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Orfanoudaki G, Markaki M, Chatzi K, Tsamardinos I, Economou A. MatureP: prediction of secreted proteins with exclusive information from their mature regions. Sci Rep 2017; 7:3263. [PMID: 28607462 PMCID: PMC5468347 DOI: 10.1038/s41598-017-03557-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/28/2017] [Indexed: 11/09/2022] Open
Abstract
More than a third of the cellular proteome is non-cytoplasmic. Most secretory proteins use the Sec system for export and are targeted to membranes using signal peptides and mature domains. To specifically analyze bacterial mature domain features, we developed MatureP, a classifier that predicts secretory sequences through features exclusively computed from their mature domains. MatureP was trained using Just Add Data Bio, an automated machine learning tool. Mature domains are predicted efficiently with ~92% success, as measured by the Area Under the Receiver Operating Characteristic Curve (AUC). Predictions were validated using experimental datasets of mutated secretory proteins. The features selected by MatureP reveal prominent differences in amino acid content between secreted and cytoplasmic proteins. Amino-terminal mature domain sequences have enhanced disorder, more hydroxyl and polar residues and less hydrophobics. Cytoplasmic proteins have prominent amino-terminal hydrophobic stretches and charged regions downstream. Presumably, secretory mature domains comprise a distinct protein class. They balance properties that promote the necessary flexibility required for the maintenance of non-folded states during targeting and secretion with the ability of post-secretion folding. These findings provide novel insight in protein trafficking, sorting and folding mechanisms and may benefit protein secretion biotechnology.
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Affiliation(s)
- Georgia Orfanoudaki
- Institute of Molecular Biology and Biotechnology-FORTH and Department of Biology-University of Crete, PO Box 1385, Heraklion, Crete, Greece
| | - Maria Markaki
- Computer Science Department, University of Crete, Heraklion, Greece
| | - Katerina Chatzi
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000, Leuven, Belgium
| | - Ioannis Tsamardinos
- Computer Science Department, University of Crete, Heraklion, Greece.,Gnosis Data Analysis PC, Heraklion, Greece
| | - Anastassios Economou
- Institute of Molecular Biology and Biotechnology-FORTH and Department of Biology-University of Crete, PO Box 1385, Heraklion, Crete, Greece. .,KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000, Leuven, Belgium.
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Alami M, Dalal K, Lelj-Garolla B, Sligar SG, Duong F. Nanodiscs unravel the interaction between the SecYEG channel and its cytosolic partner SecA. EMBO J 2007; 26:1995-2004. [PMID: 17396152 PMCID: PMC1852787 DOI: 10.1038/sj.emboj.7601661] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2005] [Accepted: 03/02/2007] [Indexed: 11/08/2022] Open
Abstract
The translocon is a membrane-embedded protein assembly that catalyzes protein movement across membranes. The core translocon, the SecYEG complex, forms oligomers, but the protein-conducting channel is at the center of the monomer. Defining the properties of the SecYEG protomer is thus crucial to understand the underlying function of oligomerization. We report here the reconstitution of a single SecYEG complex into nano-scale lipid bilayers, termed Nanodiscs. These water-soluble particles allow one to probe the interactions of the SecYEG complex with its cytosolic partner, the SecA dimer, in a membrane-like environment. The results show that the SecYEG complex triggers dissociation of the SecA dimer, associates only with the SecA monomer and suffices to (pre)-activate the SecA ATPase. Acidic lipids surrounding the SecYEG complex also contribute to the binding affinity and activation of SecA, whereas mutations in the largest cytosolic loop of the SecY subunit, known to abolish the translocation reaction, disrupt both the binding and activation of SecA. Altogether, the results define the fundamental contribution of the SecYEG protomer in the translocation subreactions and illustrate the power of nanoscale lipid bilayers in analyzing the dynamics occurring at the membrane.
