Analyses of the oligopeptide transporter gene family in poplar and grape

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Cao, Jun ^a,b   Huang, Jinling ^c   Yang, Yongping ^a   Hu, Xiangyang ^a  

^a KUNMING INSTITUTE OF BOTANY   (China)

^b JIANGSU UNIVERSITY   (China)

^c EAST CAROLINA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN; OLIGOPEPTIDE TRANSPORTER; UNCLASSIFIED DRUG; CARRIER PROTEIN; PLANT DNA;

ARTICLE; ASPEN; CHROMOSOMAL LOCALIZATION; CONTROLLED STUDY; EVOLUTIONARY ADAPTATION; GENE CLUSTER; GENE DUPLICATION; GENE EXPRESSION; GENE IDENTIFICATION; GENE STRUCTURE; GENETIC ANALYSIS; GRAPE; MICROARRAY ANALYSIS; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT DEVELOPMENT; PLANT RESPONSE; PLANT STRESS; PROTEIN ANALYSIS; PURIFYING SELECTION; ARABIDOPSIS; DNA MICROARRAY; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENETICS; MOLECULAR EVOLUTION; PLANT GENE; PLANT GENOME; RICE; VITIS;

ARABIDOPSIS; EMBRYOPHYTA; POPULUS; POPULUS TRICHOCARPA; VITACEAE; VITIS; VITIS VINIFERA;

ARABIDOPSIS; DNA, PLANT; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE EXPRESSION PROFILING; GENES, PLANT; GENOME, PLANT; MEMBRANE TRANSPORT PROTEINS; MULTIGENE FAMILY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORYZA SATIVA; PHYLOGENY; POPULUS; SEQUENCE ANALYSIS, DNA; VITIS;

EID: 80053378458     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-465     Document Type: Article

References (77)

