1
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Allen WJ, Collinson I. A unifying mechanism for protein transport through the core bacterial Sec machinery. Open Biol 2023; 13:230166. [PMID: 37643640 PMCID: PMC10465204 DOI: 10.1098/rsob.230166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/21/2023] [Indexed: 08/31/2023] Open
Abstract
Encapsulation and compartmentalization are fundamental to the evolution of cellular life, but they also pose a challenge: how to partition the molecules that perform biological functions-the proteins-across impermeable barriers into sub-cellular organelles, and to the outside. The solution lies in the evolution of specialized machines, translocons, found in every biological membrane, which act both as gate and gatekeeper across and into membrane bilayers. Understanding how these translocons operate at the molecular level has been a long-standing ambition of cell biology, and one that is approaching its denouement; particularly in the case of the ubiquitous Sec system. In this review, we highlight the fruits of recent game-changing technical innovations in structural biology, biophysics and biochemistry to present a largely complete mechanism for the bacterial version of the core Sec machinery. We discuss the merits of our model over alternative proposals and identify the remaining open questions. The template laid out by the study of the Sec system will be of immense value for probing the many other translocons found in diverse biological membranes, towards the ultimate goal of altering or impeding their functions for pharmaceutical or biotechnological purposes.
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Affiliation(s)
- William J. Allen
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Ian Collinson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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2
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Mukherjee S, Mepperi J, Sahu P, Barman DK, Kotamarthi HC. Single-Molecule Optical Tweezers As a Tool for Delineating the Mechanisms of Protein-Processing Mechanoenzymes. ACS OMEGA 2023; 8:87-97. [PMID: 36643560 PMCID: PMC9835622 DOI: 10.1021/acsomega.2c06044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Mechanoenzymes convert chemical energy from the hydrolysis of nucleotide triphosphates to mechanical energy for carrying out cellular functions ranging from DNA unwinding to protein degradation. Protein-processing mechanoenzymes either remodel the protein structures or translocate them across cellular compartments in an energy-dependent manner. Optical-tweezer-based single-molecule force spectroscopy assays have divulged information on details of chemo-mechanical coupling, directed motion, as well as mechanical forces these enzymes are capable of generating. In this review, we introduce the working principles of optical tweezers as a single-molecule force spectroscopy tool and assays developed to decipher the properties such as unfolding kinetics, translocation velocities, and step sizes by protein remodeling mechanoenzymes. We focus on molecular motors involved in protein degradation and disaggregation, i.e., ClpXP, ClpAP, and ClpB, and insights provided by single-molecule assays on kinetics and stepping dynamics during protein unfolding and translocation. Cellular activities such as protein synthesis, folding, and translocation across membranes are also energy dependent, and the recent single-molecule studies decoding the role of mechanical forces on these processes have been discussed.
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3
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Yu X, Conyne M, Lake MR, Walter KA, Min J. In silico high throughput mutagenesis and screening of signal peptides to mitigate N-terminal heterogeneity of recombinant monoclonal antibodies. MAbs 2022; 14:2044977. [PMID: 35275041 PMCID: PMC8920188 DOI: 10.1080/19420862.2022.2044977] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
N-terminal heterogeneity resulting from non-uniform signal peptide (SP) cleavage can potentially affect biologics property attributes and result in extended product development timelines. Few studies are available on engineering SPs systematically to address miscleavage issues. Herein, we developed a novel high throughput computational pipeline capable of generating millions of SP mutant sequences that uses the SignalP 5.0 deep learning model to predict which of these mutants are likely to alleviate the N-terminal miscleavage in antibodies. We optimized the parameters to target mutating one or two amino acids at the C-terminus of 84 unique SPs, exhausting all theoretically possible combinations and resulting in a library of 296,077 unique wildtype and mutant signal peptides for in silico screening of each antibody. We applied this method to five antibodies against different targets, with various extent of miscleavage (2.3% to 100%) on their Lambda light chains. In each case, multiple SP mutants were generated, with miscleavage reduced to a non-detectable level and titers comparable with or better than that of the original SPs. Pairwise mutational analysis using an in silico library enriched with high-scoring mutants revealed patterns of amino acids at the C-terminus of SPs, providing insights beyond the “Heijne rule”. To our knowledge, no similar approach that combines high throughput in silico mutagenesis and screening with SP cleavage prediction has been reported in the literature. This method can be applied to both the light chain and heavy chain of antibodies, regardless of their initial extent of miscleavage, provides optimized solutions for individual cases, and facilitates the development of antibody therapeutics. Abbreviations: Aa, amino acids; CHO, Chinese hamster ovary; CNN, convolutional neural network; CSscore, cleavage site score; CSV, comma-separated values; HC, heavy chain; HEK, human embryonic kidney; HPLC, high-performance liquid chromatography; IgG, immunoglobulin G; IGLV, immunoglobulin G Lambda variable; LC, light chain; LCMS, liquid chromatography–mass spectrometry; MS, mass spectrometry; PCR, polymerase chain reaction; PBS, phosphate-buffered saline; PEI, polyethylenimine; SP, signal peptide; SPase, signal peptidase; TCEP, tris(2-carboxyethyl) phosphine; TOF, time-of-flight.
