1
|
Kunii K, Yamanaka T, Miyamoto A, Nanatani K, Abe K. Thermostability optimization of the aspartate/alanine exchange transporter from Tetragenococcus halophilus. J Biochem 2024; 175:439-446. [PMID: 38616642 DOI: 10.1093/jb/mvad104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/20/2023] [Indexed: 12/29/2023] Open
Abstract
Aspartate/alanine exchange transporter (AspT) is a secondary transporter isolated from the lactic acid bacterium Tetragenococcus halophilus D10 strain. This transporter cooperates with aspartate decarboxylase to produce proton-motive force through decarboxylative phosphorylation. A method that successfully analyzes the AspT mechanism could serve as a prototype for elucidating the substrate transport mechanism of other exchange transporters; therefore, the purpose of this study was to search for conditions that improve the thermal stability of AspT for 3D structure analysis. We used the fluorescence size-exclusion chromatography-based thermostability assay to evaluate conditions that contribute to AspT stability. We found that the AspT thermostability was enhanced at pH 5.0 to 6.0 and in the presence of Na+ and Li+. Pyridoxal phosphate, a coenzyme of aspartate decarboxylase, also had a thermostabilizing effect on AspT. Under the conditions obtained from these results, it was possible to increase the temperature at which 50% of dimer AspT remained by 14°C. We expect these conditions to provide useful information for future structural analysis of AspT.
Collapse
Affiliation(s)
- Kota Kunii
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
| | - Takashi Yamanaka
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
| | - Akari Miyamoto
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
| | - Kei Nanatani
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
- Structural Biology Group, Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Keietsu Abe
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
- Microbial Genomics Laboratory, New Industry Creation Hatchery Center, Tohoku University, Sendai, Miyagi, 6-6-10, Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| |
Collapse
|
2
|
Conformational transition induced in the aspartate:alanine antiporter by L-Ala binding. Sci Rep 2022; 12:15871. [PMID: 36151227 PMCID: PMC9508256 DOI: 10.1038/s41598-022-19974-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 09/07/2022] [Indexed: 12/14/2022] Open
Abstract
An aspartate:alanine antiporter (AspT) from the lactic acid bacterium Tetragenococcus halophilus catalyzes the electrogenic aspartate<sup>1-</sup>:alanine<sup>0</sup> exchange reaction. Our previous kinetic analyses of transport reactions mediated by AspT in reconstituted liposomes suggested that, although the substrate transport reactions are physiologically coupled, the putative binding sites of L-aspartate (-Asp) and L-alanine (-Ala) are independently located on AspT. By using the fluorescent probe Oregon Green maleimide (OGM), which reacts specifically with cysteine, we also found that the presence of L-Asp changes the conformation of AspT. In this study, we conducted an OGM labeling assay in the presence of L-Ala. The labeling efficiency of single cysteine mutants (G62C and P79C) in transmembrane helix 3 of the AspT showed novel patterns depending on the presence of L-Ala or analogs. A concentration-dependent shift of AspT from the conformation in the presence of one substrate to that specific to the substrate added subsequently (L-Ala or L-Asp) was observed. Moreover, size-exclusion-chromatography-based thermostability assays indicated that the thermal stability of AspT in the presence of L-Ala differed from that in the presence of L-Asp. From these results, we concluded that L-Ala binding yields a conformation different from the apo or L-Asp binding conformations.
