tRNA synthetase counteracts c-Myc to develop functional vasculature

Shi, Yi; Xu, Xiaoling; Zhang, Qian; Fu, Guangsen; Mo, Zhongying; Wang, George S; Kishi, Shuji; Yang, Xiang-Lei

doi:10.7554/elife.02349

Cited by 89 publications

(121 citation statements)

References 39 publications

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“…Systematic investigation of disease-associated mutations in aaRSs is needed to ascertain their structural and functional characteristics potentially causing unusual binding (for example, protein-protein interactions) or aminoacylation behaviors. A recent case in point is that human SerRS has been demonstrated to bind to the promoter of vascular endothelial growth factor A to carry out its angiogenic functions (60). Such studies may offer a new perspective on the relevant causes of CMT.…”

Section: Discussionmentioning

confidence: 99%

Large Conformational Changes of Insertion 3 in Human Glycyl-tRNA Synthetase (hGlyRS) during Catalysis

Deng

Qin

Chen

et al. 2016

Journal of Biological Chemistry

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Glycyl-tRNA synthetase (GlyRS) is the enzyme that covalently links glycine to cognate tRNA for translation. It is of great research interest because of its nonconserved quaternary structures, unique species-specific aminoacylation properties, and noncanonical functions in neurological diseases, but none of these is fully understood. We report two crystal structures of human GlyRS variants, in the free form and in complex with tRNA Gly respectively, and reveal new aspects of the glycylation mechanism. We discover that insertion 3 differs considerably in conformation in catalysis and that it acts like a "switch" and fully opens to allow tRNA to bind in a cross-subunit fashion. The flexibility of the protein is supported by molecular dynamics simulation, as well as enzymatic activity assays. The biophysical and biochemical studies suggest that human GlyRS may utilize its flexibility for both the traditional function (regulate tRNA binding) and alternative functions (roles in diseases). Aminoacyl-tRNA synthetases (aaRSs)2 play essential roles in mediating genetic information transfer from mRNAs to proteins and attach amino acids to their cognate tRNA molecules in a two-step reaction. In the first step of the reaction, the enzymes catalyze the condensation between ATP and the specific amino acid to generate an aminoacyl-adenylate intermediate. In the second, they transfer the activated amino acid to the acceptor stem of cognate tRNA to form the product aminoacyl-tRNA. The 20 aaRSs can be grouped into two distinct classes based of the conservation of primary sequences and quaternary structures (1-7). Glycyl-tRNA synthetase (GlyRS) is a class II enzyme and possesses three conserved signature motifs at the active site. However, different from other aaRSs, the quaternary structures of GlyRSs are not conserved phylogenetically. Two oligomeric forms have been discovered in nature: whereas eukaryotic and archaeal GlyRSs form ␣2 homodimers and belong to subclass IIa, their eubacterial counterparts form ␣2␤2 heterotetramers and belong to subclass . No significant sequence homology can be found between the two subtypes. In addition to the sequence and structure diversity, studies also show that GlyRSs only aminoacylate tRNA molecules within their own kingdoms, and crossspecies glycylation is rare. This phenomenon may be attributed to the distinct discriminator base at position 73. In eukaryotes, it is an adenosine that precedes the 3Ј-CCA end, whereas in prokaryotes, a uridine is present (9,11,14,15). Therefore, the tRNA recognition mode is an interesting problem, but it is poorly understood.The human GlyRS (hGlyRS) is a class IIa synthetase and forms a homodimer using motif 1. Motifs 2 and 3, on the other hand, are responsible for recognizing the substrates glycine and ATP. Additionally, hGlyRS features an N-terminal WHEP-TRS domain, as well as several insertion domains named insertions 1-3 (9, 16), most of which are flexible in structure (17). Recent studies have shown that aaRSs have developed functions other than aminoacyl...

