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Functional Divergence and Evolutionary Dynamics of the Putative AAAP Gene Family in Brassica rapa

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Abstract

The amino acid/auxin permease (AAAP) protein family is ubiquitously present in almost all eukaryotic species and functions in various aspects of growth and development. To investigate the evolution of AAAP proteins, here 83 AAAP genes in Brassica rapa were identified, and their sequence features, and evolutionary relationships were analyzed using in silico methods. According to the phylogenetic analysis, the AAAP genes of B. rapa are divided into six clades, and these clades share relatively similar sequence features, including gene structures, conserved motifs, and domain organizations. Synteny mapping strongly suggested that segmental duplications could be responsible for the expansion of this family. Adaptive evolution analysis demonstrated that most of AAAP proteins were subject to purifying selection. However, the site Tyr257 on eight AAAP proteins from clade 2b underwent significant positive selection. Functional divergent analysis showed that type I functional divergence coefficients (θ I ) were significantly greater than zero in six pair-wise comparisons. However, functional divergence sites (Q k  > 0.95) found only in the AAAP I/II and AAAP I/III comparisons were localized mainly to the trans-membrane (TM) regions, suggesting highly divergent TM structures between these groups might be associated with group-specific functions. Our results could provide a valuable clue for further investigations of the evolutionary history and biological functions of the AAAP genes in B. rapa.

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References

  • Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modeling. Bioinformatics 22:195–201

    Article  CAS  PubMed  Google Scholar 

  • Babula D, Kaczmarek M, Barakat A, Delseny M, Quiros CF, Sadowski J (2003) Chromosomal mapping of Brassica oleracea based on ESTs from Arabidopsis thaliana: complexity of the comparative map. Mol Genet Genomics 268:656–665

    CAS  PubMed  Google Scholar 

  • Bailey TL, Williams N, Misleh C, Li WW (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34:369–373

    Article  Google Scholar 

  • Beilstein MA, Nagalingum NS, Clements MD, Manchester SR, Mathews S (2010) Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proc Natl Acad Sci U S A 107:18724–18728

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bennett MJ, Marchant A, Green HG, May ST, Ward SP, Millner PA, Walker AR, Schulz B, Feldmann KA (1996) Arabidopsis AUX1 gene: a permease-like regulator of root gravitropism. Science 273:948–950

    Article  CAS  PubMed  Google Scholar 

  • Boll M, Foltz M, Rubio-Aliaga I, Kottra G, Daniel H (2002) Functional characterization of two novel mammalian electrogenic proton-dependent amino acid co-transporters. J Biol Chem 277:22966–22973

    Article  CAS  PubMed  Google Scholar 

  • Breitkreuz KE, Shelp BJ, Fischer WN, Schwacke R, Rentsch D (1999) Identification and characterization of GABA, proline and quaternary ammonium compound transporters from Arabidopsis thaliana. FEBS Lett 450:280–284

    Article  CAS  PubMed  Google Scholar 

  • Chang HC, Bush DR (1997) Topology of NAT2, a prototypical example of a new family of amino acid transporters. J Biol Chem 272:30552–30557

    Article  CAS  PubMed  Google Scholar 

  • Chaudhry FA, Reimer RJ, Krizaj D, Barber D, Storm-Mathisen J, Copemhagen DR, Edwards RH (1999) Molecular analysis of system N suggests novel physiological roles in nitrogen metabolism and synaptic transmission. Cell 99:769–780

    Article  CAS  PubMed  Google Scholar 

  • Chen L, Bush DR (1997) LHT1, a lysine- and histidine-specific amino acid transporter in Arabidopsis. Plant Physiol 115:1127–1134

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Cheng F, Liu S, Jian Wu J, Fang L, Sun S, Liu B, Li P, Hua W, Wang XW (2011) BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biol 11:136

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Cheng F, Jian Wu J, Fang L, Sun S, Liu B, Lin K, Bonnema G, Wang XW (2012) Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa. PLoS One 7(5):e36442

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Cheung F, Trick M, Drou N, Lim YP, Park JY, Kwon SJ, Kim JA, Scott R, Pires JC, Paterson AH, Town C, Bancroft I (2009) Comparative analysis between homoeologous genome segments of Brassica napus and its progenitor species reveals extensive sequence-level divergence. Plant Cell 21:1912–1928