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Affiliation(s)
- Xin Yu
- Drug Discovery Science and Technology, AbbVie Bioresearch Center, Worcester, MA, US
| | - Merlinda Conyne
- Drug Discovery Science and Technology, AbbVie Inc, North Chicago, IL, US
| | - Marc R Lake
- Drug Discovery Science and Technology, AbbVie Inc, North Chicago, IL, US
| | - Karl A Walter
- Drug Discovery Science and Technology, AbbVie Inc, North Chicago, IL, US
| | - Jing Min
- Drug Discovery Science and Technology, AbbVie Bioresearch Center, Worcester, MA, US
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4
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Roumia AF, Tsirigos KD, Theodoropoulou MC, Tamposis IA, Hamodrakas SJ, Bagos PG. OMPdb: A Global Hub of Beta-Barrel Outer Membrane Proteins. FRONTIERS IN BIOINFORMATICS 2021; 1:646581. [PMID: 36303794 PMCID: PMC9581022 DOI: 10.3389/fbinf.2021.646581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/18/2021] [Indexed: 11/14/2022] Open
Abstract
OMPdb (www.ompdb.org) was introduced as a database for β-barrel outer membrane proteins from Gram-negative bacteria in 2011 and then included 69,354 entries classified into 85 families. The database has been updated continuously using a collection of characteristic profile Hidden Markov Models able to discriminate between the different families of prokaryotic transmembrane β-barrels. The number of families has increased ultimately to a total of 129 families in the current, second major version of OMPdb. New additions have been made in parallel with efforts to update existing families and add novel families. Here, we present the upgrade of OMPdb, which from now on aims to become a global repository for all transmembrane β-barrel proteins, both eukaryotic and bacterial.
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Affiliation(s)
- Ahmed F. Roumia
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | | | | | - Ioannis A. Tamposis
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Stavros J. Hamodrakas
- Section of Cell Biology and Biophysics, Department of Biology, School of Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Pantelis G. Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- *Correspondence: Pantelis G. Bagos
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5
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The SecA motor generates mechanical force during protein translocation. Nat Commun 2020; 11:3802. [PMID: 32732903 PMCID: PMC7393111 DOI: 10.1038/s41467-020-17561-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/07/2020] [Indexed: 12/31/2022] Open
Abstract
The Sec translocon moves proteins across lipid bilayers in all cells. The Sec channel enables passage of unfolded proteins through the bacterial plasma membrane, driven by the cytosolic ATPase SecA. Whether SecA generates mechanical force to overcome barriers to translocation posed by structured substrate proteins is unknown. Here, we kinetically dissect Sec-dependent translocation by monitoring translocation of a folded substrate protein with tunable stability at high time resolution. We find that substrate unfolding constitutes the rate-limiting step during translocation. Using single-molecule force spectroscopy, we also define the response of the protein to mechanical force. Relating the kinetic and force measurements reveals that SecA generates at least 10 piconewtons of mechanical force to actively unfold translocating proteins, comparable to cellular unfoldases. Combining biochemical and single-molecule measurements thus allows us to define how the SecA motor ensures efficient and robust export of proteins that contain stable structure. The ATPase SecA drives Sec-dependent protein translocation across the bacterial plasma membrane. Here, the authors combine kinetic translocation measurements with single-molecule force spectroscopy and demonstrate that the SecA motor generates mechanical force to unfold and translocate preproteins.
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6
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Abstract
ABSTRACT
Mycobacteria, including the infamous pathogen
Mycobacterium tuberculosis
, are high-GC Gram-positive bacteria with a distinctive cell envelope. Although there is a typical inner membrane, the mycobacterial cell envelope is unusual in having its peptidoglycan layer connected to a polymer of arabinogalactan, which in turn is covalently attached to long-chain mycolic acids that help form a highly impermeable mycobacterial outer membrane. This complex double-membrane, or diderm, cell envelope imparts mycobacteria with unique requirements for protein export into and across the cell envelope for secretion into the extracellular environment. In this article, we review the four protein export pathways known to exist in mycobacteria: two conserved systems that exist in all types of bacteria (the Sec and Tat pathways) and two specialized systems that exist in mycobacteria, corynebacteria, and a subset of low-GC Gram-positive bacteria (the SecA2 and type VII secretion pathways). We describe the progress made over the past 15 years in understanding each of these mycobacterial export pathways, and we highlight the need for research to understand the specific steps of protein export across the mycobacterial outer membrane.