Collapse
|
3
|
Miyamoto A, Yamanaka T, Suzuki S, Kunii K, Kurono K, Yoshimi A, Hidaka M, Ogasawara S, Nanatani K, Abe K. Oligomeric state of the aspartate:alanine transporter (AspT) from Tetragenococcus halophilus. J Biochem 2022; 172:217-224. [PMID: 35818339 PMCID: PMC9527358 DOI: 10.1093/jb/mvac057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/30/2022] [Indexed: 11/12/2022] Open
Abstract
The aspartate:alanine exchanger family of membrane transporters includes industrially important transporters such as succinate exporter and glutamate exporter. No high-resolution structure is available from this family so far, and the transport mechanism of these transporters also remains unclear. In the present study, we focus on the oligomeric status of the aspartate:alanine antiporter (AspT) of Tetragenococcus halophilus, which is the prototype of this family. To investigate the oligomeric structure of AspT, we established a system that produces high yields of highly purified AspT and determined the oligomeric structure of AspT by analysis with size exclusion chromatography coupled with multi-angle light scattering and blue native PAGE and by comparison of the wild-type AspT with a single-cysteine mutant that forms spontaneous inter-molecular thiol crosslinking. All the results consistently support the notion that AspT is a homodimer in solutions and in membranes.
Collapse
Affiliation(s)
- Akari Miyamoto
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-0845 Japan
| | - Takashi Yamanaka
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-0845 Japan
| | - Satomi Suzuki
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-0845 Japan
| | - Kota Kunii
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-0845 Japan
| | - Kenichiro Kurono
- LS-Project, Shoko Science Co., Ltd., Aoba-ku, Yokohama, 225-0012 Japan
| | - Akira Yoshimi
- Microbial Genomics Laboratory, New Industry Creation Hatchery Center, Tohoku University, Sendai, Miyagi, 980-8579, Japan
| | - Masafumi Hidaka
- Laboratory of Molecular Enzymology, Department of Molecular Cell Science, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-0845 Japan
| | - Satoshi Ogasawara
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, 263-8522 Japan.,Molecular Chirality Research Center, Chiba University, Chiba, 263-8522 Japan.,Membrane Protein Research and Molecular Chirality Research Centers, Chiba University, Chiba 263-8522, Japan
| | - Kei Nanatani
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-0845 Japan.,Structural Biology Group, Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi, 980-8573, Japan
| | - Keietsu Abe
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-0845 Japan.,Microbial Genomics Laboratory, New Industry Creation Hatchery Center, Tohoku University, Sendai, Miyagi, 980-8579, Japan
| |
Collapse
|
4
|
Sudha G, Bassot C, Lamb J, Shu N, Huang Y, Elofsson A. The evolutionary history of topological variations in the CPA/AT transporters. PLoS Comput Biol 2021; 17:e1009278. [PMID: 34403419 PMCID: PMC8396727 DOI: 10.1371/journal.pcbi.1009278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 08/27/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
CPA/AT transporters are made up of scaffold and a core domain. The core domain contains two non-canonical helices (broken or reentrant) that mediate the transport of ions, amino acids or other charged compounds. During evolution, these transporters have undergone substantial changes in structure, topology and function. To shed light on these structural transitions, we create models for all families using an integrated topology annotation method. We find that the CPA/AT transporters can be classified into four fold-types based on their structure; (1) the CPA-broken fold-type, (2) the CPA-reentrant fold-type, (3) the BART fold-type, and (4) a previously not described fold-type, the Reentrant-Helix-Reentrant fold-type. Several topological transitions are identified, including the transition between a broken and reentrant helix, one transition between a loop and a reentrant helix, complete changes of orientation, and changes in the number of scaffold helices. These transitions are mainly caused by gene duplication and shuffling events. Structural models, topology information and other details are presented in a searchable database, CPAfold (cpafold.bioinfo.se).
