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菌物学报  2015 

绒泡菌目黏菌的ITS1-5.8S-ITS2二级结构的比较分析

DOI: DOI:10.13346/j.mycosystema.130224, PP. 235-245

Keywords: 绒泡菌目,ITS,RNA二级结构,模型,互补性碱基变化,分子进化

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Abstract:

为探讨核糖体DNA转录间隔区(rDNAITS)的RNA二级结构在黏菌系统发育研究中的作用,以黏菌ITS通用引物PHYS4和PHYS5对绒泡菌目5属8种黏菌的rDNAITS进行扩增和测序,利用RNAstructure构建了ITS区的RNA二级结构模型。结果表明:ITS1在绒泡菌目黏菌中不能形成一个紧实的结构,但大部分物种都具有一段稳定的螺旋结构,可能对rRNA的成熟具有作用;5.8SrRNA的二级结构相似,由4个螺旋组成,主要为两种类型;基于5.8SrRNA和28SrRNA相互作用构建的ITS2的二级结构模型显示,它由一个封闭的多分支环和至少4个主要的螺旋组成,其中螺旋IV结构相对比较保守。由于ITS区的二级结构相比核苷酸序列更加保守,因此深入地分析其二级结构有助于认识其结构与进化的关系。

References

[1]  1 Aldrich HC, Daniel JW, 1982. Cell biology of Physarum and Didymium. Academic Press Inc. , New York. 1-480 [本文引用:
[2]  2 Alexopoulos CJ, Mims CW, Blackwell M, 1996. Introductory Mycology. 4th edition. John Wiley & Sons, Inc. ,New York. 775-808 [本文引用:
[3]  3 Annette WC, 2007. Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Research, 35: 3322-3329 [本文引用:
[4]  4 Coleman AW, Vacquier VD, 2002. Exploring the phylogenetic utility of ITS sequences for animals: a test case for abalone (Haliotis). Journal of Molecular Biology, 54: 246-257 [本文引用:
[5]  5 Fabry S, Kohler A, Coleman AW, 1999. Intraspecies analysis: comparison of ITS sequence data and gene intron sequence data with breeding data for a worldwide collection of Gonium pectorale. Journal of Molecular Biology, 48: 94-101 [本文引用:
[6]  6 Fiore-Donno AM, Berney CD, Pawlowski J, Baldauf SL, 2005. Higher-order phylogeny of plasmodial slime molds (Myxogastria) based on elongation factor 1-α and small subunit rRNA gene sequences. Journal of Eukaryotic Microbiology, 52: 201-210 [本文引用:
[7]  7 Fiore-Donno AM, Meyer M, Baldauf SL, Pawlowski J, 2008. Evolution of dark-spored Myxomycetes (slime-molds): molecules versus morphology. Molecular Phylogenetics and Evolution, 46: 878-889 [本文引用:
[8]  8 Fiore-Donno AM, Nikolaev SI, Nelson M, Pawlowski J, Cavalier-Smith T, Baldauf SL, 2010. Deep phylogeny and evolution of slime moulds (Mycetozoa). Protist, 161: 55-70 [本文引用:
[9]  9 Freire MCM, da Silva MR, Zhang XC, Almeida AMR, Stacey G, de Oliveira LO, 2012. Nucleotide polymorphism in the 5. 8S nrDNA gene and internal transcribed spacers in Phakopsora pachyrhizi viewed from structural models. Fungal Genetics and Biology, 49: 95-100 [本文引用:
[10]  10 Gottschling M, Pl?tner J, 2004. Secondary structure models of the nuclear internal transcribed spacer regions and 5. 8S rRNA in Calciodinelloideae (Peridiniaceae) and other dinoflagellates. Nucleic Acids Research, 32: 307-315 [本文引用:
[11]  11 Hausner G, Wang X, 2005. Unusual compact rDNA gene arrangements within some members of the Ascomycota: evidence for molecular co-evolution between ITS1 and ITS2. Genome, 48: 648-660 [本文引用:
[12]  12 Jacq B, 1981. Sequence homologies between eukaryotic 5. 8S rRNA and the 5’-end of prokaryotic 23S rRNA: evidence for a common evolutionary origin. Nucleic Acids Reserach, 9: 2913-2932 [本文引用:
[13]  13 Joseph N, Krauskopf E, Vera MI, Michot B, 1999. Ribosomal internal transcribed spacer 2 (ITS2) exhibits a common core of secondary structure in vertebrates and yeast. Nucleic Acids Research, 27: 4533-4540 [本文引用:
[14]  14 Kirk PM, Cannon PF, Minter DW, Stalpers JA, 2008. Ainsworth & Bisby’s dictionary of the fungi. 10th edition. CAB International, Egham. 767 [本文引用:
[15]  15 Larue B, Gaudreau C, Bagre HO, Charpentier G, 2009. Generalized structure and evolution of ITS1 and ITS2 rDNA in black ?ies (Diptera: Simuliidae). Molecular Phylogenetics and Evolution, 53: 749-757 [本文引用:
[16]  16 Liu JS, Schardl CL, 1994. A conserved sequence in internal transcribed spacer 1 of plant nuclear rRNA genes. Plant Molecular Biology, 26: 775-778 [本文引用:
[17]  17 Liu Y, Cui XL, Li WJ, Peng Q, 2006. Application of secondary structure in phylogenetic analysis of Micrbiology. Microbiology China, 33: 146-150 (in Chinese) [本文引用:
[18]  18 Martin GW, Alexopoulos CJ, 1969. The myxomycetes. University of Iowa Press, Iowa. 1-561 [本文引用:
[19]  19 Martin MP, Lado C, Sjohansen S, 2003. Primers are designed for amplification and direct sequencing of ITS region of rDNA from Myxomycetes. Mycologia, 95: 474-479 [本文引用:
[20]  20 Maroteaux L, Herzog M, Soyer-Gobillard MO, 1985. Molecular organization of dinoagellate ribosomal DNA: evolutionary implications of the deduced 5. 8S rRNA secondary structure. Biosystems, 18: 307-319 [本文引用:
[21]  21 Mai JC, Coleman AW, 1997. The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants. Journal of Molecular Evolution, 44: 258-271 [本文引用:
[22]  22 Müller T, Philippi N, Dand ekar T, Schultz J, Wolf M, 2007. Distinguishing species. RNA, 13: 1469-1472 [本文引用:
[23]  23 Musters W, Boon K, Sand e CA, Heerikhuizen H, Planta RJ, 1990. Functional analysis of transcribed spacers of yeast ribosomal DNA. EMBO Journal, 9: 2989-2996 [本文引用:
[24]  24 Nazar RN, 2004. Ribosomal RNA processing and ribosome biogenesis in eukaryotes. IUBMB Life, 56: 457-465 [本文引用:
[25]  25 Nues RW, Rientjes J, Sand e CA, Zerp SF, Sluiter C, Venema J, Planta RJ, Raué HA, 1994. Separate structural elements within internal transcribed spacer 1 of Saccharomyces cerevisiae precursor ribosomal RNA direct the formation of 17S and 26S rRNA. Nucleic Acids Research, 22: 912-919 [本文引用:
[26]  26 Réblová M, Untereiner WA, Réblová K, 2013. Novel evolutionary lineages revealed in the Chaetothyriales (Fungi) based on multigene phylogenetic analyses and comparison of ITS secondary structure. PLoS One, 8: e63547. doi: DOI:10.1371/journal.pone.0063547 [本文引用:
[27]  27 Sand e CA, Kwa M, Nues RW, Heerikhuizen H, Raué HA, Planta RJ, 1992. Functional analysis of internal transcribed spacer 2 of Saccharomyces cerevisiae ribosomal DNA. Journal of Molecular Biology, 223: 899-910 [本文引用:
[28]  28 Schultz J, Maisel S, Gerlach D, Muller T, Wolf M, 2005. A common core of secondary structure of the internal transcribed spacers (ITS2) throughout the Eukaryota. RNA, 11: 361-364 [本文引用:
[29]  29 Schlotterer C, Hauser MT, Haeseler A, Tautz D, 1994. Comparative evolutionary analysis of rDNA ITS regions in Drosophila. Molecular Biology and Evolution, 11: 513-522 [本文引用:
[30]  30 Tinoco I, Ulenbeck OC, Levine MD, 1971. Estimation of secondary structure in ribonucleic acids. Nature, 230: 362-367 [本文引用:
[31]  31 Tinoco I, Borer PN, Dengler B, Levin MD, Uhlenbeck OC, Crothers DM, Bralla J, 1973. Improved estimation of secondary structure in ribonucleic acids. Nature New Biololgy, 246(150): 40-41 [本文引用:
[32]  32 Vollmer SV, Palumbi SR, 2004. Testing the utility of internally transcribed spacer sequences in coral phylogenetics. Molecular Ecology, 13: 2763-2772 [本文引用:
[33]  33 Wolf M, Achtziger M, Schultz J, Dand ekar T, Müller T, 2005. Homology modeling revealed more than 20, 000 rRNA internal transcribed spacer 2 (ITS2) secondary structures. RNA, 11: 1616-1623 [本文引用:
[34]  34 Wolf M, Friedrich J, Dand ekar T, Müller T, 2005. CBC analyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures. In Silico Biology, 5: 291-294 [本文引用:
[35]  35 Young I, Coleman AW, 2004. The advantages of the ITS2 region of the nuclear rDNA cistron for analysis of phylogenetic relationships of insects: a Drosophila example. Journal of Molecular Biology, 30: 236-242 [本文引用:
[36]  36 Zuker M, Stiegler P, 1981. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Reserach, 9: 133-148 [本文引用:
[37]  37 刘杨, 崔晓龙, 李文均, 彭谦, 2006. RNA二级结构在微生物系统发育分析上的应用. 微生物学通报, 33(2): 146-150 [本文引用:

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