探討酵母菌aminoacyl-tRNA synthetases的生化功能及演化

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張嘉珮(Chia-pei Chang) 查詢紙本館藏

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論文名稱

探討酵母菌aminoacyl-tRNA synthetases的生化功能及演化
(Study of the biological functions and evolution of yeast aminoacyl-tRNA synthetases)

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★ 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

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摘要(中)

先前研究指出酵母菌的一些tRNA synthetase有一富含離胺酸的附加區段，但是在相對應的大腸桿菌酵素中則無，推測此附加區段可能和tRNA結合有關。酵母菌的valyl-tRNA synthetase (ValRS)中也含有N端的附加區段。我們發現這個附加區段具有非專一性的tRNA鍵結能力，刪除此附加區段會影響酵素的tRNA鍵結能力、胺醯化活性、及互補能力，由此可知附加區段對酵素的重要性。如文獻所知，酵母菌使用non-AUG作為轉譯起始點的例子仍不多，我們發現除了AAG及AGG外，其他和AUG只差一個核苷酸的密碼皆可能作為轉譯起始密碼，除此之外我們發現不同的non-AUG轉譯起始密碼可能偏好不同的周圍序列。酵母菌的ALA1基因使用AUG和non-AUG作為轉譯起始密碼同時做出細胞質及粒線體的alanyl-tRNA synthetase (AlaRS)異構酵素，我們想知道其他酵母菌是否也利用類似機制做出AlaRS。結果發現除了Vanderwaltozyma polyspora以外其他酵母菌也都是利用一個基因同時做出細胞質及粒線體的AlaRS異構型，然而在V. polyspora的細胞核中則有兩個不同的AlaRS基因，一個做細胞質酵素，另一個則做粒線體酵素。演化分析發現所有酵母菌的AlaRS都源自於粒線體，因此推測V. polyspora的AlaRS基因可能經歷至少兩次的基因重組，首先源自粒線體的基因獲得細胞質功能成為雙重功能的基因，而其同源基因（源自古生菌）隨即消失，接著雙重功能的基因又經歷全基因體的複製，產生兩個雙功能的基因，最後其中一個保留細胞質功能，另一個則保留粒線體功能。

摘要(英)

Previous studies show that many yeast aminoacyl-tRNA synthetases (aaRSs) contain a lysine-rich polypeptide extension or appended domain, which is absent from their bacterial relatives. Yeast valyl-tRNA synthetase (ValRS) possesses an N-terminal appended domain. This domain acts as an auxiliary tRNA-binding domain. Deletion of this domain from ValRS impaired its tRNA-binding, aminoacylation, and complementation activities. This finding underscores the necessity of an appended domain for functioning of a yeast aaRS. So far, only a few examples of non-AUG initiation have been identified in yeast. Our results show that, except for AAG and AGG, all triplets that differ from AUG by a single nucleotide were able to serve as an initiator in yeast. Moreover, each non-AUG initiator codon appeared to have its own favorite sequence context. In yeast, the ALA1 gene encodes the cytoplasmic and mitochondrial isoforms of AlaRS through alternative initiation from an AUG and an upstream non-AUG codon. Interestingly, except for Vanderwaltozyma polyspora, all yeast species studied contained a single dual-functional AlaRS gene. In contrast, V. polyspora contained two distinct nuclear AlaRS genes, one specifying the cytoplasmic form and the other its mitochondrial counterpart. A phylogenetic analysis revealed that all yeast AlaRS genes, including those in V. polyspora, are of mitochondrial origin. These and other results imply that the AlaRS genes in V. polyspora underwent a major genetic recombination at least twice. First, the mitochondrion-type gene gained cytoplasmic function and became a dual-functional gene, while its orthologue was lost. Later, the dual-functional gene of mitochondrial origin was duplicated into two copies during the whole-genome duplication event, each retaining a single function (cytoplasmic or mitochondrial).

關鍵字(中)

★ 轉譯起始點
★ 附加區段
★ tRNA合成酵素

關鍵字(英)

★ aminoacyl-tRNA synthetase
★ appended domain
★ translation initiator

論文目次

Table of Contents
中文摘要 i
Abstract ii
誌謝 iii
Table of Contents iv
List of Figures vi
List of Tables viii
Overall introduction 1
Chapter I - Promoting the formation of an active synthetase/tRNA complex by a non-specific tRNA-binding domain 6
Abstract 7
Introduction 8
Materials and Methods 11
Results 15
Discussion 21
Chapter II - A single sequence context cannot satisfy all non-AUG initiator codons in yeast 24
Abstract 25
Introduction 26
Materials and Methods 29
Results 32
Discussion 37
Chapter III - Alanyl-tRNA synthetase genes of Vanderwaltozyma polyspora arose from duplication of a dual-functional predecessor of mitochondrial origin 39
Abstract 40
Introduction 41
Materials and Methods 44
Result 47
Discussion 52
Summary 54
References 56
List of Figures
Figure 1. Ads of yeast and human ValRSs. 66
Figure 2. Complementation assays for Wt and mutant yeast VAS1 constructs. 67
Figure 3. Aminoacylation assays for Wt and mutant yeast ValRSs. 68
Figure 4. Gel mobility-shift assays for the tRNA-binding activities of the Ad, and Wt and mutant yeast ValRSs. 69
Figure 5. Converting E. coli GlnRS into a functional yeast enzyme. 71
Figure 6. Rescuing a defective yeast ValRS mutant with the Ad of human ValRS. 72
Figure 7. Screening for all feasible non-AUG initiation codons. 73
Figure 8. Comparing the efficiencies of various non-AUG initiator codons in ALA1. 75
Figure 9. Rescuing a cryptic translation initiation site in ALA1. 76
Figure 10. Comparing the efficiencies of various non-AUG initiator codons in GRS1. 78
Figure 11. Comparison of the efficiencies of various non-AUG initiator codons using lacZ as a reporter. 79
Figure 12. Alignment of N-terminal presequences of yeast AlaRSs. 81
Figure 13. Comparison of the acceptor stems of yeast tRNAAla isoacceptors. 82
Figure 14. Cross-specific complementation assays for various yeast AlaRS genes. 83
Figure 15. Mapping of the translation initiator codons of VpALA1 and VpALA2. 84
Figure 16. Analysis of endogenous VpALA1 and VpALA2 mRNAs by RT-PCR. 85
Figure 17. Phylogenetic analysis of the relationships of VpAlaRS1, VpAlaRS2, and other AlaRSs. 86
List of Tables
Table 1: Kinetic parameters for aminoacylation of tRNAVal by wild-type and mutant ValRSa 87

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指導教授

王健家(Chien-chia Wang)

審核日期

2011-6-29

推文