Collapse
Affiliation(s)
- Govindarajan Sudha
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Claudio Bassot
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - John Lamb
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Nanjiang Shu
- Bioinformatics Short-term Support and Infrastructure (BILS), Science for Life Laboratory, Sweden
| | - Yan Huang
- Science for Life Laboratory, Karolinska Institutet, Stockholm University, Solna, Sweden
| | - Arne Elofsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| |
Collapse
|
5
|
Suzuki S, Nanatani K, Abe K. R76 in transmembrane domain 3 of the aspartate:alanine transporter AspT is involved in substrate transport. Biosci Biotechnol Biochem 2016; 80:744-7. [PMID: 26849958 DOI: 10.1080/09168451.2015.1123609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The L-aspartate:L-alanine antiporter of Tetragenococcus halophilus (AspT) possesses an arginine residue (R76) within the GxxxG motif in the central part of transmembrane domain 3 (TM3)-a residue that has been estimated to transport function. In this study, we carried out amino acid substitutions of R76 and used proteoliposome reconstitution for analyzing the transport function of each substitution. Both l-aspartate and l-alanine transport assays showed that R76K has higher activity than the AspT-WT (R76), whereas R76D and R76E have lower activity than the AspT-WT. These results suggest that R76 is involved in AspT substrate transport.
Collapse
Affiliation(s)
- Satomi Suzuki
- a Department of Microbial Biotechnology , Graduate School of Agricultural Science, Tohoku University , Sendai , Japan
| | - Kei Nanatani
- a Department of Microbial Biotechnology , Graduate School of Agricultural Science, Tohoku University , Sendai , Japan
| | - Keietsu Abe
- a Department of Microbial Biotechnology , Graduate School of Agricultural Science, Tohoku University , Sendai , Japan
| |
Collapse
|
6
|
A cell-free translocation system using extracts of cultured insect cells to yield functional membrane proteins. PLoS One 2014; 9:e112874. [PMID: 25486605 PMCID: PMC4259328 DOI: 10.1371/journal.pone.0112874] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 10/17/2014] [Indexed: 11/24/2022] Open
Abstract
Cell-free protein synthesis is a powerful method to explore the structure and function of membrane proteins and to analyze the targeting and translocation of proteins across the ER membrane. Developing a cell-free system based on cultured cells for the synthesis of membrane proteins could provide a highly reproducible alternative to the use of tissues from living animals. We isolated Sf21 microsomes from cultured insect cells by a simplified isolation procedure and evaluated the performance of the translocation system in combination with a cell-free translation system originating from the same source. The isolated microsomes contained the basic translocation machinery for polytopic membrane proteins including SRP-dependent targeting components, translocation channel (translocon)-dependent translocation, and the apparatus for signal peptide cleavage and N-linked glycosylation. A transporter protein synthesized with the cell-free system could be functionally reconstituted into a lipid bilayer. In addition, single and double labeling with non-natural amino acids could be achieved at both the lumen side and the cytosolic side in this system. Moreover, tail-anchored proteins, which are post-translationally integrated by the guided entry of tail-anchored proteins (GET) machinery, were inserted correctly into the microsomes. These results showed that the newly developed cell-free translocation system derived from cultured insect cells is a practical tool for the biogenesis of properly folded polytopic membrane proteins as well as tail-anchored proteins.
Collapse
|
7
|
Rusden AD, Stephenson DP, Verma NK. Topological investigation of glucosyltransferase V in Shigella flexneri using the substituted cysteine accessibility method. Biochemistry 2013; 52:2655-61. [PMID: 23534399 DOI: 10.1021/bi400168h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modification of the lipopolysaccharide O-antigen of Shigella converts the serotype, which is significant as acquired immune responses are serotype specific. Glucosyltransferases (Gtrs) modify the O-antigen by the addition of glucosyl-groups; however the precise mechanism of O-antigen modification is not fully understood. This study aims to substantiate inferences made on the GtrV topological structure using the substituted cysteine accessibility method (SCAM). Twenty-one amino acid residues were tested to clarify three features of GtrV: the extramembrane regions, a proposed reentrant loop, and a membrane border region. Overall, the results agreed with a previous topology proposed for GtrV. The topology of GtrV consists of 11 extramembrane regions with a cytoplasmic N-terminus, periplasmic C-terminus and 9 transmembrane (TM) helices. The existence of a reentrant loop between TM helices IV and V was verified, and the cytoplasmic membrane border region of TM helix II was examined in depth.