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7
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SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat Biotechnol 2019; 37:420-423. [PMID: 30778233 DOI: 10.1038/s41587-019-0036-z] [Citation(s) in RCA: 2512] [Impact Index Per Article: 502.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 01/16/2019] [Indexed: 11/08/2022]
Abstract
Signal peptides (SPs) are short amino acid sequences in the amino terminus of many newly synthesized proteins that target proteins into, or across, membranes. Bioinformatic tools can predict SPs from amino acid sequences, but most cannot distinguish between various types of signal peptides. We present a deep neural network-based approach that improves SP prediction across all domains of life and distinguishes between three types of prokaryotic SPs.
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Structural Similarities and Differences between Two Functionally Distinct SecA Proteins, Mycobacterium tuberculosis SecA1 and SecA2. J Bacteriol 2015; 198:720-30. [PMID: 26668263 DOI: 10.1128/jb.00696-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 12/01/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED While SecA is the ATPase component of the major bacterial secretory (Sec) system, mycobacteria and some Gram-positive pathogens have a second paralog, SecA2. In bacteria with two SecA paralogs, each SecA is functionally distinct, and they cannot compensate for one another. Compared to SecA1, SecA2 exports a distinct and smaller set of substrates, some of which have roles in virulence. In the mycobacterial system, some SecA2-dependent substrates lack a signal peptide, while others contain a signal peptide but possess features in the mature protein that necessitate a role for SecA2 in their export. It is unclear how SecA2 functions in protein export, and one open question is whether SecA2 works with the canonical SecYEG channel to export proteins. In this study, we report the structure of Mycobacterium tuberculosis SecA2 (MtbSecA2), which is the first structure of any SecA2 protein. A high level of structural similarity is observed between SecA2 and SecA1. The major structural difference is the absence of the helical wing domain, which is likely to play a role in how MtbSecA2 recognizes its unique substrates. Importantly, structural features critical to the interaction between SecA1 and SecYEG are preserved in SecA2. Furthermore, suppressor mutations of a dominant-negative secA2 mutant map to the surface of SecA2 and help identify functional regions of SecA2 that may promote interactions with SecYEG or the translocating polypeptide substrate. These results support a model in which the mycobacterial SecA2 works with SecYEG. IMPORTANCE SecA2 is a paralog of SecA1, which is the ATPase of the canonical bacterial Sec secretion system. SecA2 has a nonredundant function with SecA1, and SecA2 exports a distinct and smaller set of substrates than SecA1. This work reports the crystal structure of SecA2 of Mycobacterium tuberculosis (the first SecA2 structure reported for any organism). Many of the structural features of SecA1 are conserved in the SecA2 structure, including putative contacts with the SecYEG channel. Several structural differences are also identified that could relate to the unique function and selectivity of SecA2. Suppressor mutations of a secA2 mutant map to the surface of SecA2 and help identify functional regions of SecA2 that may promote interactions with SecYEG.
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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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10
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Protein export by the mycobacterial SecA2 system is determined by the preprotein mature domain. J Bacteriol 2012. [PMID: 23204463 DOI: 10.1128/jb.02032-12] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
At the core of the bacterial general secretion (Sec) pathway is the SecA ATPase, which powers translocation of unfolded preproteins containing Sec signal sequences through the SecYEG membrane channel. Mycobacteria have two nonredundant SecA homologs: SecA1 and SecA2. While the essential SecA1 handles "housekeeping" export, the nonessential SecA2 exports a subset of proteins and is required for Mycobacterium tuberculosis virulence. Currently, it is not understood how SecA2 contributes to Sec export in mycobacteria. In this study, we focused on identifying the features of two SecA2 substrates that target them to SecA2 for export, the Ms1704 and Ms1712 lipoproteins of the model organism Mycobacterium smegmatis. We found that the mature domains of Ms1704 and Ms1712, not the N-terminal signal sequences, confer SecA2-dependent export. We also demonstrated that the lipid modification and the extreme N terminus of the mature protein do not impart the requirement for SecA2 in export. We further showed that the Ms1704 mature domain can be efficiently exported by the twin-arginine translocation (Tat) pathway. Because the Tat system exports only folded proteins, this result implies that SecA2 substrates can fold in the cytoplasm and suggests a putative role of SecA2 in enabling export of such proteins. Thus, the mycobacterial SecA2 system may represent another way that bacteria solve the problem of exporting proteins that can fold in the cytoplasm.