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Clark JA, Amara SG (2005) Amino acid neurotransmitter transporters: structure, function, and molecular diversity. BioEssays 15:323–332

    Article  Google Scholar 

  • Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14:755–763

    Article  CAS  PubMed  Google Scholar 

  • Fischer WN, Kwart M, Hummel S, Frommer WB (1995) Substrate specificity and expression profile of amino acid transporters (AAPs) in Arabidopsis. J Biol Chem 270:16315–16320

    Article  CAS  PubMed  Google Scholar 

  • Fischer WN, Loo DD, Koch W, Ludewig U, Boorer KJ, Tegeder M, Rentsch D, Wright EM, Frommer WB (2002) Low and high affinity amino acid H+-cotransporters for cellular import of neutral and charged amino acids. Plant J 29:717–731

    Article  CAS  PubMed  Google Scholar 

  • Foster J, Lee YH, Tegeder M (2008) Distinct expression of members of the LHT amino acid transporter family in flowers indicates specific roles in plant reproduction. Sex Plant Reprod 21:143–152

    Article  CAS  Google Scholar 

  • Fournier D, Andrade-Navarro MA (2011) PDBpaint, a visualization webservice to tag protein structures with sequence annotations. Bioinformatics 27:2605–2606

    CAS  PubMed  Google Scholar 

  • Frommer WB, Hummel S, Riesmeier JW (1993) Expression cloning in yeast of a cDNA encoding a broad specificity amino acid permease from Arabidopsis thaliana. Proc Natl Acad Sci U S A 90:5944–5948

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Frommer WB, Hummel S, Unseld M, Ninnemann O (1995) Seed and vascular expression of a high-affinity transporter for cationic amino acids in Arabidopsis. Proc Natl Acad Sci U S A 92:12036–12040

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Grallath S, Weimar T, Meyer A, Gumy C, Suter-Grotemeyer M, Neuhaus JM, Rentsch D (2005) The AtProT family. Compatible solute transporters with similar substrate specificity but differential expression patterns. Plant Physiol 137:117–126

    Google Scholar 

  • Gu X (1999) Statistical methods for testing functional divergence after gene duplication. Mol Biol Evol 16:1664–1674

    Article  CAS  PubMed  Google Scholar 

  • Gu X (2003) Functional divergence in protein (family) sequence evolution. Genetica 118:133–141

    Article  CAS  PubMed  Google Scholar 

  • Gu X, Vander-Velden K (2002) DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. Bioinformatics 18:500–501

    Article  CAS  PubMed  Google Scholar 

  • Guo AY, Zhu QH, Chen X, Luo JC (2007) GSDS: a gene structure display server. Yi Chuan (Chinese) 29:1023–1026

    Article  CAS  Google Scholar 

  • Hirner A, Ladwig F, Stransky H, Okumoto S, Keinath M, Harms A, Frommer WB, Koch W (2006) Arabidopsis LHT1 is a high-affinity transporter for cellular amino acid uptake in both root epidermis and leaf mesophyll. Plant Cell 18:1931–1946

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hsu LC, Chiou TJ, Chen L, Bush DR (1993) Cloning a plant amino acid transporter by functional complementation of a yeast amino acid transport mutant. Proc Natl Acad Sci U S A 90:7441–7445

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Johnston JS, Pepper AE, Hall AE, Chen ZJ, Hodnett G, Drabek J, Lopez R, Price HJ (2005) Evolution of genome size in Brassicaceae. Ann Bot 95:229–235

    Article  CAS  PubMed  Google Scholar 

  • Kong H, Landherr LL, Frohlich MW, Leebens-Mack J, Ma H, dePamphilis CW (2007) Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth. Plant J 50:873–885

    Article  CAS  PubMed  Google Scholar 

  • Lagercrantz U, Lydiate DJ (1996) Comparative genome mapping in Brassica. Genetics 144:1903–1910

    CAS  PubMed  Google Scholar 

  • Lan TH, DelMonte TA, Reischmann KP, Hyman J, Kowalski SP, McFerson J, Kresovich S, Paterson AH (2000) An EST-enriched comparative map of Brassica oleracea and Arabidopsis thaliana. Genome Res 10:776–788

