酵母菌的可誘導GlyRS之特性

以作者查詢圖書館館藏

、以作者查詢臺灣博碩士

、以作者查詢全國書目

、勘誤回報

、線上人數：13

、訪客IP：18.117.91.153

姓名

吳怡樺(Yi-Hua Wu) 查詢紙本館藏

畢業系所

生命科學系

論文名稱

酵母菌的可誘導GlyRS之特性
(Characterization of an inducible yeast glycyl-tRNA synthetase gene)

相關論文

★ Kineosphaera limosa 菌株中 phaC 基因之序列分析	★ 剪力和組織蛋白去乙醯酶在動靜脈廔管失效扮演的角色
★ Classification of powdery mildews on ornamental plants in northern Taiwan	★ 秀麗隱桿線蟲線粒體AlaRS通過非傳統模式識別T型無臂tRNAAla
★ 探討DNA損傷反應與慢性暴露4-胺基聯苯產生之肝臟毒性	★ Bacillus thuringiensis contains two prolyl-tRNA synthetases of different origins
★ Recognition of tRNA His isoacceptors by human HisRS isoforms	★ Functional replacement of yeast nuclear and mitochondrial RNase P by a protein-only RNase P
★ Functional characterization of a noncanonical ProRS in Toxoplasma gondii	★ tRNA aminoacylation by a naturally occurring mini-AlaRS
★ Functional Repurposing of C-Ala Domains	★ Recognition of a non-canonical tRNAAla by a non-canonical alanyl-tRNA synthetase
★ 探討Alanyl-tRNA synthetase的演化及專一性	★ 酵母菌valyl-tRNA synthetase附加區段的生物功能之探討
★ 探討酵母菌glycyl-tRNA合成酵素的非傳統生物功能	★ 探討酵母菌Valyl-tRNA synthetase的生化活性

檔案

[Endnote RIS 格式]

[Bibtex 格式]

[相關文章]

[文章引用]

[完整記錄]

[館藏目錄]

[檢視]

[下載]

本電子論文使用權限為同意立即開放。
已達開放權限電子全文僅授權使用者為學術研究之目的，進行個人非營利性質之檢索、閱讀、列印。
請遵守中華民國著作權法之相關規定，切勿任意重製、散佈、改作、轉貼、播送，以免觸法。

摘要(中)

Aminoacyl-tRNA synthetases(簡稱aaRSs)其催化生成aminoacyl-tRNAs，提供蛋白質生合成的原料。它們是一群不可或缺且古老的酵素家族，存在於自然界所有的生物體內，正因如此，我們便可利用它們做演化研究的依據。之前的研究指出，酵母菌(Saccharomyces cerevisiae)的細胞核內有編碼兩種不同的GlyRS基因，分別為GRS1基因(解碼glycyl-tRNA synthetase1，簡稱GlyRS1)和GRS2基因(解碼glycyl-tRNA synthetase2，簡稱GlyRS2)。其中蛋白質GlyRS1，即具有細胞質和粒線體的功能，且與GlyRS2做蛋白質序列比較發現明顯地多了一段嵌入肽鏈(insertion peptide) ，此外，兩種蛋白質在結構和序列上並無明顯差異；而GRS2基因平常於酵母菌體內不表現，類似「假基因(Pseudogene)」，其看似演化留下的痕跡(在高等真核生物並無此基因，且所有已知酵母菌菌株中，只有S. cerevisiae和V. polyspora具有GRS2基因)，但我們發現若以生物技術所獲得其表現的蛋白質GlyRS2，竟然具有催化活性，因此其所扮演的角色及生理意義，遂成為我們研究的終極目的。首先，我們發現GRS2基因在一些極端條件下(高溫、存在酒精、氧化壓力等)，會被誘導使表現量上升，且由實驗結果可知其蛋白質GlyRS2在高溫條件具有較佳的活性及穩定性；接著，藉由從各種不同面向的生物體內和體外實驗結果證明「嵌入肽鏈」對GlyRS1重要性，並與GlyRS2做比較，再更進一步討論GlyRS1和GlyRS2之間演化上的關係；最後，我們由體外實驗結果發現GlyRS2於酸性和存在酒精條件下，催化活性並無明顯變化，反而GlyRS1催化活性大受影響，此結果間接解釋了GlyRS2真正的生理功能，以及為何它在演化這條漫漫長路上罕見地被保留至今，其可能與釀酒酵母菌S. cerevisiae的發酵作用有關。