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11
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Abstract
The conserved general secretion (Sec) pathway carries out most protein export in bacteria and is powered by the essential ATPase SecA. Interestingly, mycobacteria and some Gram-positive bacteria possess two SecA proteins: SecA1 and SecA2. In these species, SecA1 is responsible for exporting most proteins, whereas SecA2 exports only a subset of substrates and is implicated in virulence. However, despite the impressive body of knowledge about the canonical SecA1, less is known concerning SecA2 function. Here, we review our current understanding of the different types of SecA2 systems and outline future directions for their study.
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Affiliation(s)
- Meghan E Feltcher
- Department of Microbiology and Immunology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-27290, USA
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12
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Chen N, Hong FL, Wang HH, Yuan QH, Ma WY, Gao XN, Shi R, Zhang RJ, Sun CS, Wang SB. Modified recombinant proteins can be exported via the Sec pathway in Escherichia coli. PLoS One 2012; 7:e42519. [PMID: 22912705 PMCID: PMC3418276 DOI: 10.1371/journal.pone.0042519] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 07/10/2012] [Indexed: 01/29/2023] Open
Abstract
The correct folding of a protein is a pre-requirement for its proper posttranslational modification. The Escherichia coli Sec pathway, in which preproteins, in an unfolded, translocation-competent state, are rapidly secreted across the cytoplasmic membrane, is commonly assumed to be unfavorable for their modification in the cytosol. Whether posttranslationally modified recombinant preproteins can be efficiently transported via the Sec pathway, however, remains unclear. ACP and BCCP domain (BCCP87) are carrier proteins that can be converted into active phosphopantetheinylated ACP (holo-ACP) and biotinylated-BCCP (holo-BCCP) by AcpS and BirA, respectively. In the present study, we show that, when ACP or BCCP87 is fused to the C-terminus of secretory protein YebF or MBP, the resulting fusion protein preYebF-ACP, preYebF-BCCP87, preMBP-ACP or preMBP-BCCP87 can be modified and then secreted. Our data demonstrate that posttranslational modification of preYebF-ACP, preYebF-BCCP87 preMBP-ACP and preMBP-BCCP87 can take place in the cytosol prior to translocation, and the Sec machinery accommodates these previously modified fusion proteins. High levels of active holo-ACP and holo-BCCP87 are achieved when AcpS or BirA is co-expressed, especially when sodium azide is used to retard their translocation across the inner membrane. Our results also provide an alternative to achieve a high level of modified recombinant proteins expressed extracellularly.
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Affiliation(s)
- Nan Chen
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Fu-Lin Hong
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Hai-Hong Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Qi-Hang Yuan
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Wan-Yan Ma
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Xu-Na Gao
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Rui Shi
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Rui-Juan Zhang
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Chang-Sheng Sun
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
| | - Sheng-Bin Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong, P. R. China
- * E-mail:
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13
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Gumbart J, Schreiner E, Wilson DN, Beckmann R, Schulten K. Mechanisms of SecM-mediated stalling in the ribosome. Biophys J 2012; 103:331-41. [PMID: 22853911 DOI: 10.1016/j.bpj.2012.06.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Revised: 06/01/2012] [Accepted: 06/05/2012] [Indexed: 02/05/2023] Open
Abstract
Nascent-peptide modulation of translation is a common regulatory mechanism of gene expression. In this mechanism, while the nascent peptide is still in the exit tunnel of the ribosome, it induces translational pausing, thereby controlling the expression of downstream genes. One example is SecM, which inhibits peptide-bond formation in the ribosome's peptidyl transferase center (PTC) during its own translation, upregulating the expression of the protein translocase SecA. Although biochemical experiments and cryo-electron microscopy data have led to the identification of some residues involved in SecM recognition, the full pathway of interacting residues that connect SecM to the PTC through the ribosome has not yet been conclusively established. Here, using the cryo-electron microscopy data, we derived the first (to our knowledge) atomic model of the SecM-stalled ribosome via molecular-dynamics flexible fitting, complete with P- and A-site tRNAs. Subsequently, we carried out simulations of native and mutated SecM-stalled ribosomes to investigate possible interaction pathways between a critical SecM residue, R163, and the PTC. In particular, the simulations reveal the role of SecM in altering the position of the tRNAs in the ribosome, and thus demonstrate how the presence of SecM in the exit tunnel induces stalling. Finally, steered molecular-dynamics simulations in which SecM was pulled toward the tunnel exit suggest how SecA interacting with SecM from outside the ribosome relieves stalling.
