange path. In SecA, release of magnesium might be required to destabilize the ADP binding site prior to release of the nucleotide. GENERAL SIGNIFICANCE We identified dynamic hydrogen-bond networks that help control nucleotide exchange in SecA, and stabilize ADP at an intermediate site that could explain slow release. The reaction coordinate of the protein motor involves complex rearrangements of a hydrogen-bond network at the active site, with perturbation of the magnesium ion site likely occurring prior to the release of ADP.
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Motions of the SecA protein motor bound to signal peptide: Insights from molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:416-427. [DOI: 10.1016/j.bbamem.2017.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 11/03/2017] [Accepted: 11/07/2017] [Indexed: 12/31/2022]
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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: 57] [Impact Index Per Article: 8.1] [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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Khalili Yazdi A, Namjoshi S, Hackett J, Ghonaim N, Shilton BH. Characterization of a polypeptide-binding site in the DEAD Motor of the SecA ATPase. FEBS Lett 2017; 591:3378-3390. [DOI: 10.1002/1873-3468.12832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/18/2017] [Accepted: 08/22/2017] [Indexed: 11/07/2022]
Affiliation(s)
| | - Sarita Namjoshi
- Department of Biochemistry; University of Western Ontario; London Canada
| | - Jesse Hackett
- Department of Biochemistry; University of Western Ontario; London Canada
| | - Nour Ghonaim
- Department of Biochemistry; University of Western Ontario; London Canada
| | - Brian H. Shilton
- Department of Biochemistry; University of Western Ontario; London Canada
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Yazdi AK, Vezina GC, Shilton BH. An alternate mode of oligomerization for E. coli SecA. Sci Rep 2017; 7:11747. [PMID: 28924213 PMCID: PMC5603524 DOI: 10.1038/s41598-017-11648-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/29/2017] [Indexed: 11/08/2022] Open
Abstract
SecA is the ATPase of preprotein translocase. SecA is a dimer in solution and changes in its oligomeric state may function in preprotein translocation. The SecA-N68 construct, in which the C-terminal helical domains of SecA are deleted, was used to investigate the mechanism of SecA oligomerization. SecA-N68 is in equilibrium between monomers, dimers, and tetramers. Subunit interactions in the SecA-N68 tetramer are mediated entirely by unstructured regions at its N- and C-termini: when the termini are deleted to yield SecA-N68∆NC, the construct is completely monomeric. This monomeric construct yielded crystals diffracting to 2.6 Å that were used to solve the structure of SecA-N68, including the "preprotein crosslinking domain" (PPXD) that was missing from previous E. coli SecA structures. The SecA-N68 structure was combined with small angle X-ray scattering (SAXS) data to construct a model of the SecA-N68 tetramer that is consistent with the essential roles of the extreme N- and C-termini in oligomerization. This mode of oligomerization, which depends on binding of the extreme N-terminus to the DEAD motor domains, NBD1 and NBD2, was used to model a novel parallel and flexible SecA solution dimer that agrees well with SAXS data.
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Affiliation(s)
- Aliakbar Khalili Yazdi
- Department of Biochemistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Grant C Vezina
- Department of Biochemistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Brian H Shilton
- Department of Biochemistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada.
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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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Milenkovic S, Bondar AN. Mechanism of conformational coupling in SecA: Key role of hydrogen-bonding networks and water interactions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:374-85. [PMID: 26607006 DOI: 10.1016/j.bbamem.2015.11.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 11/05/2015] [Accepted: 11/18/2015] [Indexed: 11/16/2022]
Abstract
SecA uses the energy yielded by the binding and hydrolysis of adenosine triphosphate (ATP) to push secretory pre-proteins across the plasma membrane in bacteria. Hydrolysis of ATP occurs at the nucleotide-binding site, which contains the conserved carboxylate groups of the DEAD-box helicases. Although crystal structures provide valuable snapshots of SecA along its reaction cycle, the mechanism that ensures conformational coupling between the nucleotide-binding site and the other domains of SecA remains unclear. The observation that SecA contains numerous hydrogen-bonding groups raises important questions about the role of hydrogen-bonding networks and hydrogen-bond dynamics in long-distance conformational couplings. To address these questions, we explored the molecular dynamics of SecA from three different organisms, with and without bound nucleotide, in water. By computing two-dimensional hydrogen-bonding maps we identify networks of hydrogen bonds that connect the nucleotide-binding site to remote regions of the protein, and sites in the protein that respond to specific perturbations. We find that the nucleotide-binding site of ADP-bound SecA has a preferred geometry whereby the first two carboxylates of the DEAD motif bridge via hydrogen-bonding water. Simulations of a mutant with perturbed ATP hydrolysis highlight the water-bridged geometry as a key structural element of the reaction path.
