Genome-wide identification and comparative analysis of the TUBBY-like protein gene family in maize

详细信息    查看全文

• 作者：Chen Yulong ; Dai Wei ; Sun Baoming ; Zhao Yang ; Ma Qing
• 关键词：Maize ; Microsynteny ; Phylogenetic analysis ; Stress ; induced expression ; TLP genes
• 刊名：Genes & Genomics
• 出版年：2016
• 出版时间：January 2016
• 年：2016
• 卷：38
• 期：1
• 页码：25-36
• 全文大小：1,731 KB
• 参考文献：Akihiro I, Nishina PM, Naggerten K (2002) The tubby-like proteins, a family with roles in neuronal development and function. J Cell Sci 115:9–14
  Bailey TL, Williams N, Misleh C, Li WW (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34:W369–W373CrossRef PubMed PubMedCentral
  Baskin DG, Wilcox BJ, Figlewicz DP, Dm D (1988) Insulin and insulin-like growth factors in the CNS. Trends Neurosci 11:107–111CrossRef PubMed
  Bateman A, Finn RD, Sims PJ, Wiedmer T, Biegert A, Söding J (2009) Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors. Bioinformatics 25:159–162CrossRef PubMed PubMedCentral
  Boggon TJ, Shan WS, Santagata S, Myers SC, Shapiro L (1999) Implication of tubby proteins as transcription factors by structure-based functional analysis. Science 286:2119–2125CrossRef PubMed
  Cannon SB, Mitra A, Baumgarten A, Young ND, May G (2004) The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol 4:10CrossRef PubMed PubMedCentral
  Coleman DL, Eicher EM (1990) Fat (fat) and tubby (tub): two autosomal recessive mutations causing obesity syndromes in the mouse. J Hered 81:424–427PubMed
  Deleu W, González V, Monfort A, Bendahmane A, Puigdomènech P, Arús P, Garcia-Mas J (2007) Structure of two melon regions reveals high microsynteny with sequenced plant species. Mol Genet Genom 278:611–622CrossRef
  Gagne JM, Downes BP, Shiu SH, Durski AM, Vierstra RD (2002) The F-box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in Arabidopsis. Proc Natl Acad Sci USA 99:11519–11524CrossRef PubMed PubMedCentral
  Guo AY, Zhu QH, Chen X, Luo JC (2007) GSDS: a gene structure display server. Hereditas 29:1023–1026CrossRef PubMed
  Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, Sharma P, Kapoor S, Tyagi AK, Jp K (2007) F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 143:1467–1483CrossRef PubMed PubMedCentral
  Kapeller R, Moriarty A, Strauss A, Stubdal H, Theriault K, Siebert E, Chickering T, Morgenstern JP, Tartaglia LA, Lillie J (1999) Tyrosine phosphorylation of Tub and its association with Src Homology 2 domain-containing proteins implicate Tub in intracellular signaling by insulin. J Biol Chem 274:24980–24986CrossRef PubMed
  Kleyn PW, Fan W, Kovats SG, Lee JJ, Pulido JC, Wu Y, Berkemeier LR, Misumi DJ, Holmgren L et al (1996) Identification and characterization of the mouse obesity gene tubby: a member of a novel gene family. Cell 2:281–290CrossRef
  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 50:873–885CrossRef PubMed
  Lai CP, Lee CL, Chen PH, Wu SH, Yang CC, Shaw JF (2004) Molecular analyses of the Arabidopsis TUBBY-like protein gene family. Plant Physiol 134:1586–1597CrossRef PubMed PubMedCentral
  Letunic I, Doerks T, Bork P (2012) SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res 40:D302–D305CrossRef PubMed PubMedCentral
  Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452CrossRef PubMed
  Liu Q (2008) Identification of rice TUBBY-like genes and their evolution. FEBS J 275:163–171CrossRef PubMed
  Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290:1151–1155CrossRef PubMed
  Mf W (1998) The IRS-signalling system: a network of docking proteins that mediate insulin action. Mol Cell Biochem 182:3–11CrossRef
  Moore RC, Purugganan MD (2003) The early stages of duplicate gene evolution. Proc Natl Acad Sci USA 100:15682–15687CrossRef PubMed PubMedCentral
  Mural RJ, Adams EWM, Smith HO, Miklos GL, Wides R, Halpern A, Li PW, Sutton GG, Nadeau J et al (2002) A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science 296:1661–1671CrossRef PubMed
  Noben-Trauth K, Naggert JK, North MA, Pm N (1996) A candidate gene for the mouse mutation tubby. Nature 380:534–538CrossRef PubMed
  North MA, Naggert JK, Yan Y, Noben-Trauth K, Nishina PM (1997) Molecular characterization of TUB, TULP1, and TULP2, members of the novel tubby gene family and their possible relation to ocular diseases. Proc Natl Acad Sci USA 94:3128–3133CrossRef PubMed PubMedCentral
  Ohlemiller KK, Hughes RM, Mosinger-Ogilvie J, Speck JD, Grosof DH, Ms S (1995) Cochlear and retinal degeneration in the tubby mouse. NeuroReport 6:845–849CrossRef PubMed
  Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J (2012) The Pfam protein families database. Nucleic Acids Res 40:D290–D301CrossRef PubMed PubMedCentral
  Rogozin IB, Wolf YI, Sorokin AV, Mirkin BG, Koonin EV (2003) Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr Biol 13:1512–1517CrossRef PubMed
  Santagata S, Boggon TJ, Baird CL, Gomez CA, Zhao J, Shan WS, Myszka DG, Shapiro L (2001) G-protein signaling through tubby proteins. Science 292:2041–2050CrossRef PubMed
  Sato S, Nakamura Y, Kaneko T, Asamizu E, Kato T, Nakao M, Sasamoto S, Watanabe A, Ono A, Kawashima K (2008) Genome structure of the legume, Lotus japonicus. DNA Res 15:227–239CrossRef PubMed PubMedCentral
  Sekhon RS, Lin H, Childs KL, Hansey CN, Buell CR, De Leon N, Kaeppler SM (2011) Genome-wide atlas of transcription during maize development. Plant J 66:553–563CrossRef PubMed
  Sekhon RS, Briskine R, Hirsch CN, Myers CL, Springer NM, Buell CR, de Leon N, Kaeppler SM (2013) Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays. PLoS One 8:e61005CrossRef PubMed PubMedCentral
  Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Molecular Evolutionary Genetics Analysis Software version 6.0. Mol Biol Evol 30:2725–2729CrossRef PubMed PubMedCentral
  Thompson JD, Higgins DG, Tj G (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680CrossRef PubMed PubMedCentral
  Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Dg H (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882CrossRef PubMed PubMedCentral
  Ullrich A, Schlessinger J (1990) Signal transduction by receptors with tyrosine kinase activity. Cell 61:203–212CrossRef PubMed
  Wang X, Shi X, Hao B, Ge S, Luo J (2005) Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol 165:937–946CrossRef PubMed
  Wardhan V, Jahan K, Gupta S, Chennareddy S, Datta A, Chakraborty S, Chakraborty N (2012) Overexpression of CaTLP1, a putative transcription factor in chickpea (Cicer arietinum L.), promotes stress tolerance. Plant Mol Biol 79:479–493CrossRef PubMed
  Yang Z, Zhou Y, Wang X, Gu S, Yu J, Liang G, Yan C, Xu C (2008) Genomewide comparative phylogenetic and molecular evolutionary analysis of tubby-like protein family in Arabidopsis, rice, and poplar. Genomics 92:246–253CrossRef PubMed
  Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3:e38CrossRef PubMed PubMedCentral
  