摘要(英)

Aminoacyl-tRNA synthetases (aaRSs) participate in producing aminoacyl-tRNAs (aa-tRNAs) which are the precursors in protein synthesis. They are a large and old family of housekeeping enzymes that are pivotal in protein translation and other vital cellular processes in the overall organisms. Thus, aaRSs are useful proteins to study evolution. In previous studies, Saccharomyces cerevisiae possesses two distinct nuclear glycyl-tRNA synthetase (GlyRS) genes, GRS1 and GRS2. GRS1 encodes GlyRS1 which contains both cytoplasmic and mitochondrial activities, while GRS2 (which encodes GlyRS2) is dysfunctional and not required for growth. They are much alike, but are distinguished by an insertion peptide of GlyRS1 that is absent from GlyRS2 and other eukaryotic homologues. In the past, GRS2 was considered as a pseudogene-like gene and only exists in S. cerevisiae and V. polyspora. However, we observed that in vitro purified GlyRS2 had the aminoacylation ability. The exciting results made us curious of the biological function of GlyRS2 in yeast and discuss why GlyRS2 has survived during the GlyRSs’ evolution? First, we herein present evidence that the expression of GRS2 was drastically induced in the some stress conditions (ex: heat shock, alcohol and hydrogen peroxide addition). In addition, GlyRS2 was more stable and more active under heat shock conditions than under normal conditions. Second, we proved that the insertion peptide of GlyRS1 facilitates both productive docking and catalysis of cognate tRNAs in vivo and in vitro. Further, we found that GlyRS2 is an active enzyme essentially resembling the insertion peptide-deleted form of GlyRS1. And a phylogenetic analysis showed that GRS1 and GRS2 are paralogues that arose from a gene duplication event relatively recently. Finally, we found that GlyRS2 has more stable aminoacylation activity than GlyRS1 in the acidic and alcohol-added conditions. The results show the possibly biological function of GlyRS2 in yeast and explain why GlyRS2 is kept during the evolution of GlyRS family.

關鍵字(中)

★ glycyl-tRNA synthetase
★ GlyRS1
★ GlyRS2
★ pseudogene-like gene
★ stress-inducible gene
★ gene duplication
★ insertion peptide
★ fermentation
★ whole-genome duplication

關鍵字(英)

★ glycyl-tRNA synthetase
★ GlyRS1
★ GlyRS2
★ pseudogene-like gene
★ stress-inducible gene
★ gene duplication
★ insertion peptide
★ fermentation
★ whole-genome duplication

論文目次

中文摘要 i
Abstract ii
Declaration iii
誌謝 iv
Table of Contents v
List of Tables vii
List of Figures viii
Overall introduction 1
Chapter I - Saccharomyces cerevisiae possesses a stress-inducible glycyl-tRNA synthetase gene ........................................................................................................................................ 6
Abstract 7
Introduction 8
Materials and Methods 10
Results 12
Discussion 15
Chapter II - An insertion peptide of yeast glycyl-tRNA synthetase facilitates both productive docking and catalysis of cognate tRNAs ............................................................................. 17
Abstract 18
Introduction 19
Materials and Methods 21
Results 24
Discussion 29

Chapter III - The biological functions of Saccharomyces cerevisiae glycyl-tRNA synthetase 2
.............................................................................................................................................. 31
Abstract 32
Introduction 33
Materials and Methods 36
Results 38
Discussion 43
Summary 46
References 47
Appendix 82

