AlaRS透過其C端區域結合L構型tRNA的肘部

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安媞卡(Titi Rindi Antika) 查詢紙本館藏

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論文名稱

AlaRS透過其C端區域結合L構型tRNA的肘部
(Evolutionary gain of C-Ala enables AlaRS to target the tRNAAla elbow)

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至系統瀏覽論文 (2024-8-1以後開放)

摘要(中)

Alanyl-tRNA synthetase (AlaRS)是細胞內必要的轉譯酵素之一，它的主要功能是將丙胺酸(alanine)接到相對應的tRNAAla上。AlaRS藉由辨識tRNAAla acceptor stem上的G3:U70鹼基配對來維持其tRNAAla辨識的專一性，這種辨認方式存在幾乎所有物種中。AlaRS的結構含有四個功能區域(包含催化、tRNA辨識、校正、及C-Ala)，而且在演化上一直保持這四個功能區域，因此不論是原核或真核生物的AlaRS都是由四個功能區域組成。然而，不同於胺基端的其他三個功能區域，他們在序列及功能上都非常保守，C端區域 (C-Ala)在序列和功能上有著顯著差異。例如，大腸桿菌C-Ala參與了tRNA結合，並參與AlaRS二聚體的形成，但人類細胞質C-Ala卻不參與tRNA結合，而且人類AlaRS是以單體的形式存在。更有趣的是，人類C-Ala雖然失去結合tRNA的能力，卻獲得DNA結合能力。在本論文中，我們發現線蟲C. elegans細胞質C-Ala同時具有tRNA和DNA的結合能力，而且此 C-Ala 能夠結合許多不同種類的tRNA，但是明顯地偏好tRNAAla。我們進一步的實驗發現線蟲C-Ala 可以專一性地辨識tRNAAla D-loop上的G18。值得注意的是：這二個鹼基在演化上非常保守，且參與了tRNA L構型的形成，因此這二個鹼基也廣泛存在非tRNAAla的D-loop上。雖然線蟲粒線體AlaRS的C-Ala比其細胞質AlaRS的C-Ala 短小許多(大約只有四分之一大小)，卻也可以同時與DNA及其同源tRNAAla D-loop結合。這項研究解釋了C-Ala如何透過與tRNAAla的D-loop結合，促進 AlaRS 的tRNAAla結合能力及胺醯化活性。

摘要(英)

Alanyl-tRNA synthetase (AlaRS) is the enzyme responsible for charging alanine to its cognate tRNAAla. AlaRS is prominent for its ability to specifically recognize tRNAAla through a wobble base pair in the acceptor stem, G3:U70, which is highly conserved in nearly all organisms. AlaRS retains a highly-conserved four-domain structure. Nevertheless, its C-terminal domain (C-Ala) is significantly diverged in sequence and function. For example, E. coli C-Ala mediates tRNA binding and dimerization, while human cytoplasmic C-Ala poorly binds tRNA and forms a monomer. Instead, human C-Ala retains a strong DNA-binding activity. We showed herein that the nematode C. elegans cytoplasmic C-Ala robustly binds both tRNA and DNA. Despite the fact that this C-Ala can bind many different tRNAs with appreciable affinities, with a distinct preference to tRNAAla. As it turns out, Ce-C-Alac specifically recognized the conserved invariant base G18 in the D-loop of tRNAAla through a highly conserved lysine residue, K934. While its mitochondrial counterpart is only one fourth the size of a regular C-Ala domain, it can also bind DNA and its cognate tRNAAla. This study underscores the molecular mechanism of how C-Ala targets AlaRS to the elbow-containing tRNAAla and facilitates its aminoacylation.

關鍵字(中)

★ 丙氨酰-tRNA 合成酶
★ tRNA
★ C-Ala
★ 秀麗隱桿線蟲
★ tRNA 結合區域
★ DNA 結合區域

關鍵字(英)

★ Alanyl-tRNA synthetase
★ tRNA
★ C-Ala
★ C. elegans
★ tRNA-binding domain
★ DNA-binding domain