    Article  CAS  PubMed  Google Scholar 

  • Lee YH, Foster J, Chen J, Voll LM, Weber APM, Tegeder M (2007) AAP1 transports uncharged amino acids into roots of Arabidopsis. Plant J 50:305–319

    Article  CAS  PubMed  Google Scholar 

  • Letunic I, Bork P (2011) Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39:W475–W478

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Lu Y, Song Z, Lü K, Lian X, Cai H (2012) Molecular characterization, expression and functional analysis of the amino acid transporter gene family (OsAATs) in rice. Acta Physiol Plant 34:1943–1962

    Article  CAS  Google Scholar 

  • Lukens L, Zou F, Lydiate D, Parkin I, Osborn T (2003) Comparison of a Brassica oleracea genetic map with the genome of Arabidopsis thaliana. Genetics 164:359–372

    CAS  PubMed  Google Scholar 

  • Lysak MA, Koch MA, Pecinka A, Schubert I (2005) Chromosome triplication found across the tribe Brassiceae. Genome Res 15:516–525

    Article  CAS  PubMed  Google Scholar 

  • Lysak MA, Cheung K, Kitschke M, Bureš P (2007) Ancestral chromosomal blocks are triplicated in Brassiceae species with varying chromosome number and genome size. Plant Physiol 145:402–410

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Mai B, Lipp M (1994) Cloning and chromosomal organization of a gene encoding a putative amino-acid permease from Saccharomyces cerevisiae. Gene 143(1):129–133

    Article  CAS  PubMed  Google Scholar 

  • McIntire SH, Reimer RJ, Schuske K, Edwards RH, Jorgensen EM (1997) Identification and characterization of the vesicular GABA transporter. Nature 389:870–876

    Article  CAS  PubMed  Google Scholar 

  • Mun JH, Kwon SJ, Yang TJ, Seol YJ, Jin M, Kim JA, Lim MH, Kim JS, Baek S, Choi BS, Yu HJ, Kim DS, Kim N, Lim KB, Lee SI, Hahn JH, Lim YP, Bancroft I, Park BS (2009) Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biol 10:111

    Article  Google Scholar 

  • Niemelä T, Seppänen M, Jauhianen L, Tulisalo U (2006) Yield potential of spring turnip rape synthetics and composite hybrids compared with open-pollinated commercial cultivars. Can J Plant Sci 86:693–700

    Article  Google Scholar 

  • Okumoto S, Schmidt R, Tegeder M, Fischer WN, Rentsch D, Frommer WB, Koch W (2002) High affinity amino acid transporters specifically expressed in xylem parenchyma and developing seeds of Arabidopsis. J Biol Chem 277:45338–45346

    Article  CAS  PubMed  Google Scholar 

  • Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer ELL, Eddy SR, Bateman A, Finn RD (2012) The Pfam protein families database. Nucleic Acids Res 40:290–301

    Article  Google Scholar 

  • Rentsch D, Hirner B, Schmelzer E, Frommer WB (1996) Salt stress-induced proline transporters and salt stress-repressed broad specificity amino acid permeases identified by suppression of a yeast amino acid permease-targeting mutant. Plant Cell 8:1437–1446

    CAS  PubMed Central  PubMed  Google Scholar 

  • Rentsch D, Schmidt S, Tegeder M (2007) Transporters for uptake and allocation of organic nitrogen compounds in plants. FEBS Lett 581:2281–2289

    Article  CAS  PubMed  Google Scholar 

  • Riechmann JL, Heard J, Martin G, Reuber L, Jiang CZ, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, Creelman R, Pilgrim BP, Zhang JZ, Ghandehari D, Sherman BK, Yu GL (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290:2105–2110

    Article  CAS  PubMed  Google Scholar 

  • Sagné C, Mestikawy SEI, Isambert M, Hamon M, Henry J, Giros B, Gasnier B (1997) Cloning of a functional vesicular GABA and glycine transporter by screening of genome databases. FEBS Lett 417:177–183