參考文獻

1. Burbaum JJ, Schimmel P. 1991. Structural relationships and the classification of aminoacyl-tRNA synthetases. J. Biol. Chem. 266:16965-16968.
2. Carter CW Jr. 1993. Cognition, mechanism, and evolutionary relationships in aminoacyl-tRNA synthetases. Annu. Rev. Biochem. 62:715-748.
3. Giege R, Sissler M, Florentz C. 1998. Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res. 26:5017-5035.
4. Giege R. 2006. The early history of tRNA recognition by aminoacyl-tRNA synthetases. J. Bioscience. 31:477-488.
5. Dietrich A, Weil JH, Marechal-Drouard L. 1992. Nuclear-encoded transfer RNAs in plant mitochondria. Annu. Rev. Cell Biol. 8:115-131.
6. Tang HL, Yeh LS, Chen NK, Ripmaster T, Schimmel P, Wang CC. 2004. Translation of a yeast mitochondrial tRNA synthetase initiated at redundant non-AUG codons. J. Biol. Chem. 279:49656-49663.
7. Huang HY, Tang HL, Chao HY, Yeh LS, Wang CC. 2006. An unusual pattern of protein expression and localization of yeast alanyl-tRNA synthetase isoforms.
Mol. Microbiol. 60:189-198.
8. Chang KJ, Wang CC. 2004. Translation initiation from a naturally occurring non-AUG codon in Saccharomyces cerevisiae. J. Biol. Chem. 279:13778-13785.
9. Natsoulis G, Hilger F, Fink GR. 1986. The HTS1 gene encodes both the cytoplasmic and mitochondrial histidine tRNA synthetases of S. cerevisiae. Cell. 46:235-243.
10. Chatton B, Walter P, Ebel JP, Lacroute F, Fasiolo F. 1988. The yeast VAS1 gene encodes both mitochondrial and cytoplasmic valyl-tRNA synthetases. J. Biol. Chem. 263:52-57.
11. Min B, Pelaschier JT, Graham DE, Tumbula-Hansen D, Söll D. 2002. Transfer RNA-dependent amino acid biosynthesis: an essential route to asparagine formation. Proc. Natl. Acad. Sci. U. S. A. 99:2678-2683.
12. Gagnon Y, Lacoste L, Champagne N, Lapointe J. 1996. Widespread use of the glu-tRNAGln transamidation pathway among bacteria. A member of the alpha purple bacteria lacks glutaminyl-tRNA synthetase. J. Biol. Chem. 271:14856-14863.
13. Eriani G, Delarue M, Poch O, Gangloff J, Moras D. 1990. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 347:203-206.
14. Schimmel P. 1987. Aminoacyl tRNA synthetases: general scheme of structure-function relationships in the polypeptides and recognition of transfer RNAs. Annu. Rev. Biochem. 56:125-158.
15. Ostrem DL, Berg P. 1970. Glycyl-tRNA synthetase: an oligomeric protein containing dissimilar subunits. Proc. Natl. Acad. Sci. U. S. A. 67:1967-1974.
16. Mazauric MH, Reinbolt J, Lorber B, Ebel C, Keith G, Giege R, Kern D. 1996. An example of non-conservation of oligomeric structure in prokaryotic aminoacyl-tRNA synthetases. Biochemical and structural properties of glycyl-tRNA synthetase from Thermus thermophilus. Eur. J. Biochem. 241:814-826.
17. Shiba K, Schimmel P, Motegi H, Noda T. 1994. Human glycyl-tRNA synthetase. Wide divergence of primary structure from bacterial counterpart and species-specific aminoacylation. J. Biol. Chem. 269:30049-30055.
18. Nada S, Chang PK, Dignam JD. 1993. Primary structure of the gene for glycyl-tRNA synthetase from Bombyx mori. J. Biol. Chem. 268:7660-7667.
19. Chien CI, Chen YW, Wu YH, Chang CY, Wang TL, Wang CC. 2014. Functional substitution of a eukaryotic glycyl-tRNA synthetase with an evolutionarily unrelated bacterial cognate enzyme. PLoS One. 9:e94659.