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Affiliation(s)
- Meriem Alami
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, Faculty of Medicine, University of British Columbia, British Columbia, Canada
| | - Kush Dalal
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, Faculty of Medicine, University of British Columbia, British Columbia, Canada
| | - Barbara Lelj-Garolla
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, Faculty of Medicine, University of British Columbia, British Columbia, Canada
| | - Stephen G Sligar
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Franck Duong
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, Faculty of Medicine, University of British Columbia, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia, Canada V6T 1Z3. Tel.: +1 604 822 5975; Fax: +1 604 822 5227; E-mail:
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Papanikou E, Karamanou S, Baud C, Frank M, Sianidis G, Keramisanou D, Kalodimos CG, Kuhn A, Economou A. Identification of the Preprotein Binding Domain of SecA. J Biol Chem 2005; 280:43209-17. [PMID: 16243836 DOI: 10.1074/jbc.m509990200] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SecA, the preprotein translocase ATPase, has a helicase DEAD motor. To catalyze protein translocation, SecA possesses two additional flexible domains absent from other helicases. Here we demonstrate that one of these "specificity domains" is a preprotein binding domain (PBD). PBD is essential for viability and protein translocation. PBD mutations do not abrogate the basal enzymatic properties of SecA (nucleotide binding and hydrolysis), nor do they prevent SecA binding to the SecYEG protein conducting channel. However, SecA PBD mutants fail to load preproteins onto SecYEG, and their translocation ATPase activity does not become stimulated by preproteins. Bulb and Stem, the two sterically proximal PBD substructures, are physically separable and have distinct roles. Stem binds signal peptides, whereas the Bulb binds mature preprotein regions as short as 25 amino acids. Binding of signal or mature region peptides or full-length preproteins causes distinct conformational changes to PBD and to the DEAD motor. We propose that (a) PBD is a preprotein receptor and a physical bridge connecting bound preproteins to the DEAD motor, and (b) preproteins control the ATPase cycle via PBD.
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Affiliation(s)
- Efrosyni Papanikou
- Institute of Molecular Biology and Biotechnology, F.O.R.T.H., University of Crete, P.O. Box 1527, GR-711 10 Iraklio, Crete, Greece
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Vrontou E, Economou A. Structure and function of SecA, the preprotein translocase nanomotor. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1694:67-80. [PMID: 15546658 DOI: 10.1016/j.bbamcr.2004.06.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2003] [Revised: 06/03/2004] [Accepted: 06/17/2004] [Indexed: 11/22/2022]
Abstract
Most secretory proteins that are destined for the periplasm or the outer membrane are exported through the bacterial plasma membrane by the Sec translocase. Translocase is a complex nanomachine that moves processively along its aminoacyl polymeric substrates effectively pumping them to the periplasmic space. The salient features of this process are: (a) a membrane-embedded "clamp" formed by the trimeric SecYEG protein, (b) a "motor" provided by the dimeric SecA ATPase, (c) regulatory subunits that optimize catalysis and (d) both chemical and electrochemical metabolic energy. Significant recent strides have allowed structural, biochemical and biophysical dissection of the export reaction. A model incorporating stepwise strokes of the translocase nanomachine at work is discussed.
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Affiliation(s)
- Eleftheria Vrontou
- Laboratory Unicellular, Organisms Group, Institute of Molecular Biology and Biotechnology, FO.R.T.H. and Department of Biology, University of Crete, Vassilika Vouton, P.O. Box 1527, GR-711 10 Iraklio, Crete, Greece
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Abstract
The targeting of proteins into and across biological membranes to their correct cellular locations is mediated by a variety of transport pathways. These systems must couple the thermodynamically unfavorable processes of substrate translocation and integration with the expenditure of metabolic energy, using the free energy of ATP and GTP hydrolysis and/or a transmembrane protonmotive force. Several recent advances in our knowledge of the structure and function of these transport systems have provided insights into the mechanisms of energy transduction, force generation and energy use by different protein transport pathways.
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Affiliation(s)
- Nathan N Alder
- Department of Medical Biochemistry and Genetics, Texas A&M University System Health Science Center, College Station, TX 77843, USA
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De Keyzer J, Van Der Does C, Driessen AJM. Kinetic analysis of the translocation of fluorescent precursor proteins into Escherichia coli membrane vesicles. J Biol Chem 2002; 277:46059-65. [PMID: 12226104 DOI: 10.1074/jbc.m208449200] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein secretion in Escherichia coli is mediated by translocase, a multi-subunit membrane protein complex with SecA as ATP-driven motor protein and the SecYEG complex as translocation pore. A fluorescent assay was developed to facilitate kinetic studies of protein translocation. Single cysteine mutants of proOmpA were site-specific labeled with fluorescent dyes, and the SecA and ATP-dependent translocation into inner membrane vesicles and SecYEG proteoliposomes was monitored by means of protease accessibility and in gel fluorescent imaging. The translocation of fluorescently labeled proOmpA was largely independent on the position and the size of the fluorescent label (up to a size of 13-16 A). A fluorophore at the +4 position blocked translocation, but inhibition was completely relieved in the PrlA4 mutant. The kinetics of translocation of the fluorescently labeled proOmpA could be directly monitored by means of fluorescence quenching. Inner membrane vesicles containing wild-type SecYEG were found to translocate proOmpA with a turnover of 4.5 molecules proOmpA/SecYEG complex/min and an apparent K(m) of 180 nm, whereas the PrlA4 mutant showed an almost 10-fold increase in turnover rate and a 3-fold increase of the apparent K(m) for proOmpA translocation.
