酵母菌組蛋白的物種專一性生物素化

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：4

、訪客IP：3.142.249.238

姓名

唐蒂琪(Duong Ngoc Kieu Thi) 查詢紙本館藏

畢業系所

生命科學系

論文名稱

酵母菌組蛋白的物種專一性生物素化
(Species-specific biotinylation of yeast histones)

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
★ 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	★ 酵母菌轉譯起始機制的研究

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)

x中文摘要

生物素化是種必需的維生素與蛋白質的特定賴氨酸殘基共價結合的生物素化作用，由酵母中的生物素蛋白連接酶（BPL1）介導。生物素化是一種罕見的翻譯後修飾，通常發生在位於廣泛分化物種中羧化酶內共有序列（A / V）MKM中的特定賴氨酸殘基上。雖然釀酒酵母的Arc1p缺少共有序列（A / V）MKM，但它在其SSKD處被生物素化。更有趣的是，儘管白色念珠菌（CaH2B）的組蛋白蛋白缺乏（A / V）MKM和SSKD，它們可以在體內生物素化，而釀酒酵母（ScH2B）的組蛋白不能。從Western blot檢測HRP-Streptavidin，我們的結果表明，CaH2B的生物素化似乎是溫度依賴性的;將生長溫度從20℃升高至37℃顯著增加其生物素化水平。基於外源生物素補充劑（〜0.2μg/ L至200μg/ L）的增強，組蛋白的生物素化水平也增加。儘管測試了10種BPL1（ScBPL1，CaBPL1，SpBPL1，PsBPL1，VpBPL1，KlBPL1，LeBPL1，PgBPL1，TpBPL1 ，DhBPL1）可以成功替代ScBPL1敲除菌株，但是它們都不能在釀酒酵母體內對天然組蛋白或CaH2B轉化體進行生物素化。然而，體外生物素化測定結果表明，CaBPL1和ScBPL1都能直接將生物素附著到組蛋白H2B上。這些結果表明釀酒酵母可能含有它們自己的機制來抑制生物素蛋白連接酶在體內對蛋白質組蛋白的生物素化。
關鍵詞：組蛋白，H2B，生物素蛋白連接酶，白色念珠菌，生物素化

摘要(英)

Abstract

Biotinylation, which is covalent binding of a biotin - an essential vitamin to a specific lysine residue of a protein, is mediated by biotin protein ligase (BPL1) in yeast. Biotinylation is a rare post-translational modification and normally occurs in a specific lysine residue positioned in the consensus sequence (A/V)MKM within carboxylases in widely divergent species. While Arc1p of Saccharomyces cerevisiae lacks the consensus sequence (A/V)MKM, it is biotinylated at its SSKD. More interestingly, even though the histone proteins of Candida albicans (CaH2B) lack both (A/V)MKM and SSKD, they can be biotinylated in vivo while histone proteins of S. cerevisiae (ScH2B) cannot. Judging from Western blot probed with HRP-Streptavidin, our results showed that the biotinylation of CaH2B appears to be temperature-dependent; rising the growth temperature from 20oC to 37oC dramatically increased its biotinylation level. Biotinylation level of histones also increased based on the enhancement of exogenous biotin supplement (~0.2 µg/L to 200 μg/L). Despite ten of BPL1s tested (S. cerevisiae BPL1 INVSc1, C. albicans BPL1 SC 5314, S. pombe BPL1 972, and all wild-type of P. stipitis BPL1, V. polyspora BPL1, K. lactis BPL1, L. elongisporus BPL1, P. guilliermondii BPL1, T. phaffii BPL1, D. hansennii BPL1) can successfully substitute ScBPL1 knockout strain, none of them can biotinylate the native histone protein or CaH2B transformants in S. cerevisiae. However, result from in vitro biotinylation assay showed that both of the CaBPL1 and ScBPL1 could attach biotin into the histone protein H2B directly. These results suggesting that S. cerevisiae might contain their own mechanism to inhibit biotinylation of protein histone by biotin protein ligase in vivo.

Keywords: Histone, H2B, biotin protein ligase, Candida albicans, biotinylation

關鍵字(中)

★ 組蛋白
★ H2B
★ 生物素蛋白連接酶
★ 白色念珠菌
★ 生物素化

關鍵字(英)