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Affiliation(s)
- James Gumbart
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA
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14
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Celedon JM, Cline K. Intra-plastid protein trafficking: how plant cells adapted prokaryotic mechanisms to the eukaryotic condition. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:341-51. [PMID: 22750312 DOI: 10.1016/j.bbamcr.2012.06.028] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/11/2012] [Accepted: 06/20/2012] [Indexed: 12/14/2022]
Abstract
Protein trafficking and localization in plastids involve a complex interplay between ancient (prokaryotic) and novel (eukaryotic) translocases and targeting machineries. During evolution, ancient systems acquired new functions and novel translocation machineries were developed to facilitate the correct localization of nuclear encoded proteins targeted to the chloroplast. Because of its post-translational nature, targeting and integration of membrane proteins posed the biggest challenge to the organelle to avoid aggregation in the aqueous compartments. Soluble proteins faced a different kind of problem since some had to be transported across three membranes to reach their destination. Early studies suggested that chloroplasts addressed these issues by adapting ancient-prokaryotic machineries and integrating them with novel-eukaryotic systems, a process called 'conservative sorting'. In the last decade, detailed biochemical, genetic, and structural studies have unraveled the mechanisms of protein targeting and localization in chloroplasts, suggesting a highly integrated scheme where ancient and novel systems collaborate at different stages of the process. In this review we focus on the differences and similarities between chloroplast ancestral translocases and their prokaryotic relatives to highlight known modifications that adapted them to the eukaryotic situation. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
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Affiliation(s)
- Jose M Celedon
- Horticultural Sciences Department and Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL 32611, USA
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15
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Abstract
Outer membrane protein A (OmpA) of Escherichia coli is a paradigm for the biogenesis of outer membrane proteins; however, the structure and assembly of OmpA have remained controversial. A review of studies to date supports the hypothesis that native OmpA is a single-domain large pore, while a two-domain narrow-pore structure is a folding intermediate or minor conformer. The in vitro refolding of OmpA to the large-pore conformation requires isolation of the protein from outer membranes with retention of an intact disulfide bond followed by sufficient incubation in lipids at temperatures of ≥ 26 °C to overcome the high energy of activation for refolding. The in vivo maturation of the protein involves covalent modification of serines in the eighth β-barrel of the N-terminal domain by oligo-(R)-3-hydroxybutyrates as the protein is escorted across the cytoplasm by SecB for post-translational secretion across the secretory translocase in the inner membrane. After cleavage of the signal sequence, protein chaperones, such as Skp, DegP and SurA, guide OmpA across the periplasm to the β-barrel assembly machinery (BAM) complex in the outer membrane. During this passage, a disulfide bond is formed between C290 and C302 by DsbA, and the hydrophobicity of segments of the C-terminal domain, which are destined for incorporation as β-barrels in the outer membrane bilayer, is increased by covalent attachment of oligo-(R)-3-hydroxybutyrates. With the aid of the BAM complex, OmpA is then assembled into the outer membrane as a single-domain large pore.
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Affiliation(s)
- Rosetta N Reusch
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.
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16
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de Souza GA, Leversen NA, Målen H, Wiker HG. Bacterial proteins with cleaved or uncleaved signal peptides of the general secretory pathway. J Proteomics 2011; 75:502-10. [PMID: 21920479 DOI: 10.1016/j.jprot.2011.08.016] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 08/16/2011] [Accepted: 08/18/2011] [Indexed: 11/29/2022]
Abstract
Correct protein compartmentalization is a key step for molecular function and cell viability, and this is especially true for membrane and externalized proteins of bacteria. Recent proteomic reports of Bacillus subtilis have shown that many proteins with Sec-like signal peptides and absence of a transmembrane helix domain are still observed in membrane-enriched fractions, but further evidence about signal peptide cleavage or soluble protein contamination is still needed. Here we report a proteomic screening of identified peptides in culture filtrate, membrane fraction and whole cell lysate of Mycobacterium tuberculosis. We were able to detect peptide sequencing evidence that shows that the predicted signal peptide was kept uncleaved for several types of proteins such as mammalian cell entry (Mce) proteins and PE or PE-PGRS proteins. Label-free quantitation of all proteins identified in each fraction showed that the majority of these proteins with uncleaved signal peptides are, indeed, enriched in the Triton X-114 lipid phase. Some of these proteins are likely to be located in the inner membrane while others may be outer membrane proteins.
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Affiliation(s)
- Gustavo A de Souza
- Section for Microbiology and Immunology, the Gade Institute, University of Bergen, N-5021 Bergen, Norway
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17
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SecA, a remarkable nanomachine. Cell Mol Life Sci 2011; 68:2053-66. [PMID: 21479870 PMCID: PMC3101351 DOI: 10.1007/s00018-011-0681-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Revised: 03/22/2011] [Accepted: 03/28/2011] [Indexed: 01/03/2023]
Abstract
Biological cells harbor a variety of molecular machines that carry out mechanical work at the nanoscale. One of these nanomachines is the bacterial motor protein SecA which translocates secretory proteins through the protein-conducting membrane channel SecYEG. SecA converts chemically stored energy in the form of ATP into a mechanical force to drive polypeptide transport through SecYEG and across the cytoplasmic membrane. In order to accommodate a translocating polypeptide chain and to release transmembrane segments of membrane proteins into the lipid bilayer, SecYEG needs to open its central channel and the lateral gate. Recent crystal structures provide a detailed insight into the rearrangements required for channel opening. Here, we review our current understanding of the mode of operation of the SecA motor protein in concert with the dynamic SecYEG channel. We conclude with a new model for SecA-mediated protein translocation that unifies previous conflicting data.