• 作者单位：Chen Yulong (1)
  Dai Wei (1)
  Sun Baoming (1)
  Zhao Yang (1)
  Ma Qing (1)
  
  1. Key Laboratory of Crop Biology of Anhui Province, Anhui Agricultural University, Hefei, 230036, China
  
• 刊物主题：Microbial Genetics and Genomics; Plant Genetics & Genomics; Animal Genetics and Genomics; Human Genetics;
• 出版者：Springer Netherlands
• ISSN：2092-9293

文摘

The evolutionary history of TUBBY-like proteins (TLPs), which contain a highly conserved tubby domain, can be traced to the early stages of eukaryote evolution, on account of the identification of this gene family in organisms from single-celled to multicellular eukaryotes. While genome-wide structural and evolutionary analyses of the entire TLP gene family have recently been reported in Arabidopsis and rice, little is known about TLP genes in maize. To gain insight into how TLP genes have evolved in maize, we conducted comprehensive analysis of the molecular evolution of TLP genes in this crop. A total of 15 TLP genes (ZmTLP1–15) were identified in maize by genome-wide screening. This family was classified into four subfamilies based on phylogenetic relationships, protein domains, and motif organization. Gene duplication and chromosomal location analysis indicated that segmental duplication has played a major role in the expansion of the maize TLP family. The ZmTLP genes exhibited differential expression profiles under ABA, NaCl, 42, 4 °C, and PEG stress treatment. We performed microsynteny analysis across three gramineous species based on comparisons of the specific regions containing TLP genes, revealing numerous microsyntenic gene pairs among maize, rice, and sorghum, which suggests that the flanking regions of TLP genes may be derived from a common ancient Gramineae ancestor.