A novel TctA citrate transporter from an activated sludge metagenome: Structural and mechanistic predictions for the TTT family

Proteins: Structure, Function and Bioinformatics

Volumn 82, Issue 9, 2014, Pages 1756-1764

  Batista García, Ramón Alberto ^a   Sánchez Reyes, Ayixon ^a   Millán Pacheco, César ^a   González Zuñiga, Víctor Manuel ^b   Juárez, Soledad ^b   Folch Mallol, Jorge Luis ^a   Pastor, Nina ^a  

^a UNIVERSIDAD AUTÓNOMA DEL ESTADO DE MORELOS   (Mexico)

^b INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

Author keywords

Citrate; Docking; Gene phylogeny; Metagenomic; Molecular modeling; TctA

Indexed keywords

BACTERIAL PROTEIN; TCTA CITRATE TRANSPORTER; TRIPARTITE TRICARBOXYLATE TRANSPORTER; UNCLASSIFIED DRUG; CARRIER PROTEIN; CITRATE-BINDING TRANSPORT PROTEIN; CITRIC ACID; PROTEIN BINDING; SEWAGE;

ACTIVATED SLUDGE; AGAR GEL ELECTROPHORESIS; AMINO ACID SEQUENCE; ARTICLE; BETAPROTEOBACTERIA; BORDETELLA; COMAMONAS; COMAMONAS TESTOSTERONI; CONTROLLED STUDY; CORYNEBACTERIUM; DNA LIBRARY; METAGENOMICS; MICROBIAL COMMUNITY; MOLECULAR DYNAMICS; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTEIN STRUCTURE; SALMONELLA; SEWAGE TREATMENT PLANT; STEREOCHEMISTRY; BINDING SITE; CHEMISTRY; ENZYMOLOGY; GENE LIBRARY; GENETICS; ISOLATION AND PURIFICATION; METAGENOME; MICROBIOLOGY; MOLECULAR DOCKING; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; SEWAGE; ULTRASTRUCTURE;

BETAPROTEOBACTERIA; COMAMONAS TESTOSTERONI;

AMINO ACID SEQUENCE; BINDING SITES; CARRIER PROTEINS; CITRIC ACID; COMAMONAS TESTOSTERONI; GENE LIBRARY; METAGENOME; MOLECULAR DOCKING SIMULATION; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; REPETITIVE SEQUENCES, AMINO ACID; SEQUENCE ALIGNMENT; SEWAGE;

EID: 84906317393     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24529     Document Type: Article

References (33)