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18
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Målen H, De Souza GA, Pathak S, Søfteland T, Wiker HG. Comparison of membrane proteins of Mycobacterium tuberculosis H37Rv and H37Ra strains. BMC Microbiol 2011; 11:18. [PMID: 21261938 PMCID: PMC3033788 DOI: 10.1186/1471-2180-11-18] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 01/24/2011] [Indexed: 01/24/2023] Open
Abstract
Background The potential causes for variation in virulence between distinct M. tuberculosis strains are still not fully known. However, differences in protein expression are probably an important factor. In this study we used a label-free quantitative proteomic approach to estimate differences in protein abundance between two closely related M. tuberculosis strains; the virulent H37Rv strain and its attenuated counterpart H37Ra. Results We were able to identify more than 1700 proteins from both strains. As expected, the majority of the identified proteins had similar relative abundance in the two strains. However, 29 membrane-associated proteins were observed with a 5 or more fold difference in their relative abundance in one strain compared to the other. Of note, 19 membrane- and lipo-proteins had higher abundance in H37Rv, while another 10 proteins had a higher abundance in H37Ra. Interestingly, the possible protein-export membrane protein SecF (Rv2586c), and three ABC-transporter proteins (Rv0933, Rv1273c and Rv1819c) were among the more abundant proteins in M. tuberculosis H37Rv. Conclusion Our data suggests that the bacterial secretion system and the transmembrane transport system may be important determinants of the ability of distinct M. tuberculosis strains to cause disease.
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Affiliation(s)
- Hiwa Målen
- Section for Microbiology and Immunology, the Gade Institute, University of Bergen, Bergen, Norway
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19
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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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20
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Brady LJ, Maddocks SE, Larson MR, Forsgren N, Persson K, Deivanayagam CC, Jenkinson HF. The changing faces of Streptococcus antigen I/II polypeptide family adhesins. Mol Microbiol 2010; 77:276-86. [PMID: 20497507 PMCID: PMC2909373 DOI: 10.1111/j.1365-2958.2010.07212.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Streptococcus mutans antigen I/II (AgI/II) protein was one of the first cell wall-anchored adhesins identified in Gram-positive bacteria. It mediates attachment of S. mutans to tooth surfaces and has been a focus for immunization studies against dental caries. The AgI/II family polypeptides recognize salivary glycoproteins, and are also involved in biofilm formation, platelet aggregation, tissue invasion and immune modulation. The genes encoding AgI/II family polypeptides are found among Streptococcus species indigenous to the human mouth, as well as in Streptococcus pyogenes, S. agalactiae and S. suis. Evidence of functionalities for different regions of the AgI/II proteins has emerged. A sequence motif within the C-terminal portion of Streptococcus gordonii SspB (AgI/II) is bound by Porphyromonas gingivalis, thus promoting oral colonization by this anaerobic pathogen. The significance of other epitopes is now clearer following resolution of regional crystal structures. A new picture emerges of the central V (variable) region, predicted to contain a carbohydrate-binding trench, being projected from the cell surface by a stalk formed by an unusual association between an N-terminal alpha-helix and a C-terminal polyproline helix. This presentation mode might be important in determining functional conformations of other Gram-positive surface proteins that have adhesin domains flanked by alpha-helical and proline-rich regions.
