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Henderson RC, Gao F, Jayanthi S, Kight A, Sharma P, Goforth RL, Heyes CD, Henry RL, Suresh Kumar TK. Domain Organization in the 54-kDa Subunit of the Chloroplast Signal Recognition Particle. Biophys J 2016; 111:1151-1162. [PMID: 27653474 PMCID: PMC5034345 DOI: 10.1016/j.bpj.2016.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 07/29/2016] [Accepted: 08/02/2016] [Indexed: 10/21/2022] Open
Abstract
Chloroplast signal recognition particle (cpSRP) is a heterodimer composed of an evolutionarily conserved 54-kDa GTPase (cpSRP54) and a unique 43-kDa subunit (cpSRP43) responsible for delivering light-harvesting chlorophyll binding protein to the thylakoid membrane. While a nearly complete three-dimensional structure of cpSRP43 has been determined, no high-resolution structure is yet available for cpSRP54. In this study, we developed and examined an in silico three-dimensional model of the structure of cpSRP54 by homology modeling using cytosolic homologs. Model selection was guided by single-molecule Förster resonance energy transfer experiments, which revealed the presence of at least two distinct conformations. Small angle x-ray scattering showed that the linking region among the GTPase (G-domain) and methionine-rich (M-domain) domains, an M-domain loop, and the cpSRP43 binding C-terminal extension of cpSRP54 are predominantly disordered. Interestingly, the linker and loop segments were observed to play an important role in organizing the domain arrangement of cpSRP54. Further, deletion of the finger loop abolished loading of the cpSRP cargo, light-harvesting chlorophyll binding protein. These data highlight important structural dynamics relevant to cpSRP54's role in the post- and cotranslational signaling processes.
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Affiliation(s)
- Rory C Henderson
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Feng Gao
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Srinivas Jayanthi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Alicia Kight
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas
| | - Priyanka Sharma
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas
| | - Robyn L Goforth
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas
| | - Colin D Heyes
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas
| | - Ralph L Henry
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas
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Breaking on through to the other side: protein export through the bacterial Sec system. Biochem J 2013; 449:25-37. [PMID: 23216251 DOI: 10.1042/bj20121227] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
More than one-third of cellular proteomes traffic into and across membranes. Bacteria have invented several sophisticated secretion systems that guide various proteins to extracytoplasmic locations and in some cases inject them directly into hosts. Of these, the Sec system is ubiquitous, essential and by far the best understood. Secretory polypeptides are sorted from cytoplasmic ones initially due to characteristic signal peptides. Then they are targeted to the plasma membrane by chaperones/pilots. The translocase, a dynamic nanomachine, lies at the centre of this process and acts as a protein-conducting channel with a unique property; allowing both forward transfer of secretory proteins but also lateral release into the lipid bilayer with high fidelity and efficiency. This process, tightly orchestrated at the expense of energy, ensures fundamental cell processes such as membrane biogenesis, cell division, motility, nutrient uptake and environmental sensing. In the present review, we examine this fascinating process, summarizing current knowledge on the structure, function and mechanics of the Sec pathway.
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Ariosa AR, Duncan SS, Saraogi I, Lu X, Brown A, Phillips GJ, Shan SO. Fingerloop activates cargo delivery and unloading during cotranslational protein targeting. Mol Biol Cell 2012; 24:63-73. [PMID: 23135999 PMCID: PMC3541965 DOI: 10.1091/mbc.e12-06-0434] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
During protein targeting by the signal recognition particle (SRP), signals from cargo binding in the SRP's M domain must be communicated to its GTPase domain to initiate the membrane delivery of cargo. In this study, a conserved fingerloop lining the signal sequence–binding groove of SRP is shown to provide a key link in this molecular communication. During cotranslational protein targeting by the signal recognition particle (SRP), information about signal sequence binding in the SRP's M domain must be effectively communicated to its GTPase domain to turn on its interaction with the SRP receptor (SR) and thus deliver the cargo proteins to the membrane. A universally conserved “fingerloop” lines the signal sequence–binding groove of SRP; the precise role of this fingerloop in protein targeting has remained elusive. In this study, we show that the fingerloop plays important roles in SRP function by helping to induce the SRP into a more active conformation that facilitates multiple steps in the pathway, including efficient recruitment of SR, GTPase activation in the SRP•SR complex, and most significantly, the unloading of cargo onto the target membrane. On the basis of these results and recent structural work, we propose that the fingerloop is the first structural element to detect signal sequence binding; this information is relayed to the linker connecting the SRP's M and G domains and thus activates the SRP and SR for carrying out downstream steps in the pathway.