1. Busch W, Saier MH. The IUBMB-Endorsed transporter classification system. Mol Biotech 2002, 27(3):253-262.
2. Saier MH, Yen MR, Noto K, Tamang DG, Elkan C. The Transporter Classification Database: recent advances. Nucleic Acids Res 2009, (37 Database):D274-278.
3. Hauser M, Narita V, Donhardt AM, Naider F, Becker JM. Multiplicity and regulation of genes encoding peptide transporters in Saccharomyces cerevisiae. Mol Membr Biol 2001, 18(1):105-112.
4. Rea PA. Plant ATP-binding cassette transporters. Annu Rev Plant Biol 2007, 58:347-375. 10.1146/annurev.arplant.57.032905.105406, 17263663.
5. Wang R, Liu D, Crawford NM. The Arabidopsis CHL1 protein plays a major role in high-affinity nitrate uptake. Proc Natl Acad Sci USA 1998, 95(25):15134-15139. 10.1073/pnas.95.25.15134, 24588, 9844028.
6. Chiang CS, Stacey G, Tsay YF. Mechanisms and functional properties of two peptide transporters, AtPTR2 and fPTR2. J Biol Chem 2004, 279(29):30150-30157. 10.1074/jbc.M405192200, 15138259.
7. Lubkowitz MA, Hauser L, Breslav M, Naider F, Becker JM. An oligopeptide transport gene from Candida albicans. Microbiol 1997, 143(Pt2):387-396.
8. Lubkowitz MA, Barnes D, Breslav M, Burchfield A, Naider F, Becker JM. Schizosaccharomyces pombe isp4 encodes a transporter representing a novel family of oligopeptide transporters. Mol Microbiol 1998, 28(4):729-741.
9. Curie C, Panaviene Z, Loulergue C, Dellaporta SL, Briat JF, Walker EL. Maize yellow stripe1 encodes a membrane protein directly involved in Fe(III) uptake. Nature 2001, 409(6818):346-349. 10.1038/35053080, 11201743.
10. Roberts LA, Pierson AJ, Panavise Z, Walker EL. Yellow Stripe1 expanded roles for the Maize iron-phytosiderophore transporter. Plant Physiol 2004, 135(1):112-120. 10.1104/pp.103.037572, 429338, 15107503.
11. DiDonato RJ, Roberts LA, Sanderson T, Eisley RB, Walker EL. Arabidopsis Yellow Stripe-Like2 (YSL2): a metal-regulated gene encoding a plasma membrane transporter of nicotianamine-metal complexes. Plant J 2004, 39(3):403-414. 10.1111/j.1365-313X.2004.02128.x, 15255869.
12. Koike S, Inoue H, Mizuno D, Takahashi M, Nakanishi H, Mori S, Nishizawa NK. OsYSL2 is a rice metal-nicotianamine transporter that is regulated by iron and expressed in the phloem. Plant J 2004, 39(3):415-424. 10.1111/j.1365-313X.2004.02146.x, 15255870.
13. Murata Y, Ma JF, Yamaji F, Ueno D, Nomoto K, Iwashita T. A specific transporter for iron(III)-phytosiderophore in barley roots. Plant J 2006, 46(4):563-572. 10.1111/j.1365-313X.2006.02714.x, 16640594.
14. Aoyama T, Kobayashi T, Takahashi M, Nagasaka S, Usuda K, Kakei Y, Ishimaru Y, Nakanishi H, Mori S, Nishizawa NK. OsYSL18 is a rice iron(III)-deoxymugineic acid transporter specifically expressed in reproductive organs and phloem of lamina joints. Plant Mol Biol 2009, 70(6):681-692. 10.1007/s11103-009-9500-3, 2706380, 19468840.
15. Lee S, Chiecko JC, Kim SA, Walker EL, Lee Y, Guerinot ML, An G. Disruption of OsYSL15 leads to iron inefficiency in rice plants. Plant Physiol 2009, 150(2):786-800. 10.1104/pp.109.135418, 2689993, 19376836.
16. Ishimaru Y, Masuda H, Bashir K, Inoue H, Tsukamoto T, Takahashi M, Nakanishi H, Aoki N, Hirose T, Ohsugi R, Nishizawa NK. Rice metal-nicotianamine transporter, OsYSL2, is required for the long-distance transport of iron and manganese. Plant J 2010, 62(3):379-390. 10.1111/j.1365-313X.2010.04158.x, 20128878.
17. Stacey MG, Patel A, McClain WE, Mathieu M, Remley M, Rogers EE, Gassmann W, Blevins DG, Stacey G. The Arabidopsis AtOPT3 protein functions in metal homeostasis and movement of iron to developing seeds. Plant Physiol 2008, 146(2):589-601. 2245856, 18083798.
18. Koh S, Wiles AM, Sharp JS, Naider FR, Becker JM, Stacey G. An oligopeptide transporter gene family in Arabidopsis. Plant Physiol 2002, 128(1):21-29. 10.1104/pp.010332, 148940, 11788749.