Collapse
Affiliation(s)
- Anthony D Rusden
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | | | | |
Collapse
|
8
|
Krupnik T, Sobczak-Elbourne I, Lolkema JS. Turnover and accessibility of a reentrant loop of the Na+-glutamate transporter GltS are modulated by the central cytoplasmic loop. Mol Membr Biol 2011; 28:462-72. [PMID: 21995702 DOI: 10.3109/09687688.2011.624989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
GltS of Escherichia coli is a secondary transporter that catalyzes Na+-glutamate symport. The structural model of GltS shows two homologous domains with inverted membrane topology that are connected by a central loop that resides in the cytoplasm. Each domain contains a reentrant loop structure. Accessibility of the Cys residues in two GltS mutants in which Pro351 and Asn356 in the reentrant loop in the C-terminal domain were replaced by Cys is demonstrated to be sensitive to the catalytic state supporting a role for the reentrant loops in catalysis. Saturating concentrations of the substrate L-glutamate protected both mutants against inactivation by thiol reagents, while the presence of the co-ion Na+ stimulated the inactivation of both mutants. Insertion of the 10 kDa biotin acceptor domain (BAD) of oxaloacetate decarboxylase of Klebsiella pneumoniae in the central cytoplasmic loop blocked the access pathway from the periplasmic side of the membrane to the cysteine residues in mutants P351C and N356C in the reentrant loop. Kinetically, insertion of BAD increased the maximal rate of uptake 2.7-fold while leaving the apparent affinity constants for L-glutamate and Na+ unaltered. The data suggests that insertion of BAD in the central loop results in conformational changes at the translocation site that lower the activation energy of the translocation step without affecting the access pathway from the periplasmic side for substrate and co-ions. It is concluded that changes in the central loop that connects the two domains may have a regulatory function on the activity of the transporter.
Collapse
Affiliation(s)
- Tomas Krupnik
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | | | | |
Collapse
|
9
|
Gresock MG, Savenkova MI, Larsen RA, Ollis AA, Postle K. Death of the TonB Shuttle Hypothesis. Front Microbiol 2011; 2:206. [PMID: 22016747 PMCID: PMC3191458 DOI: 10.3389/fmicb.2011.00206] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Accepted: 09/15/2011] [Indexed: 11/23/2022] Open
Abstract
A complex of ExbB, ExbD, and TonB couples cytoplasmic membrane (CM) proton motive force (pmf) to the active transport of large, scarce, or important nutrients across the outer membrane (OM). TonB interacts with OM transporters to enable ligand transport. Several mechanical models and a shuttle model explain how TonB might work. In the mechanical models, TonB remains attached to the CM during energy transduction, while in the shuttle model the TonB N terminus leaves the CM to deliver conformationally stored potential energy to OM transporters. Previous studies suggested that TonB did not shuttle based on the activity of a GFP-TonB fusion that was anchored in the CM by the GFP moiety. When we recreated the GFP-TonB fusion to extend those studies, in our hands it was proteolytically unstable, giving rise to potentially shuttleable degradation products. Recently, we discovered that a fusion of the Vibrio cholerae ToxR cytoplasmic domain to the N terminus of TonB was proteolytically stable. ToxR-TonB was able to be completely converted into a proteinase K-resistant conformation in response to loss of pmf in spheroplasts and exhibited an ability to form a pmf-dependent formaldehyde crosslink to ExbD, both indicators of its location in the CM. Most importantly, ToxR-TonB had the same relative specific activity as wild-type TonB. Taken together, these results provide conclusive evidence that TonB does not shuttle during energy transduction. We had previously concluded that TonB shuttles based on the use of an Oregon Green(®) 488 maleimide probe to assess periplasmic accessibility of N-terminal TonB. Here we show that the probe was permeant to the CM, thus permitting the labeling of the TonB N-terminus. These former results are reinterpreted in the context that TonB does not shuttle, and suggest the existence of a signal transduction pathway from OM to cytoplasm.