20. Koerner TJ, Myers AM, Lee S, Tzagoloff A. 1987. Isolation and characterization of the yeast gene coding for the alpha subunit of mitochondrial phenylalanyl-tRNA synthetase. J. Biol. Chem. 262:3690-3696.
21. Klipcan L, Finarov I, Moor N, Safro MG. 2010. Structural aspects of phenylalanylation and quality control in three major forms of phenylalanyl-tRNA synthetase. J. Amino Acids. 2010:983503.
22. Turner RJ, Lovato M, Schimmel P. 2000. One of two genes encoding glycyl-tRNA synthetase in Saccharomyces cerevisiae provides mitochondrial and cytoplasmic functions. J. Biol. Chem. 275:27681-27688.
23. Chen SJ, Lee CY, Lin ST, Wang CC. 2011. Rescuing a dysfunctional homologue of a yeast glycyl-tRNA synthetase gene. ACS Chem. Biol. 6:1182-1187.
24. Chen SJ, Wu YH, Huang HY, Wang CC. 2012. Saccharomyces cerevisiae possesses a stress-inducible glycyl-tRNA synthetase gene. PLoS One. 7:e33363.
25. Kellis M, Birren BW, Lander ES. 2004. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature. 428:617-624.
26. Dietrich FS, Voegeli S, Brachat S, Lerch A, Gates K, Steiner S, Mohr C, Pohlmann R, Luedi P, Choi S, Wing RA, Flavier A, Gaffney TD, Philippsen P. 2004. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science. 304:304-307.
27. Wolfe K. 2004. Evolutionary genomics: yeasts accelerate beyond BLAST. Curr. Biol. 14: R392-394.
28. Cliften PF. 2005. After the duplication: gene loss and adaptation in Saccharomyces genomes. Genetics. 172:863-872.
29. Turunen O, Seelke R, Macosko J. 2009. In silico evidence for functional specialization after genome duplication in yeast. FEMS Yeast Res. 9:16-31.
30. Clark RL, Neidhardt FC. 1990. Roles of the two lysyl-tRNA synthetases of Escherichia coli: analysis of nucleotide sequences and mutant behavior. J. Bacteriol. 172:3237-3243.
31. Ibba M, Morgan S, Curnow AW, Pridmore DR, Vothknecht UC, Gardner W, Lin W, Woese CR, Söll D. 1997. A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases. Science. 278:1119-1122.
32. Kitabatake M, Ali K, Demain A, Sakamoto K, Yokoyama S, Söll D. 2002. Indolmycin resistance of Streptomyces coelicolor A3(2) by induced expression of one of its two tryptophanyl-tRNA synthetases. J. Biol. Chem. 277:23882-23887.
33. Buddha MR, Keery KM, Crane BR. 2004. An unusual tryptophanyl tRNA synthetase interacts with nitric oxide synthase in Deinococcus radiodurans. Proc. Natl. Acad. Sci. U. S. A. 101:15881-15886.
34. Piškur J, Rozpedowska E, Polakova S, Merico A, Compagno C. 2006. How did Saccharomyces evolve to become a good brewer? Trends Genet. 22:183-186.
35. Merico A, Sulo P, Piškur J, Compagno C. 2007. Fermentative lifestyle in yeasts belonging to the Saccharomyces complex. FEBS J. 274:976-989.
36. Dashko S, Zhou N, Compagno C, Piškur J. 2014. Why, when, and how did yeast evolve alcoholic fermentation? FEMS Yeast Research. 14:826-832.
37. Stanley D, Bandara A, Fraser S, Chambers PJ, Stanley GA. 2010. The ethanol stress response and ethanol tolerance of Saccharomyces cerevisiae. J. Appl. Microbiol. 109:13-24.
38. Zhao XQ, Bai FW. 2009. Mechanisms of yeast stress tolerance and its manipulation for efficient fuel ethanol production. J. Biotechnol. 144:23-30.
39. Aguilera F, Peinado RA, Millan C, Ortega JM, Mauricio JC. 2006. Relationship between ethanol tolerance, H+-ATPase activity and the lipid composition of the plasma membrane in different wine yeast strains. Int. J. Food Microbiol. 110:34-42.