19. Cagnac O, Bourbouloux A, Chakrabarty D, Zhang MY, Delrot S. AtOPT6 transports glutathione derivatives and is induced by primisulfuron. Plant Physiol 2004, 135(3):1378-1387. 10.1104/pp.104.039859, 519055, 15247401.
20. Stacey MG, Osawa H, Patel A, Gassmann W, Stacey G. Expression analyses of Arabidopsis oligopeptide transporters during seed germination, vegetative growth and reproduction. Planta 2006, 223(2):291-305. 10.1007/s00425-005-0087-x, 16151844.
21. Pike S, Patel A, Stacey G, Gassmann W. Arabidopsis OPT6 is an oligopeptide transporter with exceptionally broad substrate specificity. Plant Cell Physiol 2009, 50(11):1923-1932. 10.1093/pcp/pcp136, 19808809.
22. Bogs J, Bourbouloux A, Cagnac O, Wachter A, Rausch T, Delrot S. Functional characterization and expression analysis of a glutathione transporter, BjGT1, from Brassica juncea: evidence for regulation by heavy metal exposure. Plant Cell Environ 2003, 26(10):1703-1711.
23. Vasconcelos MW, Li GW, Lubkowitz MA, Grusak MA. Characterization of the PT clade of oligopeptide transporters in rice. The Plant Genome 2008, 1(2):77-88.
24. Zhang MY, Bourbouloux A, Cagnac O, Srikanth CV, Rentsch D, Bachhawat AK, Delrot S. A novel family of transporters mediating the transport of glutathione derivatives in plants. Plant Physiol 2004, 134(1):482-491. 10.1104/pp.103.030940, 316327, 14730075.
25. Lubkowitz M. The Oligopeptide Transporters: A Small Gene Family with a Diverse Group of Substrates and Functions?. Mol Plant 2011, 4(3):407-415. 10.1093/mp/ssr004, 21310763.
26. Gomolplitinant KM, Saier MH. Evolution of the oligopeptide transporter family. J Membr Biol 2011, 240(2):89-110. 10.1007/s00232-011-9347-9, 3061005, 21347612.
27. Marchler-Bauer A, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, He S, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Tasneem A, Thanki N, Yamashita RA, Zhang D, Zhang N, Bryant SH. CDD: specific functional annotation with the Conserved Domain Database. Nucleic Acids Res 2009, (37 Database):D205-210.
28. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 2011, (39 Database):D225-229.
29. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003, 52:696-704. 10.1080/10635150390235520, 14530136.
30. Lartillot N, Lepage T, Blanquart S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 2009, 25:2286-2288. 10.1093/bioinformatics/btp368, 19535536.
31. Hu R, Qi G, Kong Y, Kong D, Gao Q, Zhou G. Comprehensive analysis of NAC domain transcription factor gene family in Populus trichocarpa. BMC Plant Biol 2010, 10:145. 3017804, 20630103.
32. Afoufa-Bastien D, Medici A, Jeauffre J, Coutos-Thévenot P, Lemoine R, Atanassova R, Laloi M. The Vitis vinifera sugar transporter gene family: phylogenetic overview and macroarray expression profiling. BMC Plant Biol 2010, 10:245. 10.1186/1471-2229-10-245, 3095327, 21073695.
33. Le Jean M, Schikora A, Mari S, Briat JF, Curie C. A loss-of-function mutation in AtYSL1 reveals its role in iron and nicotianamine seed loading. Plant J 2005, 44(5):769-782. 10.1111/j.1365-313X.2005.02569.x, 16297069.
34. Waters BM, Chu HH, Didonato RJ, Roberts LA, Eisley RB, Lahner B, Salt DE, Walker EL. Mutations in Arabidopsis yellow stripe-like1 and yellow stripe-like3 reveal their roles in metal ion homeostasis and loading of metal ions in seeds. Plant Physiol 2006, 141(4):1446-1458. 10.1104/pp.106.082586, 1533956, 16815956.
35. Chu HH, Chiecko J, Punshon T, Lanzirotti A, Lahner B, Salt DE, Walker EL. Successful reproduction requires the function of Arabidopsis Yellow Stripe-Like1 and Yellow Stripe-Like3 metal-nicotianamine transporters in both vegetative and reproductive structures. Plant Physiol 2010, 154(1):197-210. 10.1104/pp.110.159103, 2938154, 20625001.
36. Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W. GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol 2004, 136(1):2621-2632. 10.1104/pp.104.046367, 523327, 15375207.
37. Sterck L, Rombauts S, Jansson S, Sterky F, Rouze P, Van de Peer Y. EST data suggest that poplar is an ancient polyploid. New Phytol 2005, 67(1):165-170.
38. Wolfe KH, Gouy M, Yang YW, Sharp PM, Li WH. Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc Natl Acad Sci USA 1989, 86(16):6201-6205. 10.1073/pnas.86.16.6201, 297805, 2762323.
39. Crane PR, Friis EM, Pedersen KR. The origin and early diversification of angiosperms. Nature 1995, 374(6517):27-33.
40. Kellogg EA. Evolutionary history of the grasses. Plant Physiol 2001, 125(3):1198-1205. 10.1104/pp.125.3.1198, 1539375, 11244101.
41. Jaillon O, Aury J-M, Noel B, Policrit A, Clepet C, Casagrande A, Choisne N, Aubourg C, Vitulo N, Jubin C, et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 2007, 449(7161):463-467. 10.1038/nature06148, 17721507.
42. Hardison RC. A brief history of hemoglobins: plant, animal, protist, and bacteria. Proc Natl Acad Sci USA 1996, 93(12):5675-5679. 10.1073/pnas.93.12.5675, 39118, 8650150.
43. Lin H, Zhu W, Silva JC, Gu X, Buell CR. (2006) Intron gain and loss in segmentally duplicated genes in rice. Genome Biol 2006, 7(5):R41. 10.1186/gb-2006-7-5-r41, 1779517, 16719932.
44. Cao J, Shi F, Liu X, Huang G, Zhou M. Phylogenetic analysis and evolution of aromatic amino acid hydroxylase. FEBS Lett 2010, 584(23):4775-4782. 10.1016/j.febslet.2010.11.005, 21073869.
45. Li W, Liu B, Yu L, Feng D, Wang H, Wang J. Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants. BMC Evol Biol 2009, 9:90. 10.1186/1471-2148-9-90, 2688005, 19416520.
46. Cao J, Shi F, Liu X, Jia J, Zeng J, Huang G. Genome-wide identification and evolutionary analysis of Arabidopsis Sm genes family. J Biomol Struct Dyn 2011, 28(4):535-544.
47. Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci USA 2003, 100(20):11484-11489. 10.1073/pnas.1932072100, 208784, 14500911.
48. Mehan MR, Freimer NB, Ophoff RA. A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture. Hum Genomics 2004, 1(5):335-344.
49. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 2006, 313(5793):1596-1604. 10.1126/science.1128691, 16973872.
50. Licausi F, Giorgi FM, Zenoni S, Osti F, Pezzotti M, Perata P. Genomic and transcriptomic analysis of the AP2/ERF superfamily in Vitis vinifera. BMC Genomics 2010, 11:719. 10.1186/1471-2164-11-719, 3022922, 21171999.
51. Blanc G, Hokamp K, Wolfe KH. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res 2003, 13(2):137-144. 10.1101/gr.751803, 420368, 12566392.
52. Guyot R, Keller B. Ancestral genome duplication in rice. Genome 2004, 47(3):610-614. 10.1139/g04-016, 15190378.
53. Bailey TL, Williams N, Misleh C, Li WW. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 2006, (34 Web Server):W369-373.
54. Prince VE, Picket FB. Splitting pairs: the diverging fates of duplicated genes. Nat Rev Genet 2002, 3(11):827-837. 10.1038/nrg928, 12415313.
55. Blanc G, Wolfe KH. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 2004, 16(7):1679-1691. 10.1105/tpc.021410, 514153, 15208398.
56. Deluc LG, Grimplet J, Wheatley MD, Tillett RL, Quilici DR, Osborne C, Schooley DA, Schlauch KA, Cushman JC, Cramer GR. Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development. BMC Genomics 2007, 8:429. 10.1186/1471-2164-8-429, 2220006, 18034876.
57. Deluc LG, Quilici DR, Decendit A, Grimplet J, Wheatley MD, Schlauch KA, Mérillon JM, Cushman JC, Cramer GR. Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay. BMC Genomics 2009, 10:212. 10.1186/1471-2164-10-212, 2701440, 19426499.