★ Histone
★ H2B
★ biotin protein ligase
★ Candida albicans
★ biotinylation

論文目次

Table of Contents

中文摘要 i
Abstract ii
Acknowledgement iii
Table of Contents iv
List of figures vi
List of Tables vii
Abbreviations viii
I. Introduction 1
1. Post-translational modification 1
2. Biotin 1
3. Biotin protein ligase 2
4. Targets of biotinylation 3
5. Biological function of histone biotinylation from various species 5
II. Materials and methods 8
1. Strains and culture media 8
2. Plasmid constructions 8
3. Complementation assays for cytoplasmic function and in vivo biotinylation assays 9
4. Western blot with HRP-anti-His6 Ab, HRP-anti mouse IgG-anti H2B, Streptavidin-HRP 10
5. Purification of His6-tagged Proteins 11
6. In vitro biotinylation assays 13
III. Results 14
1. Only C. albicans histones are biotinylated among 10 yeast species tested 14
2. Biotinylation of histone in C. albicans is biotin concentration dependent 14
3. Biotinylation of histone in C. albicans is temperature dependent 15
4. Rescue of ScBPL1 knockout strain by BPL1s of other yeasts in vivo 15
5. Co-transformation of CaH2B and yeast BPL1s into a ScBPL1 knockout strain 16
6. Purification of BPL1 and H2B 17
7. In vitro biotinylation of H2B by BPL1 18
IV. Discussion 19
FIGURES 23
TABLES 32
REFERENCES 33
Appendixes 36
Appendix 1. Schematic structure of the three classes biotin protein ligase 36
Appendix 2. Sequence alignment of the biotin domains of biotin carboxylase from diverse organisms. 36
Appendix 3. Biotinylation of Arc1p. 37
Appendix 4. Sequence of C. albicans Histone H2B. The sites of biotinylation are in bold 38
Appendix 5. Sequence of C. albicans Histone H4. The sites of biotinylation are in bold 38
Appendix 6. Plasmid list 39