40. Cartwright CP, Veazey FJ, Rose AH. 1987. Effect of ethanol on activity of the plasma-membrane ATPase in, and accumulation of glycine by, Saccharomyces cerevisiae. J. Gen. Microbiol. 133:857-865.
41. Rosa MF, Sa-Correia I. 1996. Intracellular acidification does not account for inhibition of Saccharomyces cerevisiae growth in the presence of ethanol. FEMS Microbiol. Lett. 135:271-274.
42. Borodina I, Nielsen J. 2014. Advances in metabolic engineering of yeast Saccharomyces cerevisiae for production of chemicals. Biotechnol. J. 9:609-620.
43. Orij R, Postmus J, Ter Beek A, Brul S, Smits GJ. 2009. In vivo measurement of cytosolic and mitochondrial pH using a pH-sensitive GFP derivative in Saccharomyces cerevisiae reveals a relation between intracellular pH and growth. Microbiology. 155:268-278.
44. Viana T, Loureiro-Dias MC, Loureiro V, Prista C. 2012. Peculiar H+ homeostasis of Saccharomyces cerevisiae during the late stages of wine fermentation.
Appl. Environ. Microbiol. 78:6302-6308.
45. Wu YH, Chang CP, Chien CI, Tseng YK, Wang CC. 2013. An insertion peptide in yeast glycyl-tRNA synthetase facilitates both productive docking and catalysis of cognate tRNAs. Mol. Cell. Biol. 33:3515-3523.
46. Mirande M. 2010. Processivity of translation in the eukaryote cell: role of aminoacyl-tRNA synthetases. FEBS Lett. 584:443-447.
47. Wang CC, Schimmel P. 1999. Species barrier to RNA recognition overcome with nonspecific RNA binding domains. J. Biol. Chem. 274:16508-16512.
48. Frugier M, Moulinier L, Giege R. 2000. A domain in the N-terminal extension of class IIb eukaryotic aminoacyl-tRNA synthetases is important for tRNA binding. EMBO J. 19:2371-2380.
49. Chang CP, Lin G, Chen SJ, Chiu WC, Chen WH, Wang CC. 2008. Promoting the formation of an active synthetase/tRNA complex by a nonspecific tRNA-binding domain. J. Biol. Chem. 283:30699-30706.
50. Grant TD, Snell EH, Luft JR, Quartley E, Corretore S, Wolfley JR, Snell ME, Hadd A, Perona JJ, Phizicky EM, Grayhack EJ. 2012. Structural conservation of an ancient tRNA sensor in eukaryotic glutaminyl-tRNA synthetase. Nucleic Acids Res. 40:3723-3731.
51. Martinis S, Schimmel P. 1991. In Escherichia coli and Salmonella: Cellular and Molecular Biology, ed Neidhardt FC (American Society for Microbiology, Washington, D.C.), 2nd ed. pp. 887-901.
52. Pelchat M, Lapointe J. 1999. Aminoacyl-tRNA synthetase genes of Bacillus subtilis: organization and regulation. Biochem. Cell Biol. 77:343-347.
53. Chen SJ, Lin G, Chang KJ, Yeh LS, Wang CC. 2008. Translational efficiency of a non-AUG initiation codon is significantly affected by its sequence context in yeast. J. Biol. Chem. 283:3173-3180.
54. Chen SJ, Ko CY, Yen CW, Wang CC. 2009. Translational efficiency of redundant ACG initiator codons is enhanced by a favorable sequence context and remedial initiation. J. Biol. Chem. 284:818-827.
55. Hsiao SP, Chen SL. 2010. Myogenic regulatory factors regulate M-cadherin expression by targeting its proximal promoter elements. Biochem. J. 428:223-233.
56. Fersht AR, Ashford JS, Bruton CJ, Jakes R, Koch GL, Hartley BS. 1975. Active site titration and aminoacyl adenylate binding stoichiometry of aminoacyl-tRNA synthetases. Biochemistry-Us. 14:1-4.
57. Mirande M. 1991. Aminoacyl-tRNA synthetase family from prokaryotes and eukaryotes: structural domains and their implications. Prog. Nucleic. Acid Res. Mol. Biol. 40:95-142.