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Affiliation(s)
- L. Jeannine Brady
- Department of Oral Biology, University of Florida, Gainesville FL 32610, USA
| | - Sarah E. Maddocks
- School of Oral and Dental Sciences, University of Bristol, Bristol BS9 2RD, UK
| | - Matthew R. Larson
- Department of Physiology and Biophysics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Nina Forsgren
- Department of Odontology, Umeå University, SE-901 87 Umeå, Sweden
| | - Karina Persson
- Department of Odontology, Umeå University, SE-901 87 Umeå, Sweden
| | - Champion C. Deivanayagam
- Center for Biophysical Sciences and Engineering, and Department of Vision Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Howard F. Jenkinson
- School of Oral and Dental Sciences, University of Bristol, Bristol BS9 2RD, UK
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21
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Transport of preproteins by the accessory Sec system requires a specific domain adjacent to the signal peptide. J Bacteriol 2010; 192:4223-32. [PMID: 20562303 DOI: 10.1128/jb.00373-10] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The accessory Sec (SecA2/Y2) systems of streptococci and staphylococci are dedicated to the transport of large serine-rich repeat (SRR) glycoproteins to the bacterial cell surface. The means by which the glycosylated preproteins are selectively recognized by the accessory Sec system have not been fully characterized. In Streptococcus gordonii, the SRR glycoprotein GspB has a 90-residue amino-terminal signal sequence that is essential for transport by SecA2/Y2 but is not sufficient to mediate the transport of heterologous proteins by this specialized transporter. We now report that a preprotein must remain at least partially unfolded prior to transport by the accessory Sec system. In addition, a region of approximately 20 residues from the amino-terminal end of mature GspB (the accessory Sec transport or AST domain) is essential for SecA2/Y2-dependent transport. The replacement of several AST domain residues with glycine strongly interferes with export, which suggests that a helical conformation may be important. Analysis of GspB variants with alterations in the AST domain, in combination with the results with a SecY2 variant, indicates that the AST domain is essential both for targeting to the SecA2/Y2 translocase and for initiating translocation through the SecY2 channel. The combined results suggest a unique mechanism that ensures the transport of a single substrate by the SecA2/Y2 system.
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22
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Thermodynamics of the protein translocation. Methods Enzymol 2009. [PMID: 21609866 DOI: 10.1016/s0076-6879(09)66012-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Many proteins synthesized in bacteria are secreted from the cytoplasm into the periplasm to function in the cell envelope or in the extracellular medium. The Sec translocase is a primary and evolutionary conserved secretion pathway in bacteria. It catalyzes the translocation of unfolded proteins across the cytoplasmic membrane via the pore-forming SecYEG complex. This process is driven by the proton motive force and ATP hydrolysis facilitated by the SecA motor protein. Current insights in the mechanism of protein translocation are largely based on elaborate multidisciplinary studies performed during the last three decades. To understand the process dynamics, the thermodynamic principles of translocation and the subunit interactions need to be addressed. Isothermal titration calorimetry has been widely applied to study thermodynamics of biological interactions, their stability, and driving forces. Here, we describe the examples that exploit this method to investigate key interactions among components of the Sec translocase and suggest further potential applications of calorimetry.
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du Plessis DJF, Berrelkamp G, Nouwen N, Driessen AJM. The lateral gate of SecYEG opens during protein translocation. J Biol Chem 2009; 284:15805-14. [PMID: 19366685 DOI: 10.1074/jbc.m901855200] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The SecYEG translocon of Escherichia coli mediates the translocation of preproteins across the cytoplasmic membrane. Here, we have examined the role of the proposed lateral gate of the translocon in translocation. A dual cysteine cross-linking approach allowed the introduction of cross-linker arms of various lengths between adjoining aminoacyl positions of transmembrane segments 2b and 7 of the lateral gate. Oxidation and short spacer linkers that fix the gate in the closed state abolished preprotein translocation, whereas long spacer linkers support translocation. The cross-linking data further suggests that SecYEG lateral gate opening and activation of the SecA ATPase are coupled processes. It is concluded that lateral gate opening is a critical step during SecA-dependent protein translocation.
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Affiliation(s)
- David J F du Plessis
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
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Abstract
The persistent difficulties in the production of protein at high levels in heterologous systems, as well as the inability to understand pathologies associated with protein aggregation, highlight our limited knowledge on the mechanisms of protein folding in vivo. Attempts to improve yield and quality of recombinant proteins are diverse, frequently involving optimization of the cell growth temperature, the use of synonymous codons and/or the co-expression of tRNAs, chaperones and folding catalysts among others. Although protein secondary structure can be determined largely by the amino acid sequence, protein folding within the cell is affected by a range of factors beyond amino acid sequence. The folding pathway of a nascent polypeptide can be affected by transient interactions with other proteins and ligands, the ribosome, translocation through a pore membrane, redox conditions, among others. The translation rate as well as the translation machinery itself can dramatically affect protein folding, and thus the structure and function of the protein product. This review addresses current efforts to better understand how the use of synonymous codons in the mRNA and the availability of tRNAs can modulate translation kinetics, affecting the folding, the structure and the biological activity of proteins.