參考文獻

REFERENCES

1. Madsen, C. T., Sylvestersen, K. B., Young, C., Larsen, S. C., Poulsen, J. W., Andersen, M. A., Palmqvist, E. A., Hey-Mogensen, M., Jensen, P. B., Treebak, J. T., Lisby, M., and Nielsen, M. L. (2015) Biotin starvation causes mitochondrial protein hyperacetylation and partial rescue by the SIRT3-like deacetylase Hst4p. Nat Commun 6, 7726
2. Chapman-Smith, A., and Cronan, J. E., Jr. (1999) In vivo enzymatic protein biotinylation. Biomol Eng 16, 119-125
3. Sternicki, L. M., Wegener, K. L., Bruning, J. B., Booker, G. W., and Polyak, S. W. (2017) Mechanisms Governing Precise Protein Biotinylation. Trends Biochem Sci 42, 383-394
4. Tong, L. (2013) Structure and function of biotin-dependent carboxylases. Cell Mol Life Sci 70, 863-891
5. Healy, S., Perez-Cadahia, B., Jia, D., McDonald, M. K., Davie, J. R., and Gravel, R. A. (2009) Biotin is not a natural histone modification. Biochim Biophys Acta 1789, 719-733
6. Chang, C. Y., Chang, C. P., Chakraborty, S., Wang, S. W., Tseng, Y. K., and Wang, C. C. (2016) Modulating the Structure and Function of an Aminoacyl-tRNA Synthetase Cofactor by Biotinylation. J Biol Chem 291, 17102-17111
7. Kim, H. S., Hoja, U., Stolz, J., Sauer, G., and Schweizer, E. (2004) Identification of the tRNA-binding protein Arc1p as a novel target of in vivo biotinylation in Saccharomyces cerevisiae. J Biol Chem 279, 42445-42452
8. Kuroishi, T., Rios-Avila, L., Pestinger, V., Wijeratne, S. S., and Zempleni, J. (2011) Biotinylation is a natural, albeit rare, modification of human histones. Mol Genet Metab 104, 537-545
9. Camporeale, G., Giordano, E., Rendina, R., JanosZempleni, and Eissenberg, J. C. (2006) Drosophila holocarboxylase synthetase is a chromosomal protein required for normal histone biotinylation, gene transcription patterns, lifespan and heat tolerance. The Journal of Nutrition 136, 2735-2742
10. Hasim, S., Tati, S., Madayiputhiya, N., Nandakumar, R., and Nickerson, K. W. (2013) Histone biotinylation in Candida albicans. FEMS Yeast Res 13, 529-539
11. Peters, D. M., Griffin, J. B., Stanley, J. S., Beck, M. M., and Zempleni, J. (2002) Exposure to UV light causes increased biotinylation of histones in Jurkat cells. American Journal of Phisiology-Cell Physiology 283, c878-c884
12. Shechter, D., Dormann, H. L., Allis, C. D., and Hake, S. B. (2007) Extraction, purification and analysis of histones. Nature protocols 2, 1445-1457
13. Hymes, J., Fleischhauer, K., and Wolf, B. (1995) Biotinylation of histones by human serum biotinidase: assessment of biotinyl-transferase activity in sera from normal individuals and children with biotinidase deficiency. Biochemical and molecular medicine 56, 76-83
14. White, C. L., Suto, R. K., and Luger, K. (2001) Structure of the yeast nucleosome core partical reveals fundamental changes in internucleosome interactions. The EMBO Journal 20, 5207-5218
15. Chang, C. P., Lin, G., Chen, S. J., Chiu, W. C., Chen, W. H., and Wang, C. C. (2008) Promoting the formation of an active synthetase/tRNA complex by a nonspecific tRNA-binding domain. J Biol Chem 283, 30699-30706
16. Dyer, P. N., Edayathumangalam, R. S., White, C. L., Bao, Y., Chakravarthy, S., Muthurajan, U. M., and Luger, K. (2004) Reconstitution of nucleosome core particles from recombinant histones and DNA. Methods in enzymology 375, 23-44
17. Klinker, H., Haas, C., Harrer, N., Becker, P. B., and Mueller-Planitz, F. (2014) Rapid purification of recombinant histones. PloS one 9, e104029
18. Purushothaman, S., Annamalai, K., Tyagi, A. K., and Surolia, A. (2011) Diversity in functional organization of class I and class II biotin protein ligase. PloS one 6, e16850
19. Choi-Rhee, E., Schulman, H., and Cronan, J. E. (2004) Promiscuous protein biotinylation by Escherichia coli biotin protein ligase. Protein Sci 13, 3043-3050
20. Ahmad Hussin, N., Pathirana, R. U., Hasim, S., Tati, S., Scheib-Owens, J. A., and Nickerson, K. W. (2016) Biotin Auxotrophy and Biotin Enhanced Germ Tube Formation in Candida albicans. Microorganisms 4
21. Pendini, N. R., Bailey, L. M., Booker, G. W., Wilce, M. C., Wallace, J. C., and Polyak, S. W. (2008) Biotin protein ligase from Candida albicans: expression, purification and development of a novel assay. Arch Biochem Biophys 479, 163-169
22. Polyak, S. W., Chapman-Smith, A., Brautigan, P. J., and Wallace, J. C. (1999) Biotin protein ligase from Saccharomyces cerevisiae. The N-terminal domain is required for complete activity. J Biol Chem 274, 32847-32854
23. Kobza, K., Sarath, G., and Zempleni, J. (2008) Prokaryotic BirA ligase biotinylates K4, K9, K18 and K23 in histone H3. BMB reports 41, 310-315
24. Athappilly, F. K., and Hendrickson, W. A. (1995) Structure of the biotinyl domain of acetyl-coenzyme A carboxylase determined by MAD phasing. Structure (London, England : 1993) 3, 1407-1419
25. Yao, X., Wei, D., Soden, C., Summers, M. F., and Beckett, D. (1997) Structure of the Carboxy-Terminal Fragment of the Apo-Biotin Carboxyl Carrier Subunit of Escherichia coli Acetyl-CoA Carboxylase. Biochemistry 36, 15089-15100
26. Campeau, E., and Gravel, R. A. (2001) Expression in Escherichia coli of N- and C-terminally deleted human holocarboxylase synthetase. Influence of the N-terminus on biotinylation and identification of a minimum functional protein. J Biol Chem 276, 12310-12316
27. Alva, V., Ammelburg, M., Soding, J., and Lupas, A. N. (2007) On the origin of the histone fold. BMC Struct Biol 7, 17
28. Pick, H., Kilic, S., and Fierz, B. (2014) Engineering chromatin states: chemical and synthetic biology approaches to investigate histone modification function. Biochim Biophys Acta 1839, 644-656
29. Chen, X., Chou, H. H., and Wurtele, E. S. (2013) Holocarboxylase synthetase 1 physically interacts with histone h3 in Arabidopsis. Scientifica (Cairo) 2013, 983501
30. Lemos-Carolino, M., Madeira-Lopes, A., and Van Uden, N. (1982) The temperature profile of the pathogenic yeast Candida albicans. Zeitschrift fur allgemeine Mikrobiologie 22, 705-709
31. Nadeem, S. G., Shafiq, A., Hakim, S. T., Anjum, Y., and U. Kazm, S. (2013) Effect of Growth Media, pH and Temperature on Yeast to Hyphal Transition in Candida albicans. Open Journal of Medical Microbiology 03, 185-192
32. Hazen, K. C., and Cutler, J. E. (1979) Autoregulation of Germ Tube Formation by Candida albicans. Infection and Immunity 24, 661-666
33. J. Steven Stanley, Jacob B. Griffin, and Zempleni, J. (2001) Biotinylation of histones in human cells effects of cell prolifiration. European Journal of Biochemistry 268, 5424-5429
34. Kothapalli, N., Camporeable, G., Kueh, A., Chew, Y. C., Oommen, A. M., Griffin, J. B., and Zempleni, J. Biological functions of biotinylated histones. The Journal of Nutritional Biochemistry 16, 446-448
35. Watts, J. S., Morton, D. G., Kemphues, K. J., and Watts, J. L. (2018) The biotin-ligating protein BPL-1 is critical for lipid biosynthesis and polarization of the Caenorhabditis elegans embryo. J Biol Chem 293, 610-622

指導教授

王健家(Wang Chien-Chia)

審核日期

2018-7-10

推文