58. Wang CC, Morales AJ, Schimmel P. 2000. Functional redundancy in the nonspecific RNA binding domain of a class I tRNA synthetase. J. Biol. Chem. 275:17180-17186.
59. Francin M, Kaminska M, Kerjan P, Mirande M. 2002. The N-terminal domain of mammalian Lysyl-tRNA synthetase is a functional tRNA-binding domain. J. Biol. Chem. 277:1762-1769.
60. Francin M, Mirande M. 2006. Identity elements for specific aminoacylation of a tRNA by mammalian lysyl-tRNA synthetase bearing a nonspecific tRNA-interacting factor. Biochemistry. 45: 10153-10160.
61. Kaminska M, Deniziak M, Kerjan P, Barciszewski J, Mirande M. 2000. A recurrent general RNA binding domain appended to plant methionyl-tRNA synthetase acts as a cis-acting cofactor for aminoacylation. EMBO J. 19:6908-6917.
62. Kaminska M, Shalak V, Mirande M. 2001. The appended C-domain of human methionyl-tRNA synthetase has a tRNA-sequestering function. Biochemistry. 40:14309-14316.
63. Simos G, Segref A, Fasiolo F, Hellmuth K, Shevchenko A, Mann M, Hurt EC. 1996. The yeast protein Arc1p binds to tRNA and functions as a cofactor for the methionyl- and glutamyl-tRNA synthetases. EMBO J. 15:5437-5448.
64. Godinic V, Mocibob M, Rocak S, Ibba M, Weygand-Durasevic I. 2007. Peroxin Pex21p interacts with the C-terminal noncatalytic domain of yeast seryl-tRNA synthetase and forms a specific ternary complex with tRNA(Ser). FEBS J. 274:2788-2799.
65. Kawakami K, Ito K, Nakamura Y. 1992. Differential regulation of two genes encoding lysyl-tRNA synthetases in Escherichia coli: lysU-constitutive mutations compensate for a lysS null mutation. Mol. Microbiol. 6:1739-1745.
66. Marechal-Drouard L, Small I, Weil JH, Dietrich A. 1995. Transfer RNA import into plant mitochondria. Methods Enzymol. 260:310-327.
67. Duchene AM, Peeters N, Dietrich A, Cosset A, Small ID, Wintz H. 2001. Overlapping destinations for two dual targeted glycyl-tRNA synthetases in Arabidopsis thaliana and Phaseolus vulgaris. J. Biol. Chem. 276:15275-15283.
68. Chiu WC, Chang CP, Wen WL, Wang SW, Wang CC. 2010. Schizosaccharomyces pombe possesses two paralogous valyl-tRNA synthetase genes of mitochondrial origin. Mol. Biol. Evol. 27:1415-1424.
69. Brown JR, Doolittle WF. 1997. Archaea and the prokaryote-to-eukaryote transition. Microbiol. Mol. Biol. Rev. 61:456-502.
70. Chiu WC, Chang CP, Wang CC. 2009. Evolutionary basis of converting a bacterial tRNA synthetase into a yeast cytoplasmic or mitochondrial enzyme. J. Biol. Chem. 284:23954-23960.
71. Rinehart J, Krett B, Rubio MA, Alfonzo JD, Söll D. 2005. Saccharomyces cerevisiae imports the cytosolic pathway for Gln-tRNA synthesis into the mitochondrion. Genes Dev. 19:583-592.
72. Chang CP, Tseng YK, Ko CY, Wang CC. 2012. Alanyl-tRNA synthetase genes of Vanderwaltozyma polyspora arose from duplication of a dual-functional predecessor of mitochondrial origin. Nucleic Acids Res. 40:314-322.
73. Frechin M, Senger B, Braye M, Kern D, Martin RP, Becker HD. 2009. Yeast mitochondrial Gln-tRNA(Gln) is generated by a GatFAB-mediated transamidation pathway involving Arc1p-controlled subcellular sorting of cytosolic GluRS. Genes Dev. 23:1119-1130.
74. Nameki N, Tamura K, Asahara H, Hasegawa T. 1997. Recognition of tRNA(Gly) by three widely diverged glycyl-tRNA synthetases. J. Mol. Biol. 268:640-647.
75. Simlot MM, Pfaender P. 1973. Amino acid dependent ATP-32PPi exchange measurement. A filter paper disk method. FEBS Lett. 35:201-203.