58. Cramer GR, Ergül A, Grimplet J, Tillett RL, Tattersall EA, Bohlman MC, Vincent D, Sonderegger J, Evans J, Osborne C, Quilici D, Schlauch KA, Schooley DA, Cushman JC. Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles. Funct Integr Genomics 2007, 7(2):111-34. 10.1007/s10142-006-0039-y, 17136344.
59. Gu X. Statistical methods for testing functional divergence after gene duplication. Mol Biol Evol 1999, 16(12):1664-1674.
60. Gu X. (2001) Maximum-likelihood approach for gene family evolution under functional divergence. Mol Biol Evol 2001, 18(4):453-464.
61. Stern A, Doron-Faigenboim A, Erez E, Martz E, Bacharach E, Pupko T. Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. Nucleic Acids Res 2007, (35 Web Server):W506-511.
62. Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K. WoLF PSORT: protein localization predictor. Nucleic Acids Res 2007, (35 Web Server):W585-587.
63. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32(5):1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
64. Keane TM, Creevey CJ, Pentony MM, Naughton TJ, McLnerney JO. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol 2006, 6:29. 10.1186/1471-2148-6-29, 1435933, 16563161.
65. Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol 2008, 25:1307-1320. 10.1093/molbev/msn067, 18367465.
66. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, EvolutionaryDistance, and Maximum Parsimony Methods. Mol Biol Evol 2011,
67. Comeron JM. K-Estimator: calculation of the number of nucleotide substitutions per site and the confidence intervals. Bioinformatics 1999, 15(9):763-764. 10.1093/bioinformatics/15.9.763, 10498777.
68. Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, et al. The Genomes of Oryza sativa: a history of duplications. PLoS Biol 2005, 3(2):e38. 10.1371/journal.pbio.0030038, 546038, 15685292.
69. Lynch M, Conery JS. The evolutionary fate and consequences of duplicate genes. Science 2000, 290(5494):1151-1155. 10.1126/science.290.5494.1151, 11073452.
70. Gaut BS, Morton BR, McCaig BC, Clegg MT. Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci USA 1996, 93(19):10274-10279. 10.1073/pnas.93.19.10274, 38374, 8816790.
71. Dharmawardhana P, Brunner AM, Strauss SH. Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa. BMC Genomics 2010, 11:150. 10.1186/1471-2164-11-150, 2846914, 20199690.
72. Lund ST, Peng FY, Nayar T, Reid KE, Schlosser J. Gene expression analyses in individual grape (Vitis vinifera L.) berries during ripening initiation reveal that pigmentation intensity is a valid indicator of developmental staging within the cluster. Plant Mol Biol 2008, 68(3):301-315. 10.1007/s11103-008-9371-z, 18642093.
73. Sreekantan L, Mathiason K, Grimplet J, Schlauch K, Dickerson JA, Fennell AY. Differential floral development and gene expression in grapevines during long and short photoperiods suggests a role for floral genes in dormancy transitioning. Plant Mol Biol 2010, 73(1-2):191-205. 10.1007/s11103-010-9611-x, 20151315.
74. Wise RP, Caldo RA, Hong L, Shen L, Cannon EK, Dickerson JA. In Plant Bioinformatics-Methods and Protocols. Methods in Molecular Biology 2007, 406:347-363. Humana Press, Totowa, NJ, Edwards D.
75. Sturn A, Quackenbush J, Trajanoski Z. Genesis: cluster analysis of microarray data. Bioinformatics 2002, 18(1):207-208. 10.1093/bioinformatics/18.1.207, 11836235.
76. Doron-Faigenboim A, Stern A, Mayrose I, Bacharach E, Pupko T. Selecton: a server for detecting evolutionary forces at a single amino-acid site. Bioinformatics 2005, 21(9):2101-2103. 10.1093/bioinformatics/bti259, 15647294.
77. Hirokawa T, Boon-Chieng S, Mitaku S. SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics 1998, 14(4):378-379. 10.1093/bioinformatics/14.4.378, 9632836.