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Section: Discussionmentioning

confidence: 99%

Large Conformational Changes of Insertion 3 in Human Glycyl-tRNA Synthetase (hGlyRS) during Catalysis

Deng

Qin

Chen

et al. 2016

Journal of Biological Chemistry

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“…Recently, AARSs have been implicated in specific physiological responses, such as apoptosis (2), cellular growth (3), and angiogenesis (4). Tyrosyl-tRNA synthetase (TyrRS or YARS) is conserved in eukaryotes ranging from insects to humans, and multiple mutations have been identified in its catalytic domain.…”

Section: Dna Damage Repairmentioning

confidence: 99%

Acetylation promotes TyrRS nuclear translocation to prevent oxidative damage

Cao

Xiao

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Tyrosyl-tRNA synthetase (TyrRS) is well known for its essential aminoacylation function in protein synthesis. Recently, TyrRS has been shown to translocate to the nucleus and protect against DNA damage due to oxidative stress. However, the mechanism of TyrRS nuclear localization has not yet been determined. Herein, we report that TyrRS becomes highly acetylated in response to oxidative stress, which promotes nuclear translocation. Moreover, p300/ CBP-associated factor (PCAF), an acetyltransferase, and sirtuin 1 (SIRT1), a NAD + -dependent deacetylase, regulate the nuclear localization of TyrRS in an acetylation-dependent manner. Oxidative stress increases the level of PCAF and decreases the level of SIRT1 and deacetylase activity, all of which promote the nuclear translocation of hyperacetylated TyrRS. Furthermore, TyrRS is primarily acetylated on the K244 residue near the nuclear localization signal (NLS), and acetylation inhibits the aminoacylation activity of TyrRS. Molecular dynamics simulations have shown that the in silico acetylation of K244 induces conformational changes in TyrRS near the NLS, which may promote the nuclear translocation of acetylated TyrRS. Herein, we show that the acetylated K244 residue of TyrRS protects against DNA damage in mammalian cells and zebrafish by activating DNA repair genes downstream of transcription factor E2F1. Our study reveals a previously unknown mechanism by which acetylation regulates an aminoacyl-tRNA synthetase, thus affecting the repair pathways for damaged DNA.

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“…Several AARSs were reported to bind to DNA [16, 18, 19]. In this section, we introduce the use of genomic DNA linked cellulose beads to determine the DNA binding capacity of an AARS.…”

Section: Dna-cellulose Pull-down Assay Protocolmentioning

confidence: 99%

Studying nuclear functions of aminoacyl tRNA synthetases

Shi

Wei

Yang

2017

Methods

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Aminoacyl tRNA synthetases (AARSs) are best known for their essential role in translation in the cytoplasm. The concept that AARSs also exist in the nucleus started to draw attention around the turn of the new millennium, when aminoacylated tRNAs were first found in the nuclei of Xenopus oocytes. It is now expected that all cytoplasmic AARSs are present in the nucleus. In addition to tRNA aminoacylation, nuclear AARSs were found to regulate a spectrum of biological processes and responses, with many AARSs functioning through regulation at the level of gene transcription. In this paper, we focus on describing methods that have been successfully implemented to study AARSs in transcriptional regulation. These include a cell fractionation assay to detect nuclear localization, an in vitro DNA-cellulose pull-down assay to determine DNA binding capacity, and a chromatin immunoprecipitation (ChIP)-DNA deep sequencing assay to identify DNA binding sites. Application of these methods would expand our understanding of AARS functions and reveal critical insights on the coordination of gene transcription and translation.

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tRNA synthetase counteracts c-Myc to develop functional vasculature

Cited by 89 publications

References 39 publications

Large Conformational Changes of Insertion 3 in Human Glycyl-tRNA Synthetase (hGlyRS) during Catalysis

Large Conformational Changes of Insertion 3 in Human Glycyl-tRNA Synthetase (hGlyRS) during Catalysis

Acetylation promotes TyrRS nuclear translocation to prevent oxidative damage

Studying nuclear functions of aminoacyl tRNA synthetases

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