76. Schwede T, Kopp J, Guex N, Peitsch MC. 2003. SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res. 31:3381-3385.
77. Nangle LA, Zhang W, Xie W, Yang XL, Schimmel P. 2007. Charcot-Marie-Tooth disease-associated mutant tRNA synthetases linked to altered dimer interface and neurite distribution defect. Proc. Natl. Acad. Sci. U. S. A. 104:11239-11244.
78. Schrodinger LLC. 2010. The PyMOL Molecular Graphics System, Version 1.3r1.
79. Liao CC, Lin CH, Chen SJ, Wang CC. 2012. Trans-kingdom rescue of Gln-tRNAGln synthesis in yeast cytoplasm and mitochondria. Nucleic Acids Res. 40:9171-9181.
80. Kelly SM, Jess TJ, Price NC. 2005. How to study proteins by circular dichroism? Biochim. Biophys. Acta. 1751:119-139.
81. Mazauric MH, Keith G, Logan D, Kreutzer R, Giege R, Kern D. 1998. Glycyl-tRNA synthetase from Thermus thermophilus--wide structural divergence with other prokaryotic glycyl-tRNA synthetases and functional inter-relation with prokaryotic and eukaryotic glycylation systems. Eur. J. Biochem. 251:744-757.
82. Louis-Jeune C, Andrade-Navarro MA, Perez-Iratxeta C. 2012. Prediction of protein secondary structure from circular dichroism using theoretically derived spectra. Proteins. 80:374-381.
83. Saitou N, Nei M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
84. Logan DT, Mazauric MH, Kern D, Moras D. 1995. Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus. EMBO J. 14:4156-4167.
85. Mazauric MH, Roy H, Kern D. 1999. tRNA glycylation system from Thermus thermophilus. tRNAGly identity and functional interrelation with the glycylation systems from other phylae. Biochemistry-Us. 38:13094-13105.
86. Whelihan EF, Schimmel P. 1997. Rescuing an essential enzyme-RNA complex with a non-essential appended domain. EMBO J. 16:2968-2974.
87. Nawaz MH, Pang YL, Martinis SA. 2007. Molecular and functional dissection of a putative RNA-binding region in yeast mitochondrial leucyl-tRNA synthetase. J. Mol. Biol. 367:384-394.
88. Sarkar J, Poruri K, Boniecki MT, McTavish KK, Martinis SA. 2012. Yeast mitochondrial leucyl-tRNA synthetase CP1 domain has functionally diverged to accommodate RNA splicing at expense of hydrolytic editing. J. Biol. Chem. 287:14772-14781.
89. Van Hoek MJA, Hogeweg P. 2009. Metabolic adaptation after whole genome duplication. Mol. Biol. Evol. 26:2441-2453.
90. Zhang J, Gordon JL, Byrne KP, Wolfe KH. 2009. Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome. PLoS Genetics. 5:e1000485.
91. Byrne KP, Wolfe KH. 2007. Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after whole-genome duplication. Genetics. 175:1341-1350.
92. Shima J, Takagi H. 2009. Stress-tolerance of baker′s-yeast (Saccharomyces cerevisiae) cells: stress-protective molecules and genes involved in stress tolerance.
Biotechnol. Appl. Biochem. 53:155-164.
93. Auesukaree C, Damnernsawad A, Kruatrachue M, Pokethitiyook P, Boonchird C, Kaneko Y, Harashima S. 2009. Genome-wide identification of genes involved in tolerance to various environmental stresses in Saccharomyces cerevisiae. J. Appl. Genet. 50:301-310.
94. Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. 2003. ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 31:3784-3788.
95. Conant GC, Wolfe KH. 2007. Increased glycolytic flux as an outcome of whole-genome duplication in yeast. Mol. Syst. Biol. 3:129.