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Affiliation(s)
- Stefan Milenkovic
- Theoretical Molecular Biophysics, Department of Physics, Freie Universitaet Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics, Department of Physics, Freie Universitaet Berlin, Arnimallee 14, D-14195 Berlin, Germany.
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Rawling DC, Kohlway AS, Luo D, Ding SC, Pyle AM. The RIG-I ATPase core has evolved a functional requirement for allosteric stabilization by the Pincer domain. Nucleic Acids Res 2014; 42:11601-11. [PMID: 25217590 PMCID: PMC4191399 DOI: 10.1093/nar/gku817] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 08/16/2014] [Accepted: 08/29/2014] [Indexed: 12/24/2022] Open
Abstract
Retinoic acid-inducible gene I (RIG-I) is a pattern recognition receptor expressed in metazoan cells that is responsible for eliciting the production of type I interferons and pro-inflammatory cytokines upon detection of intracellular, non-self RNA. Structural studies of RIG-I have identified a novel Pincer domain composed of two alpha helices that physically tethers the C-terminal domain to the SF2 helicase core. We find that the Pincer plays an important role in mediating the enzymatic and signaling activities of RIG-I. We identify a series of mutations that additively decouple the Pincer motif from the ATPase core and show that this decoupling results in impaired signaling. Through enzymological and biophysical analysis, we further show that the Pincer domain controls coupled enzymatic activity of the protein through allosteric control of the ATPase core. Further, we show that select regions of the HEL1 domain have evolved to potentiate interactions with the Pincer domain, resulting in an adapted ATPase cleft that is now responsive to adjacent domains that selectively bind viral RNA.
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Affiliation(s)
- David C Rawling
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Andrew S Kohlway
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Dahai Luo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Steve C Ding
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA Department of Chemistry, Yale University, New Haven, CT 06520, USA
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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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The variable subdomain of Escherichia coli SecA functions to regulate SecA ATPase activity and ADP release. J Bacteriol 2012; 194:2205-13. [PMID: 22389482 DOI: 10.1128/jb.00039-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial SecA proteins can be categorized by the presence or absence of a variable subdomain (VAR) located within nucleotide-binding domain II of the SecA DEAD motor. Here we show that VAR is dispensable for SecA function, since the VAR deletion mutant secAΔ519-547 displayed a wild-type rate of cellular growth and protein export. Loss or gain of VAR is extremely rare in the history of bacterial evolution, indicating that it appears to contribute to secA function within the relevant species in their natural environments. VAR removal also results in additional secA phenotypes: azide resistance (Azi(r)) and suppression of signal sequence defects (PrlD). The SecAΔ(519-547) protein was found to be modestly hyperactive for SecA ATPase activities and displayed an accelerated rate of ADP release, consistent with the biochemical basis of azide resistance. Based on our findings, we discuss models whereby VAR allosterically regulates SecA DEAD motor function at SecYEG.
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du Plessis DJF, Nouwen N, Driessen AJM. The Sec translocase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:851-65. [PMID: 20801097 DOI: 10.1016/j.bbamem.2010.08.016] [Citation(s) in RCA: 205] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 08/19/2010] [Accepted: 08/20/2010] [Indexed: 11/18/2022]
Abstract
The vast majority of proteins trafficking across or into the bacterial cytoplasmic membrane occur via the translocon. The translocon consists of the SecYEG complex that forms an evolutionarily conserved heterotrimeric protein-conducting membrane channel that functions in conjunction with a variety of ancillary proteins. For posttranslational protein translocation, the translocon interacts with the cytosolic motor protein SecA that drives the ATP-dependent stepwise translocation of unfolded polypeptides across the membrane. For the cotranslational integration of membrane proteins, the translocon interacts with ribosome-nascent chain complexes and membrane insertion is coupled to polypeptide chain elongation at the ribosome. These processes are assisted by the YidC and SecDF(yajC) complex that transiently interacts with the translocon. This review summarizes our current understanding of the structure-function relationship of the translocon and its interactions with ancillary components during protein translocation and membrane protein insertion. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.
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Affiliation(s)
- David J F du Plessis
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, 9751NN Haren, The Netherlands
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Survey of the year 2008: applications of isothermal titration calorimetry. J Mol Recognit 2010; 23:395-413. [DOI: 10.1002/jmr.1025] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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