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Affiliation(s)
- Jeanine De Keyzer
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
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Roos T, Kiefer D, Hugenschmidt S, Economou A, Kuhn A. Indecisive M13 procoat protein mutants bind to SecA but do not activate the translocation ATPase. J Biol Chem 2001; 276:37909-15. [PMID: 11487581 DOI: 10.1074/jbc.m105483200] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The M13 procoat protein serves as the paradigm for the Sec-independent membrane insertion pathway. This protein is inserted into the inner membrane of Escherichia coli with two hydrophobic regions and a central periplasmic loop region of 20 amino acid residues. Extension of the periplasmic loop region renders M13 procoat membrane insertion Sec-dependent. Loop regions with 118 or more residues required SecA and SecYEG and were efficiently translocated in vivo. Two mutants having loop regions of 80 and 100 residues, respectively, interacted with SecA but failed to activate the membrane translocation ATPase of SecA in vitro. Similarly, a procoat mutant with two additional glutamyl residues in the loop region showed binding to SecA but did not stimulate the ATPase. The three mutants were also defective for precursor-stimulated binding of SecA to the membrane surface. Remarkably, the mutant proteins act as competitive inhibitors of the Sec translocase. This suggests that the region to be translocated is sensed by SecA but the activation of the SecA translocation ATPase is only successful for substrates with a minimum length of the translocated region.
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Affiliation(s)
- T Roos
- Institute of Microbiology and Molecular Biology, University of Hohenheim, D-70593 Stuttgart, Germany
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Swaving J, van Wely KH, Driessen AJ. Preprotein translocation by a hybrid translocase composed of Escherichia coli and Bacillus subtilis subunits. J Bacteriol 1999; 181:7021-7. [PMID: 10559168 PMCID: PMC94177 DOI: 10.1128/jb.181.22.7021-7027.1999] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial protein translocation is mediated by translocase, a multisubunit membrane protein complex that consists of a peripheral ATPase SecA and a preprotein-conducting channel with SecY, SecE, and SecG as subunits. Like Escherichia coli SecG, the Bacillus subtilis homologue, YvaL, dramatically stimulated the ATP-dependent translocation of precursor PhoB (prePhoB) by the B. subtilis SecA-SecYE complex. To systematically determine the functional exchangeability of translocase subunits, all of the relevant combinations of the E. coli and B. subtilis secY, secE, and secG genes were expressed in E. coli. Hybrid SecYEG complexes were overexpressed at high levels. Since SecY could not be overproduced without SecE, these data indicate a stable interaction between the heterologous SecY and SecE subunits. E. coli SecA, but not B. subtilis SecA, supported efficient ATP-dependent translocation of the E. coli precursor OmpA (proOmpA) into inner membrane vesicles containing the hybrid SecYEG complexes, if E. coli SecY and either E. coli SecE or E. coli SecG were present. Translocation of B. subtilis prePhoB, on the other hand, showed a strict dependence on the translocase subunit composition and occurred efficiently only with the homologous translocase. In contrast to E. coli SecA, B. subtilis SecA binds the SecYEG complexes only with low affinity. These results suggest that each translocase subunit contributes in an exclusive manner to the specificity and functionality of the complex.
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Affiliation(s)
- J Swaving
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9751 NN Haren, The Netherlands
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Economou A. Bacterial preprotein translocase: mechanism and conformational dynamics of a processive enzyme. Mol Microbiol 1998; 27:511-8. [PMID: 9489663 DOI: 10.1046/j.1365-2958.1998.00713.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Preprotein translocase, the membrane transporter for secretory proteins, is a processive enzyme. It comprises the membrane proteins SecYEG(DFYajC) and the peripheral ATPase SecA, which acts as a motor subunit. Translocase subunits form dynamic complexes in the lipid bilayer and build an aqueous conduit through which preprotein substrates are transported at the expense of energy. Preproteins bind to translocase and trigger cycles of ATP binding and hydrolysis that drive a transition of SecA between two distinct conformational states. These changes are transmitted to SecG and lead to inversion of its membrane topology. SecA conformational changes promote directed migration of the polymeric substrate through the translocase, in steps of 20-30 aminoacyl residues. Translocase dissociates from the substrate only after the whole preprotein chain length has been transported to the trans side of the membrane, where it is fully released.
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Affiliation(s)
- A Economou
- Institute of Molecular Biology and Biotechnology-FORTH and Department of Biology, University of Crete, Iraklio-Crete, Greece.