96. Pfeiffer T, Morley A. 2014. An evolutionary perspective on the Crabtree effect. Frontiers in Molecular Biosciences. 1:17
97. Lin CH, Lin G, Chang CP, Wang CC. 2010. A tryptophan-rich peptide acts as a transcription activation domain. BMC Mol. Biol. 11:85.
98. Partow S, Siewers V, Bjørn S, Nielsen J, Maury J. 2010. Characterization of different promoters for designing a new expression vector in Saccharomyces cerevisiae. Yeast. 27:955-964.
99. Monje-Casas F, Michan C, Pueyo C. 2004. Absolute transcript levels of thioredoxin- and glutathione-dependent redox systems in Saccharomyces cerevisiae: response to stress and modulation with growth. Biochem. J. 383:139-147.
100. De Deken RH. 1966. The Crabtree effect: a regulatory system in yeast. J. Gen. Microbiol. 44:149-156.
101. Kitagaki H. 2009. Mitochondrial-morphology-targeted breeding of industrial yeast strains for alcohol fermentation. Biotechnol. Appl. Biochem. 53:145-153.
102. Magrath C, Hyman LE. 1999. A mutation in GRS1, a glycyl-tRNA synthetase, affects 3′-end formation in Saccharomyces cerevisiae. Genetics. 152:129-141.
103. Wohlgemuth I, Pohl C, Rodnina MV. 2010. Optimization of speed and accuracy of decoding in translation. EMBO J. 29:3701-3709.
104. Meriin AB, Mense M, Colbert JD, Liang F, Bihler H, Zaarur N, Rock KL, Sherman MY. 2012. A novel approach to recovery of function of mutant proteins by slowing down translation. J. Biol. Chem. 287:34264-34272.
105. Pilpel Y, Mahlab S, Linial M. 2014. Speed controls in translating secretory proteins in eukaryotes - an evolutionary perspective. PLoS Computational Biology. 10:e1003294.
106. Novoa EM, Ribas de Pouplana L. 2012. Speeding with control: codon usage, tRNAs, and ribosomes. Trends Genet. 28:574-581.
107. Piškur J. 2001. Origin of the duplicated regions in the yeast genomes. Trends Genet. 17:302-303.
108. Hagman A, Piškur J. 2015. A Study on the fundamental mechanism and the evolutionary driving forces behind aerobic fermentation in yeast. PLoS One. 10:e0116942.
109. Lynch M, Conery JS. 2000. The evolutionary fate and consequences of duplicate genes. Science. 290:1151-1155.
110. Ohno S. 1970. Evolution by gene duplication. New York: Springer Verlag.
111. Zhang J. 2003. Evolution by gene duplication: an update. Trends in Ecology & Evolution. 18:292-298.
112. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics. 151:1531-1545.
113. Hughes AL. 1994. The evolution of functionally novel proteins after gene duplication. Proc. Biol. Sci. 256:119-124.
114. Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV. 2002. Selection in the evolution of gene duplications. Genome Biol. 3:RESEARCH0008.
115. Withers M, Wernisch L, Dos Reis M. 2006. Archaeology and evolution of transfer RNA genes in the Escherichia coli genome. RNA. 12: 933-942.
116. Blank LM, Lehmbeck F, Sauer U. 2005. Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts. FEMS Yeast Res. 5:545-558.
117. Hagman A, Sall T, Compagno C, Piškur J. 2013. Yeast "make-accumulate-consume" life strategy evolved as a multi-step process that predates the whole genome duplication. PLoS One. 8:e68734.
118. Thompson JD, Higgins DG, Gibson TJ. 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. 22:4673–4680.
119. Byrne KP, Wolfe KH. 2005. The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Research. 15:1456-1461.

指導教授

王健家、王紹文(Chien-Chia Wang Shao-Win Wang)

審核日期

2015-7-31

推文