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Affiliation(s)
- Aileen R Ariosa
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Bibi E. Early targeting events during membrane protein biogenesis in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:841-50. [PMID: 20682283 DOI: 10.1016/j.bbamem.2010.07.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2010] [Revised: 07/21/2010] [Accepted: 07/22/2010] [Indexed: 10/19/2022]
Abstract
All living cells have co-translational pathways for targeting membrane proteins. Co-translation pathways for secretory proteins also exist but mostly in eukaryotes. Unlike secretory proteins, the biosynthetic pathway of most membrane proteins is conserved through evolution and these proteins are usually synthesized by membrane-bound ribosomes. Translation on the membrane requires that both the ribosomes and the mRNAs be properly localized. Theoretically, this can be achieved by several means. (i) The current view is that the targeting of cytosolic mRNA-ribosome-nascent chain complexes (RNCs) to the membrane is initiated by information in the emerging hydrophobic nascent polypeptides. (ii) The alternative model suggests that ribosomes may be targeted to the membrane also constitutively, whereas the appropriate mRNAs may be carried on small ribosomal subunits or targeted by other cellular factors to the membrane-bound ribosomes. Importantly, the available experimental data do not rule out the possibility that cells may also utilize both pathways in parallel. In any case, it is well documented that a major player in the targeting pathway is the signal recognition particle (SRP) system composed of the SRP and its receptor (SR). Although the functional core of the SRP system is evolutionarily conserved, its composition and biological practice come with different flavors in various organisms. This review is dedicated mainly to the Escherichia (E.) coli SRP, where the biochemical and structural properties of components of the SRP system have been relatively characterized, yielding essential information about various aspects of the pathway. In addition, several cellular interactions of the SRP and its receptor have been described in E. coli, providing insights into their spatial function. Collectively, these in vitro studies have led to the current view of the targeting pathway [see (i) above]. Interestingly, however, in vivo studies of the role of the SRP and its receptor, with emphasis on the temporal progress of the pathway, elicited an alternative hypothesis [see (ii) above]. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.
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Affiliation(s)
- Eitan Bibi
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
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Reinau ME, Otzen DE. Stability and structure of the membrane protein transporter Ffh is modulated by substrates and lipids. Arch Biochem Biophys 2009; 492:48-53. [PMID: 19800309 DOI: 10.1016/j.abb.2009.09.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Revised: 09/16/2009] [Accepted: 09/28/2009] [Indexed: 10/20/2022]
Abstract
The cytosolic protein Ffh transports membrane proteins from the ribosome to the inner membrane in complex with 4.5S RNA. Here we show that native Ffh binds to the hydrophobic probe ANS in a 1 Ffh:3 ANS stoichiometry, revealing a hydrophobic binding site. Thermal precipitation of Ffh is shifted upwards by approximately 10 degrees C by ANS or substrate protein, suggesting that the hydrophobic binding site makes the protein aggregation prone. Chemical denaturation confirm that Ffh is a rather unstable protein. 4.5S RNA destabilizes Ffh further, suggesting it keeps the protein in a more open conformation than the apoprotein. Escherichia coli lipid and DOPG (and to a smaller extent DOPC) increase Ffh's alpha-helical content, possibly related to Ffh's role in guiding membrane proteins to the membrane. Binding is largely mediated by electrostatic interactions but does not protect Ffh against trypsinolysis. We conclude that Ffh is a structurally flexible and dynamic protein whose stability is significantly modulated by the environment.
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Affiliation(s)
- Marika E Reinau
- Department of Life Sciences, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark
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Peterson JM, Phillips GJ. Characterization of conserved bases in 4.5S RNA of Escherichia coli by construction of new F' factors. J Bacteriol 2008; 190:7709-18. [PMID: 18805981 PMCID: PMC2583608 DOI: 10.1128/jb.00995-08] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Accepted: 09/06/2008] [Indexed: 01/03/2023] Open
Abstract
To more clearly understand the function of conserved bases of 4.5S RNA, the product of the essential ffs gene of Escherichia coli, and to address conflicting results reported in other studies, we have developed a new genetic system to characterize ffs mutants. Multiple ffs alleles were generated by altering positions that correspond to the region of the RNA molecule that interacts directly with Ffh in assembly of the signal recognition particle. To facilitate characterization of the ffs mutations with minimal manipulation, recombineering was used to construct new F' factors to easily move each allele into different genetic backgrounds for expression in single copy. In combination with plasmids that expressed ffs in multiple copy numbers, the F' factors provided an accurate assessment of the ability of the different 4.5S RNA mutants to function in vivo. Consistent with structural analysis of the signal recognition particle (SRP), highly conserved bases in 4.5S RNA are important for binding Ffh. Despite the high degree of conservation, however, only a single base (C62) was indispensable for RNA function under all conditions tested. To quantify the interaction between 4.5S RNA and Ffh, an assay was developed to measure the ability of mutant 4.5S RNA molecules to copurify with Ffh. Defects in Ffh binding correlated with loss of SRP-dependent protein localization. Real-time quantitative PCR was also used to measure the levels of wild-type and mutant 4.5S RNA expressed in vivo. These results clarify inconsistencies from prior studies and yielded a convenient method to study the function of multiple alleles.