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Isenman L, Liebow C, Rothman S. Transport of proteins across membranes--a paradigm in transition. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1241:341-70. [PMID: 8547300 DOI: 10.1016/0304-4157(95)00009-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- L Isenman
- Department of Physiology, Tufts University School of Medicine, Boston, MA 02111, USA
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Douville K, Price A, Eichler J, Economou A, Wickner W. SecYEG and SecA are the stoichiometric components of preprotein translocase. J Biol Chem 1995; 270:20106-11. [PMID: 7650029 DOI: 10.1074/jbc.270.34.20106] [Citation(s) in RCA: 110] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The transport of large preproteins across the Escherichia coli plasma membrane is catalyzed by preprotein translocase, comprised of the peripherally bound SecA subunit and an integrally bound heterotrimeric domain consisting of the SecY, SecE, and SecG subunits. We have now placed the secY, secE, and secG genes under the control of an arabinose-inducible promoter on a multicopy plasmid. Upon induction, all three of the proteins are strongly overexpressed and recovered in the plasma membrane fraction. These membranes show a strong enhancement of 1) translocation ATPase activity, 2) preprotein translocation, 3) capacity for SecA binding, and 4) formation of the membrane-inserted form of SecA. These data establish that SecY, SecE, and SecG constitute the integral membrane domain of preprotein translocase.
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Affiliation(s)
- K Douville
- Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire 03755-3844, USA
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Arkowitz RA, Bassilana M. Protein translocation in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1197:311-43. [PMID: 7819269 DOI: 10.1016/0304-4157(94)90012-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- R A Arkowitz
- MRC Laboratory of Molecular Biology, Cambridge, UK
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Precursor-specific requirements for SecA, SecB, and delta muH+ during protein export of Escherichia coli. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)99952-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Palmen R, Driessen AJ, Hellingwerf KJ. Bioenergetic aspects of the translocation of macromolecules across bacterial membranes. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1183:417-51. [PMID: 8286395 DOI: 10.1016/0005-2728(94)90072-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Bacteria are extremely versatile in the sense that they have gained the ability to transport all three major classes of biopolymers through their cell envelope: proteins, nucleic acids, and polysaccharides. These macromolecules are translocated across membranes in a large number of cellular processes by specific translocation systems. Members of the ABC (ATP binding cassette) superfamily of transport ATPases are involved in the translocation of all three classes of macromolecules, in addition to unique transport ATPases. An intriguing aspect of these transport processes is that the barrier function of the membrane is preserved despite the fact the dimensions of the translocated molecules by far surpasses the thickness of the membrane. This raises questions like: How are these polar compounds translocated across the hydrophobic interior of the membrane, through a proteinaceous pore or through the lipid phase; what drives these macromolecules across the membrane; which energy sources are used and how is unidirectionality achieved? It is generally believed that macromolecules are translocated in a more or less extended, most likely linear form. A recurring theme in the bioenergetics of these translocation reactions in bacteria is the joint involvement of free energy input in the form of ATP hydrolysis and via proton sym- or antiport, driven by a proton gradient. Important similarities in the bioenergetic mechanisms of the translocation of these biopolymers therefore may exist.
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Affiliation(s)
- R Palmen
- Department of Microbiology, University of Amsterdam, The Netherlands
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Rusch S, Kendall D. Transport of an export-defective protein by a highly hydrophobic signal peptide. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)42249-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Affiliation(s)
- M Müller
- Institut für Physikalische Biochemie, Universität München, Germany
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Strobel SM, Cannon JG, Bassford PJ. Regions of maltose-binding protein that influence SecB-dependent and SecA-dependent export in Escherichia coli. J Bacteriol 1993; 175:6988-95. [PMID: 8226642 PMCID: PMC206826 DOI: 10.1128/jb.175.21.6988-6995.1993] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
In Escherichia coli, the efficient export of maltose-binding protein (MBP) is dependent on the chaperone SecB, whereas export of ribose-binding protein (RBP) is SecB independent. To localize the regions of MBP involved in interaction with SecB, hybrids between MBP and RBP in SecB mutant cells were constructed and analyzed. One hybrid consisted of the signal peptide and first third of the mature moiety of MBP, followed by the C-terminal two-thirds of RBP (MBP-RBP112). This hybrid was dependent upon SecB for its efficient export and exhibited a strong export defect in secA mutant cells. A hybrid between RBP and MBP with the same fusion point was also constructed (RBP-MBP116). The RBP-MBP116 hybrid remained SecB independent and only exhibited a partial export defect in secA mutant cells. In addition, MBP species with specific alterations in the early mature region were less dependent on SecB for their efficient export. The export of these altered MBP species was also less affected in secA mutant cells and in cells treated with sodium azide. These results present additional evidence for the targeting role of SecB.
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Affiliation(s)
- S M Strobel
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill 27599-7290
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