Collapse
Affiliation(s)
- Michael G. Gresock
- Department of Biochemistry and Molecular Biology, The Pennsylvania State UniversityUniversity Park, PA, USA
| | - Marina I. Savenkova
- School of Molecular Biosciences, Washington State UniversityPullman, WA, USA
| | - Ray A. Larsen
- School of Molecular Biosciences, Washington State UniversityPullman, WA, USA
| | - Anne A. Ollis
- Department of Biochemistry and Molecular Biology, The Pennsylvania State UniversityUniversity Park, PA, USA
| | - Kathleen Postle
- Department of Biochemistry and Molecular Biology, The Pennsylvania State UniversityUniversity Park, PA, USA
- School of Molecular Biosciences, Washington State UniversityPullman, WA, USA
| |
Collapse
|
10
|
Membrane topology screen of secondary transport proteins in structural class ST[3] of the MemGen classification. Confirmation and structural diversity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:72-81. [PMID: 21983116 DOI: 10.1016/j.bbamem.2011.09.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 09/22/2011] [Accepted: 09/23/2011] [Indexed: 11/22/2022]
Abstract
The MemGen structural classification of membrane proteins groups families of proteins by hydropathy profile alignment. Class ST[3] of the MemGen classification contains 32 families of transporter proteins including the IT superfamily. Transporters from 19 different families in class ST[3] were evaluated by the TopScreen experimental topology screening method to verify the structural classification by MemGen. TopScreen involves the determination of the cellular disposition of three sites in the polypeptide chain of the proteins which allows for discrimination between different topology models. For nearly all transporters at least one of the predicted localizations is different in the models produced by MemGen and predictor TMHMM. Comparison to the experimental data showed that in all cases the prediction by MemGen was correct. It is concluded that the structural model available for transporters of the [st324]ESS and [st326]2HCT families is also valid for the other families in class ST[3]. The core structure of the model consists of two homologous domains, each containing 5 transmembrane segments, which have an opposite orientation in the membrane. A reentrant loop is present in between the 4th and 5th segments in each domain. Nearly all of the identified and experimentally confirmed structural variations involve additions of transmembrane segments at the boundaries of the core model, at the N- and C-termini or in between the two domains. Most remarkable is a domain swap in two subfamilies of the [st312]NHAC family that results in an inverted orientation of the proteins in the membrane.
Collapse
|
11
|
Sasahara A, Nanatani K, Enomoto M, Kuwahara S, Abe K. Substrate specificity of the aspartate:alanine antiporter (AspT) of Tetragenococcus halophilus in reconstituted liposomes. J Biol Chem 2011; 286:29044-29052. [PMID: 21719707 DOI: 10.1074/jbc.m111.260224] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The aspartate:alanine antiporter (AspT) of the lactic acid bacterium Tetragenococcus halophilus is a member of the aspartate:alanine exchanger (AAEx) transporter family. T. halophilus AspT catalyzes the electrogenic exchange of L-aspartate(1-) with L-alanine(0). Although physiological functions of AspT were well studied, L-aspartate(1-):L-alanine(0) antiport mechanisms are still unsolved. Here we report that the binding sites of L-aspartate and L-alanine are independently present in AspT by means of the kinetic studies. We purified His(6)-tagged T. halophilus AspT and characterized its kinetic properties when reconstituted in liposomes (K(m) = 0.35 ± 0.03 mm for L-aspartate, K(m) = 0.098 ± 0 mm for D-aspartate, K(m) = 26 ± 2 mm for L-alanine, K(m) = 3.3 ± 0.2 mm for D-alanine). Competitive inhibition by various amino acids of L-aspartate or L-alanine in self-exchange reactions revealed that L-cysteine selectively inhibited L-aspartate self-exchange but only weakly inhibited L-alanine self-exchange. Additionally, L-serine selectively inhibited L-alanine self-exchange but barely inhibited L-aspartate self-exchange. The aspartate analogs L-cysteine sulfinic acid, L-cysteic acid, and D-cysteic acid competitively and strongly inhibited L-aspartate self-exchange compared with L-alanine self-exchange. Taken together, these kinetic data suggest that the putative binding sites of L-aspartate and L-alanine are independently located in the substrate translocation pathway of AspT.