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Affiliation(s)
- James M Peterson
- Department of Veterinary Microbiology, Iowa State University, 1802 University Boulevard, Building 6, Ames, IA 50011, USA
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Clérico EM, Maki JL, Gierasch LM. Use of synthetic signal sequences to explore the protein export machinery. Biopolymers 2008; 90:307-19. [PMID: 17918185 DOI: 10.1002/bip.20856] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The information for correct localization of newly synthesized proteins in both prokaryotes and eukaryotes resides in self-contained, often transportable targeting sequences. Of these, signal sequences specify that a protein should be secreted from a cell or incorporated into the cytoplasmic membrane. A central puzzle is presented by the lack of primary structural homology among signal sequences, although they share common features in their sequences. Synthetic signal peptides have enabled a wide range of studies of how these "zipcodes" for protein secretion are decoded and used to target proteins to the protein machinery that facilitates their translocation across and integration into membranes. We review research on how the information in signal sequences enables their passenger proteins to be correctly and efficiently localized. Synthetic signal peptides have made possible binding and crosslinking studies to explore how selectivity is achieved in recognition by the signal sequence-binding receptors, signal recognition particle, or SRP, which functions in all organisms, and SecA, which functions in prokaryotes and some organelles of prokaryotic origins. While progress has been made, the absence of atomic resolution structures for complexes of signal peptides and their receptors has definitely left many questions to be answered in the future.
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Affiliation(s)
- Eugenia M Clérico
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, MA 01003, USA
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Krishnan B, Szymanska A, Gierasch LM. Site-specific fluorescent labeling of poly-histidine sequences using a metal-chelating cysteine. Chem Biol Drug Des 2007; 69:31-40. [PMID: 17313455 PMCID: PMC2896745 DOI: 10.1111/j.1747-0285.2007.00463.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coupling genetically encoded target sequences with specific and selective labeling strategies has made it possible to utilize fluorescence spectroscopy in complex mixtures to investigate the structure, function, and dynamics of proteins. Thus, there is a growing need for a repertoire of such labeling approaches to deploy based on a given application and to utilize in combination with one another by orthogonal reactivity. We have developed a simple approach to synthesize a fluorescent probe that binds to a poly-histidine sequence. The amino group of cysteine was converted into nitrilotriacetate to create a metal-chelating cysteine molecule, Cys-nitrilotriacetate. Two Cys-nitrilotriacetate molecules were then cross-linked using dibromobimane to generate a fluorophore capable of binding a His-tag on a protein, NTA(2)-BM. NTA(2)-BM is a potential fluorophore for selective tagging of proteins in vivo.
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Affiliation(s)
- Beena Krishnan
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA 01003-9305, USA
| | - Aneta Szymanska
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA 01003-9305, USA
- Department of Chemistry, University of Gdansk, Sobieskiego 18, 80–952 Gdansk, Poland
| | - Lila M. Gierasch
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA 01003-9305, USA
- Department of Chemistry, University of Massachusetts Amherst, 710 N. Pleasant St, Amherst, MA 01003-9336, USA
- Corresponding author: Lila M. Gierasch,
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Abstract
The signal recognition particle (SRP) directs integral membrane and secretory proteins to the cellular protein translocation machinery during translation. The SRP is an evolutionarily conserved RNA-protein complex whose activities are regulated by GTP hydrolysis. Recent structural investigations of SRP functional domains and interactions provide new insights into the mechanisms of SRP activity in all cells, leading toward a comprehensive understanding of protein trafficking by this elegant pathway.
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Affiliation(s)
- Jennifer A Doudna
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California 94705, USA.
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Cleverley RM, Gierasch LM. Mapping the signal sequence-binding site on SRP reveals a significant role for the NG domain. J Biol Chem 2002; 277:46763-8. [PMID: 12244111 DOI: 10.1074/jbc.m207427200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We present evidence that the signal recognition particle (SRP) recognizes signal sequences via the NG domain on the SRP54 protein subunit. Using a recently developed cross-linking method (Fancy, D. A., and Kodadek, T. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 6020-6024; Correction (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 1317), we find that signal peptides cross-link to the Escherichia coli SRP protein Ffh (the homologue of the mammalian SRP54 subunit) via the NG domain. Within the NG domain, the cross-linking site maps to the ras-like C-terminal subdomain termed the G domain. This result stands in contrast to previous studies, which concluded based on nascent chain cross-linking that the signal sequence bound to the adjacent M domain. As independent evidence of a direct binding interaction between the NG domain and the signal sequence, we find that the NG domain of Ffh binds signal peptides as an isolated entity. Our results suggest that the NG domain forms a substantial part of the binding site for the signal sequence.
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Affiliation(s)
- Robert M Cleverley
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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