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Affiliation(s)
- Monica Marin
- Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
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25
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Fisher AC, DeLisa MP. Laboratory evolution of fast-folding green fluorescent protein using secretory pathway quality control. PLoS One 2008; 3:e2351. [PMID: 18545653 PMCID: PMC2396501 DOI: 10.1371/journal.pone.0002351] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2008] [Accepted: 04/28/2008] [Indexed: 11/19/2022] Open
Abstract
Green fluorescent protein (GFP) has undergone a long history of optimization to become one of the most popular proteins in all of cell biology. It is thermally and chemically robust and produces a pronounced fluorescent phenotype when expressed in cells of all types. Recently, a superfolder GFP was engineered with increased resistance to denaturation and improved folding kinetics. Here we report that unlike other well-folded variants of GFP (e.g., GFPmut2), superfolder GFP was spared from elimination when targeted for secretion via the SecYEG translocase. This prompted us to hypothesize that the folding quality control inherent to this secretory pathway could be used as a platform for engineering similar ‘superfolded’ proteins. To test this, we targeted a combinatorial library of GFPmut2 variants to the SecYEG translocase and isolated several superfolded variants that accumulated in the cytoplasm due to their enhanced folding properties. Each of these GFP variants exhibited much faster folding kinetics than the parental GFPmut2 protein and one of these, designated superfast GFP, folded at a rate that even exceeded superfolder GFP. Remarkably, these GFP variants exhibited little to no loss in specific fluorescence activity relative to GFPmut2, suggesting that the process of superfolding can be accomplished without altering the proteins' normal function. Overall, we demonstrate that laboratory evolution combined with secretory pathway quality control enables sampling of largely unexplored amino-acid sequences for the discovery of artificial, high-performance proteins with properties that are unparalleled in their naturally occurring analogues.
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Affiliation(s)
- Adam C. Fisher
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, United States of America
| | - Matthew P. DeLisa
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, United States of America
- Department of Biomedical Engineering, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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26
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Affiliation(s)
- Arnold J.M. Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, 9751 NN, Haren, The Netherlands; ,
| | - Nico Nouwen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, 9751 NN, Haren, The Netherlands; ,
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Requirements for surface expression and function of adhesin P1 from Streptococcus mutans. Infect Immun 2008; 76:2456-68. [PMID: 18362133 DOI: 10.1128/iai.01315-07] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this report, we define requirements for the successful translocation and functional maturation of the adhesin P1 of Streptococcus mutans. Conformational epitopes recognized by anti-P1 monoclonal antibodies (MAbs) were further characterized, thus facilitating the use of particular MAbs as tools to monitor the locations of various forms of the protein. We show that correct localization of P1 is dependent on structural features of the molecule itself, including a requisite A region-P region intramolecular interaction that occurs within the cell prior to secretion. P1 also was shown to be affected by several members of the protein-folding-secretion-turnover apparatus. It does not achieve a fully functional form in the absence of the trigger factor PPIase homolog RopA, and its translocation is delayed when DnaK levels are limited. In addition, dnaK message levels are differentially altered in the presence of P1 lacking the alanine-rich compared to the proline-rich repeat domains. Lastly, nonsecreted P1 lacking the P region accumulates within the cell in the absence of htrA, implying an intracellular HtrA protease function in the degradation and turnover of this particular internal-deletion polypeptide. However, the opposite effect is seen for full-length P1, suggesting a sensing mechanism and substrate-dependent alteration in HtrA's function and effect that is consistent with its known ability to switch between chaperone and protease, depending on environmental perturbations.
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28
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Tomkiewicz D, Nouwen N, Driessen AJ. Kinetics and Energetics of the Translocation of Maltose Binding Protein Folding Mutants. J Mol Biol 2008; 377:83-90. [DOI: 10.1016/j.jmb.2008.01.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Revised: 01/03/2008] [Accepted: 01/07/2008] [Indexed: 11/28/2022]
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29
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Oliver DC, Paetzel M. Crystal structure of the major periplasmic domain of the bacterial membrane protein assembly facilitator YidC. J Biol Chem 2007; 283:5208-16. [PMID: 18093969 DOI: 10.1074/jbc.m708936200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The essential bacterial membrane protein YidC facilitates insertion and assembly of proteins destined for integration into the inner membrane. It has homologues in both mitochondria and chloroplasts. Here we report the crystal structure of the Escherichia coli YidC major periplasmic domain (YidCECP1) at 2.5A resolution. This domain is present in YidC from Gram-negative bacteria and is more than half the size of the full-length protein. The structure reveals that YidCECP1 is made up of a large twisted beta-sandwich protein fold with a C-terminal alpha-helix that packs against one face of the beta-sandwich. Our structure and sequence analysis reveals that the C-terminal alpha-helix and the beta-sheet that it lays against are the most conserved regions of the domain. The region corresponding to the C-terminal alpha-helix was previously shown to be important for the protein insertase function of YidC and is conserved in other YidC-like proteins. The structure reveals that a region of YidC that was previously shown to be involved in binding to SecF maps to one edge of the beta-sandwich. Electrostatic analysis of the molecular surface for this region of YidC reveals a predominantly charged surface and suggests that the SecF-YidC interaction may be electrostatic in nature. Interestingly, YidCECP1 has significant structural similarity to galactose mutarotase from Lactococcus lactis, suggesting that this domain may have another function besides its role in membrane protein assembly.
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Affiliation(s)
- David C Oliver
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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