Collapse
Affiliation(s)
- Ayako Sasahara
- Department of Microbial Biotechnology, Laboratory of Applied Microbiology, Sendai 981-8555, Japan
| | - Kei Nanatani
- Department of Biomolecular Engineering, Laboratory of Applied Biophysical Chemistry, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, and
| | - Masaru Enomoto
- Department of Applied Bioorganic Chemistry, Laboratory of Applied Bioorganic Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan
| | - Shigefumi Kuwahara
- Department of Applied Bioorganic Chemistry, Laboratory of Applied Bioorganic Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan
| | - Keietsu Abe
- Department of Microbial Biotechnology, Laboratory of Applied Microbiology, Sendai 981-8555, Japan; Microbial Genomics Laboratory, New Industry Creation Hatchery Center, Tohoku University, Sendai, Miyagi 980-8579, Japan.
| |
Collapse
|
12
|
Huhn S, Jolkver E, Krämer R, Marin K. Identification of the membrane protein SucE and its role in succinate transport in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2010; 89:327-35. [PMID: 20809072 DOI: 10.1007/s00253-010-2855-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Revised: 08/16/2010] [Accepted: 08/16/2010] [Indexed: 11/24/2022]
Abstract
Succinic acid is excreted during anaerobiosis by many bacteria, and manifold applications are known making the biotechnological production of succinate attractive. Although the pathways for succinate formation are known, succinate export is not understood in most of the succinate producing bacteria. Here, we present a bioinformatic approach for identification of a putative succinate export system in Corynebacterium glutamicum. The subsequent screening revealed that a mutant in the gene cg2425 is impaired in succinate production or transport under anaerobic conditions. A function of the Cg2425 protein as import system was excluded. In contrast, a role of the Cg2425 protein as succinate export system was indicated by accumulation of increased amounts of internal succinate under anaerobic conditions in a Cg2425-dependent manner and a concomitant impairment of external succinate accumulation. In conclusion, we propose that Cg2425 participates in succinate export in C. glutamicum and suggest the name SucE for the protein.
Collapse
Affiliation(s)
- Stephanie Huhn
- Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany
| | | | | | | |
Collapse
|
13
|
Kanou K, Iwadate M, Hirata T, Terashi G, Umeyama H, Takeda-Shitaka M. FAMSD: A powerful protein modeling platform that combines alignment methods, homology modeling, 3D structure quality estimation and molecular dynamics. Chem Pharm Bull (Tokyo) 2010; 57:1335-42. [PMID: 19952440 DOI: 10.1248/cpb.57.1335] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The prediction of a protein three-dimensional (3D) structure is one of the most important challenges in computational structural biology. We have developed an automatic protein 3D structure prediction method called FAMSD. FAMSD is based on a comparative modeling method which consists of the following four steps: (1) generating and selecting sequence alignments between target and template proteins; (2) constructing 3D structure models based on each selected alignment; (3) selecting the best 3D structure model and (4) refining the selected model. In the FAMSD method, sequence alignment programs such as a series of BLAST programs, SP3 and SPARKS2 programs, the homology modeling program FAMS (Full Automatic Modeling System), the model quality estimation program CIRCLE and the molecular dynamics program APRICOT were used in combination to construct high quality protein models. To assess the FAMSD method we have participated in the 8th Critical Assessment of Techniques for Protein Structure Prediction (CASP8) experiment. The results of our original assessment indicate that the FAMSD method offers excellent capability in packing side-chains with the correct torsion angles while avoiding the formation of atom-atom collisions. Since side-chain packing plays a significant role in defining the biological function of proteins, this method is a valuable resource in biological, pharmaceutical and medicinal research efforts.