1. Curtis TP, Sloan WT, Scannell JW. Estimating prokaryotic diversity and its limits. PNAS 2002;99:10494-10499.
2. Daniel R. The soil metagenome: a rich resource for the discovery of novel natural products. Curr Opin Biotech 2004;15:199-204.
3. Schloss R, Patrick D, Handelsman J. Biotechnological prospects from metagenomics. Curr Opin Biotech 2003;14:303-310.
4. Simon C, Daniel R. Metagenomic analyses: past and future trends. Appl Environ Microbiol 2011;77:1153-1161.
5. Winnen B, Hvorup RN, Saier MH. The tripartite tricarboxylate transporter (TTT) family. Res Microbiol 2003;154:457-465.
6. Hosaka M, Kamimura N, Toribami S, Mori K, Fukuda M, Masai E. A novel tripartite aromatic acids transporter is essential for terephthalate uptake in Comamonas sp. strain E6. Appl Environ Microbiol 2013;79:6148-6155.
7. Widenhorn KA, Somers JM, Kay WW. Expression of the divergent tricarboxylate transport operon (tctI) of Salmonella typhimurium. J Bacteriol 1988;170:3223-3227.
8. Ricci V, Loman N, Pallen M, Ivens A, Fookes M, Langridge GC, Wain J, Piddock LJ. The TCA cycle is not required for selection or survival of multidrug-resistant Salmonella. J Antimicrob Chemother 2012;67:589-599.
9. Ma YF, Zhang Y, Zhang JY Chen DW, Zhu Y, Sheng H, Wang SY, Jiang CY, Zhao GP, Liu SJ. The complete genome of Comamonas testosteroni reveals its genetic adaptations to changing environments. Appl Environ Microbiol 2009;75:6812-6819.
10. Brocker M, Schaffer S, Mack C, Bott M. Citrate utilization by Corynebacterium glutamicum is controlled by the CitAB two-component system through positive regulation of the citrate transport genes citH and tctCBA. J Bacteriol 2009;191:3869-3880.
11. Polen T, Schluesener D, Poetsch A, Bott M, Wendisch VF. Characterization of citrate utilization in Corynebacterium glutamicum by transcriptome and proteome analysis. FEMS Microbiol Lett 2007;73:109-119.
12. Antoine R, Jacob-Dubuisson F, Drobecq H, Willery E, Lesjean S, Locht C. Overrepresentation of a gene family encoding extracytoplasmic solute receptors in Bordetella. J Bacteriol 2003;185:1470-1474.
13. Magalhaes JV. How a microbial drug transporter became essential for crop cultivation on acid soils: aluminium tolerance conferred by the multidrug and toxic compound extrusion (MATE) family. Ann Bot 2012;106:199-203.
14. Saier MH, Yen MR, Noto K, Tamang DG, Elkan C. The transporter classification database: recent advances. Nucl Acids Res 2009;3:274-278.
15. Shi Y. Common folds and transport mechanisms of secondary active transporters. Ann Rev Bioph 2013;42:51-72.
16. Kebbel F, Kurz M, Arheit M, Grutter MG, Stahlberg H. Structure and substrate-induced conformational changes of the secondary citrate/sodium symporter CitS revealed by electron crystallography. Structure 2013;21:1243-1250.
17. Berman HM, Westbrook J, Feng Z. The protein data bank. Nucl Acid Res 2000;28:235-242.
18. Felske A, Engelen B, Nubel U, Backhaus. Direct ribosome isolation from soil to extract bacterial rRNA for community analysis. Appl Environ Microbial 1996;62:4162-4167.
19. Bomeman J, Jack R. PCR primers that amplify fungul rRNA genes from environmental samples. Appl Environ Microbial 2000;66:4356-4360.
20. Cho CM, Mulchandani A, Chen W. Bacterial cell surface display of organophosphorus hydrolase for selective screening of improved hydrolysis of organophosphate nerve agents. Appl Environ Microbiol 2002;68:2026-2030.
21. Zhang Y, Skolnick J. Segment assembly, structure alignment and iterative simulation in protein structure prediction. BMC Biol 2013;11:44.
22. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K. Scalable molecular dynamics with NAMD. J Comput Chem 2005;26:1781-1802.
23. Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, #efficient |optimization, and multithreading. J Comput Chem 2010;31:455-461.
24. Tanaka Y, Hipolito CJ, Maturana AD, Ito K, Kuroda T, Higuchi T, Katoh T, Kato HE, Hattori M, Kumazaki K, Tsukazaki T, Ishitani R, Suga H, Nureki O. Structural basis for the drug extrusion mechanism by a MATE multidrug transporter. Nature 2013;496:247-251.
25. Waight AB, Pedersen BP, Schlessinger A, Bonomi M, Chau BH, Roe-Zurz Z, Risenmay AJ, Sali A, Stroud RM. Structural basis for alternating access of a eukaryotic calcium/proton exchanger. Nature 2013;99:107-110.
26. Rusell RB, Barton GH. Multiple protein sequence alignment from tertiary structure comparison. Prot Struct Funct Genet 1992;67:309-323.
27. Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph 1996: 33-38.
28. He X, Szewczyk P, Karyakin A, Evin M, Hong WX, Zhang Q, Chang G. Structure of a cation-bound multidrug and toxic compound extrusion transporter. Nature 2010;467:991-994.
29. Lu M, Symersky J, Radchenko M, Koide A, Guo Y, Nie R, Koide S. Structures of a Na+-coupled, substrate-bound MATE multidrug transporter. PNAS 2013;110:2099-2104.
30. Abramson J, Paz A, Philipson KD. It's all in the symmetry. Science 2012;335:669-670.
31. Liao J, Li H, Zeng W, Cao H, Cui Z. Structural insight into the ion-exchange mechanism of the sodium/calcium exchanger. Science 2012;335:686-690.
32. Nishizawa T, Kita S, Maturana AD, Furaya N, Hirata K, Kasuya G, Ogasawara S, Dohmae N, Iwamoto T, Ishitani R, Nureki O. Structural basis for the counter-transport mechanism of a H+/Ca2+ exchanger. Science 2013;341:168-172.
33. Wong FH, Chen JS, Reddy V, Day JL, Shlykov MA, Wakabayashi ST, Saier ST. The amino acid-polyamine-organocation superfamily. J Mol Microbiol Biotech 2012;22:105-113.