論文目次

Chinese Abstract v
English Abstract vi
Acknowledgment vii
List of Publications ix
Table of Contents x
List of Figures xiv
List of Tables xv
Abbreviations xvi
Section I: Caenorhabditis elegans C-Ala 1
Chapter I. Introduction 1
1-1. Aminoacyl-tRNAsynthetases are essential in protein synthesis 1
1-2. Alanyl-tRNA synthetase (AlaRS) preserves a conserved four-domain structure 2
1-3. AlaRS recognizes tRNAAla through a G:U base pair 3
1-4. C-Ala possesses diverse functions throughout evolution 6
1-5. Research aims 7
Chapter II. Materials and Methods 9
2-1. Construction of plasmids 9
2-2. Western blotting 10
2-3. Complementation assay 11
2-4. Purification of His6-tagged proteins 12
2-5. In vitro transcription of tRNAAla, biloopAla, and minihelixAla 13
2-6. Aminoacylation assay 14
2-7. Kinetic assay 15
2-8. Electrophoretic mobility shift assay (EMSA) 16
Chapter III. Results 17
3-1. The nematode C. elegans possesses a canonical and a noncanonical AlaRS 17
3-2. Deletion of C-Ala impairs the aminoacylation activity of CeAlaRSc 20
3-3. Fusion of C-Ala to CeAlaRSm selectively enhances its aminoacylation activity toward the L-shaped tRNAAla 23
3-4. C. elegans C-Ala is both a DNA- and a tRNA-binding domain 26
3-5. Lack of an intact C-Ala domain in CeAlaRSm resulted from secondary loss of this domain 29
3-6. C. elegans cytoplasmic and mitochondrial C-Ala domains share little similarity 32
3-7. The N and C subdomains of Ce-C-Alac are responsible for DNA and tRNA binding, respectively 35
3-8. Ce-C-Alac specifically targets the D-loop sequence of CetRNAnAla 36
3-9. Ce-C-Alam also plays an important role in tRNA binding and aminoacylation 44
Chapter IV. Discussion 49
4-1. The amino acid residues liable for G3:U70 recognition are diverged in CeAlaRSm 49
4-2. Distinct features of the prokaryotic and eukaryotic C-Ala domains 50
4-3. The nematode C-Ala is both a tRNA- and a DNA-binding domain 51
4-4. C-Ala plays an important role in tRNA binding and aminoacylation 52
4-5. The D-loop sequence of tRNAAla is recognized by C-Ala 53
4-6. Acquisition (or loss) of C-Ala is an adaptive mechanism to fit the structure of its cognate tRNA 55
4-7. C-Ala of AlaRS is coevolved with the D-loop of tRNAAla 55
Chapter V. Conclusions 57
Section II: Tupanvirus AlaRS 58
Chapter I. Introduction 58
Chapter II. Materials and Methods 60
2-1. Construction of plasmids 60
2-2. Electrophoretic mobility shift assay (EMSA) 60
2-3. Complementation assay on FOA 61
2-4. In vitro transcription of tRNAAla and microAla 61
2-5. Aminoacylation assay 62
Chapter III. Results 64
3-1. TuAlaRS harbors only the aminoacylation domain 64
3-2. TuAlaRS charges tRNAAla and microAla efficiently and specifically 66
3-3. TuAlaRS binds both tRNAAla and microAla robustly 70
3-4. TuAlaRS fails to charge C. elegans mitochondrial microAla 73
3-5. Kinetic parameters for aminoacylation of tRNAAla and microAla by TuAlaRS 73
3-6. P321 and T416 are dispensable for aminoacylation 74
3-7. TuAlaRS can functionally rescue a yeast ALA1 knockout (KO) strain 75
3-8. Phylogenetic relationship of TuAlaRS with other AlaRSs 76
Chapter IV. Discussion 79
4-1. TuAlaRS displays a G3:U70 specificity 79
4-2. Despite lacking C-Ala, TuAlaRS binds tRNAAla robustly 81
4-3. TuAlaRS may have lost its editing and C-Ala domains later during evolution 82
Chapter V. Conclusions 83
Section III: Human tRNAHis-guanylyltransferase 84
Chapter I. Introduction 84
1-1. Two distinct pathways for acquisition of G-1 to tRNAHis 84
1-2. tRNAHis recognition by Thg1 84
1-3. Mechanisms of G-1 addition in eukaryotes and archaea 85
1-4. Each Thg1 subunit possesses two nucleotide-binding pockets 86
1-5. A dual-functional human Thg1 86
Chapter II. Materials and Methods 88
2-1. Gene cloning and protein purification 88
2-2. Primer extension analysis 88
2-3. In vitro transcription of tRNAHis 89
2-4. Aminoacylation assay 90
2-5. GTP incorporation assay 90
2-6. GTPase assay 91
2-7. Complementation assay 91
Chapter III. Results 93
3-1. Mature human mitochondrial tRNAHis contains G-1 93
3-2. ATP/GTP ratios affects GTP incorporation into tRNAmHis by human Thg1 95
3-3. Human Thg1 displays tRNA-inducible GTPase activity 96
3-4. ATP inhibits the GTPase activity of human Thg1 98
3-5. GTPase activity exists in other high-eukaryotic Thg1 enzymes 101
Chapter IV. Discussion 103
4-1. ATP/GTP ratios regulate the number of GTPs incorporated into HstRNAmHis 103
4-2. Human Thg1 displays a tRNA-inducible GTPase activity 103
4-3. Human Thg1’s GTPase activity resides in the adenylylation site 104
4-4. tRNA-inducible GTPase activity exists in high-eukaryotic Thg1 enzymes 107
Chapter V. Conclusions 108
References 109
Supplementary figures
Appendix A: Primer list
Appendix B: Plasmid list

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指導教授

王健家(Wang Chien-Chia)

審核日期

2023-7-18

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