    Article  PubMed  Google Scholar 

  • Sagné C, Agulhon C, Ravassard P, Darmon M, Hamon M, Mestikawy SEI, Gasnier B, Giros B (2001) Identification and characterization of a lysosomal transporter for small neutral amino acids. Proc Natl Acad Sci U S A 98:7206–7211

    Article  PubMed Central  PubMed  Google Scholar 

  • Saier M, Yen M, Noto K, Tamang D, Elkan C (2009) The Transporter Classification Database: recent advances. Nucleic Acids Res 37:274–278

    Article  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Sugawara M, Nakanishi T, Fei YJ, Huang W, Ganapathy ME, Leibach FH, Ganapathy V (2000) Cloning of an amino acid transporter with functional characteristics and tissue expression pattern identical to that of system A. J Biol Chem 275:16473–16477

    Article  CAS  PubMed  Google Scholar 

  • Suyama M, Torrents D, Bork P (2006) PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res 34:609–612

    Article  Google Scholar 

  • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  CAS  PubMed  Google Scholar 

  • Tang H, Woodhouse MR, Cheng F, Schnable JC, Pedersen BS, Conant G, Wang X, Freeling M, Pires JC (2012) Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Genetics 190:1563–1574

    Article  CAS  PubMed  Google Scholar 

  • Tegeder M, Rentsch D (2010) Uptake and partitioning of amino acids and peptides. Mol Plant 3:997–1011

    Article  CAS  PubMed  Google Scholar 

  • Tegeder M, Ward JM (2012) Molecular evolution of plant AAP and LHT amino acid transporters. Front Plant Sci 3(21):1–8

    Google Scholar 

  • Tegeder M, Tan Q, Grennan AK, Patrick JW (2007) Amino acid transporter expression and localisation studies in pea (Pisum sativum). Funct Plant Biol 34:1019–1028

    Article  CAS  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Wang X, Wang H, Wang J, Sun R, Wu J et al (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039

    Article  CAS  PubMed  Google Scholar 

  • Ward J (2001) Identification of novel families of membrane proteins from the model plant Arabidopsis thaliana. Bioinformatics 17:560–563

    Article  CAS  PubMed  Google Scholar 

  • Wipf D, Ludewig U, Tegeder M, Rentsch D, Koch W, Frommer WB (2002) Conservation of amino acid transporters in fungi, plants and animals. Trends Biochem Sci 27:139–147

    Article  CAS  PubMed  Google Scholar 

  • Yang Z (2007) PAML4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591

    Article  CAS  PubMed  Google Scholar 

  • Yang Z, Nielsen R (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 19:908–917

    Article  CAS  PubMed  Google Scholar 

  • Yang YW, Lai KN, Tai PY, Li WH (1999) Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages. J Mol Evol 48:597–604

    Article  CAS  PubMed  Google Scholar 

  • Yang Z, Wong WSW, Nielsen R (2005) Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol 22:1107–1118

    Article  CAS  PubMed  Google Scholar 

  • Yang TJ, Kim JS, Kwon SJ, Lim KB, Choi BS, Kim JA, Jin M, Park JY, Lim MH, Kim HI, Lim YP, Kang JJ, Hong JH, Kim CB, Bhak J, Bancroft I, Park BS (2006) Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa. Plant Cell 18:1339–1347

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Young GB, Jack DL, Smith DW, Saier MH (1999) The amino acid/auxin: proton symport permease family. Biochim Biophys Acta 1415:306–322

    Article  CAS  PubMed  Google Scholar 

  • Zhang J, Nielsen R, Yang Z (2005) Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol 22:2472–2479

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This work was supported by National Natural Science Foundation of China (31271755) and the Ministry of Science and Technology of China (2006CB101600).

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  1. Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing, 100101, China

    Li-Zong Hu, Wei-Bo Yin, Yu-Hong Chen & Zan-Min Hu

  2. University of Chinese Academy of Sciences, Beijing, 100049, China

    Li-Zong Hu

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Hu, LZ., Yin, WB., Chen, YH. et al. Functional Divergence and Evolutionary Dynamics of the Putative AAAP Gene Family in Brassica rapa . Plant Mol Biol Rep 32, 517–530 (2014). https://doi.org/10.1007/s11105-013-0671-3

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