Collapse
|
14
|
Kanou K, Hirata T, Iwadate M, Terashi G, Umeyama H, Takeda-Shitaka M. HUMAN FAMSD-BASE: high quality protein structure model database for the human genome using the FAMSD homology modeling method. Chem Pharm Bull (Tokyo) 2010; 58:66-75. [PMID: 20045969 DOI: 10.1248/cpb.58.66] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Almost all proteins express their biological functions through the structural conformation of their specific amino acid sequences. Therefore, acquiring the three-dimensional structures of proteins is very important to elucidate the role of a particular protein. We had built protein structure model databases, which is called RIKEN FAMSBASE (http://famshelp.gsc.riken.jp/famsbase/). The RIKEN FAMSBASE is a genome-wide protein structure model database that contains a large number of protein models from many organisms. The HUMAN FAMSBASE that is one part of the RIKEN FAMSBASE contains many protein models for human genes, which are significant in the pharmaceutical and medicinal fields. We have now implemented an update of the human protein modeling database consisting of 242918 constructed models against the number of 20743 human protein sequences with an improved modeling method called Full Automatic protein Modeling System Developed (FAMSD). The results of our benchmark test of the FAMSD method indicated that it has an excellent capability to pack amino acid side-chains with correct torsion angles in addition to the main-chain, while avoiding the formation of atom-atom collisions that are not found in experimental structures. This new protein structure model database for human genes, which is named HUMAN FAMSD-BASE, is open to the public as a component part of the RIKEN FAMSBASE at http://mammalia.gsc.riken.jp/human_famsd/. A significant improvement of the HUMAN FAMSD-BASE in comparison with the preceding HUMAN FAMSBASE was verified in the benchmark test of this paper. The HUMAN FAMSD-BASE will have an important impact on the progress of biological science.
Collapse
|
15
|
Structural and functional importance of transmembrane domain 3 (TM3) in the aspartate:alanine antiporter AspT: topology and function of the residues of TM3 and oligomerization of AspT. J Bacteriol 2009; 191:2122-32. [PMID: 19181816 DOI: 10.1128/jb.00830-08] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AspT, the aspartate:alanine antiporter of Tetragenococcus halophilus, a membrane protein of 543 amino acids with 10 putative transmembrane (TM) helices, is the prototype of the aspartate:alanine exchanger (AAE) family of transporters. Because TM3 (isoleucine 64 to methionine 85) has many amino acid residues that are conserved among members of the AAE family and because TM3 contains two charged residues and four polar residues, it is thought to be located near (or to form part of) the substrate translocation pathway that includes the binding site for the substrates. To elucidate the role of TM3 in the transport process, we carried out cysteine-scanning mutagenesis. The substitutions of tyrosine 75 and serine 84 had the strongest inhibitory effects on transport (initial rates of l-aspartate transport were below 15% of the rate for cysteine-less AspT). Considerable but less-marked effects were observed upon the replacement of methionine 70, phenylalanine 71, glycine 74, arginine 76, serine 83, and methionine 85 (initial rates between 15% and 30% of the rate for cysteine-less AspT). Introduced cysteine residues at the cytoplasmic half of TM3 could be labeled with Oregon green maleimide (OGM), whereas cysteines close to the periplasmic half (residues 64 to 75) were not labeled. These results suggest that TM3 has a hydrophobic core on the periplasmic half and that hydrophilic residues on the cytoplasmic half of TM3 participate in the formation of an aqueous cavity in membranes. Furthermore, the presence of l-aspartate protected the cysteine introduced at glycine 62 against a reaction with OGM. In contrast, l-aspartate stimulated the reactivity of the cysteine introduced at proline 79 with OGM. These results demonstrate that TM3 undergoes l-aspartate-induced conformational alterations. In addition, nonreducing sodium dodecyl sulfate-polyacrylamide gel electrophoresis analyses and a glutaraldehyde cross-linking assay suggest that functional AspT forms homo-oligomers as a functional unit.
Collapse
|