Genes

Research

Jump to: Review

14 pages, 14465 KiB

Open AccessArticle

Tryptophan Depletion Modulates Tryptophanyl-tRNA Synthetase-Mediated High-Affinity Tryptophan Uptake into Human Cells

by Takumi Yokosawa, Aomi Sato and Keisuke Wakasugi

Genes 2020, 11(12), 1423; https://doi.org/10.3390/genes11121423 - 27 Nov 2020

Cited by 3 | Viewed by 2565

Abstract

The novel high-affinity tryptophan (Trp)-selective transport system is present at elevated levels in human interferon-γ (IFN-γ)-treated and indoleamine 2,3-dioxygenase 1 (IDO1)-expressing cells. High-affinity Trp uptake into cells results in extracellular Trp depletion and immune suppression. We have previously shown that both IDO1 and [...] Read more.

The novel high-affinity tryptophan (Trp)-selective transport system is present at elevated levels in human interferon-γ (IFN-γ)-treated and indoleamine 2,3-dioxygenase 1 (IDO1)-expressing cells. High-affinity Trp uptake into cells results in extracellular Trp depletion and immune suppression. We have previously shown that both IDO1 and tryptophanyl-tRNA synthetase (TrpRS), whose expression levels are increased by IFN-γ, have a crucial function in high-affinity Trp uptake into human cells. Here, we aimed to elucidate the relationship between TrpRS and IDO1 in high-affinity Trp uptake. We demonstrated that overexpression of IDO1 in HeLa cells drastically enhances high-affinity Trp uptake upon addition of purified TrpRS protein to uptake assay buffer. We also clarified that high-affinity Trp uptake by Trp-starved cells is significantly enhanced by the addition of TrpRS protein to the assay buffer. Moreover, we showed that high-affinity Trp uptake is also markedly elevated by the addition of TrpRS protein to the assay buffer of cells overexpressing another Trp-metabolizing enzyme, tryptophan 2,3-dioxygenase (TDO2). Taken together, we conclude that Trp deficiency is crucial for high-affinity Trp uptake mediated by extracellular TrpRS. Full article

(This article belongs to the Special Issue tRNAs in Biology)

► Show Figures

Figure 1

22 pages, 3434 KiB

Open AccessArticle

Multi-Omics Database Analysis of Aminoacyl-tRNA Synthetases in Cancer

by Justin Wang, Ingrid Vallee, Aditi Dutta, Yu Wang, Zhongying Mo, Ze Liu, Haissi Cui, Andrew I. Su and Xiang-Lei Yang

Genes 2020, 11(11), 1384; https://doi.org/10.3390/genes11111384 - 22 Nov 2020

Cited by 13 | Viewed by 3375

Abstract

Aminoacyl-tRNA synthetases (aaRSs) are key enzymes in the mRNA translation machinery, yet they possess numerous non-canonical functions developed during the evolution of complex organisms. The aaRSs and aaRS-interacting multi-functional proteins (AIMPs) are continually being implicated in tumorigenesis, but these connections are often limited [...] Read more.

Aminoacyl-tRNA synthetases (aaRSs) are key enzymes in the mRNA translation machinery, yet they possess numerous non-canonical functions developed during the evolution of complex organisms. The aaRSs and aaRS-interacting multi-functional proteins (AIMPs) are continually being implicated in tumorigenesis, but these connections are often limited in scope, focusing on specific aaRSs in distinct cancer subtypes. Here, we analyze publicly available genomic and transcriptomic data on human cytoplasmic and mitochondrial aaRSs across many cancer types. As high-throughput technologies have improved exponentially, large-scale projects have systematically quantified genetic alteration and expression from thousands of cancer patient samples. One such project is the Cancer Genome Atlas (TCGA), which processed over 20,000 primary cancer and matched normal samples from 33 cancer types. The wealth of knowledge provided from this undertaking has streamlined the identification of cancer drivers and suppressors. We examined aaRS expression data produced by the TCGA project and combined this with patient survival data to recognize trends in aaRSs’ impact on cancer both molecularly and prognostically. We further compared these trends to an established tumor suppressor and a proto-oncogene. We observed apparent upregulation of many tRNA synthetase genes with aggressive cancer types, yet, at the individual gene level, some aaRSs resemble a tumor suppressor while others show similarities to an oncogene. This study provides an unbiased, overarching perspective on the relationship of aaRSs with cancers and identifies certain aaRS family members as promising therapeutic targets or potential leads for developing biological therapy for cancer. Full article

(This article belongs to the Special Issue tRNAs in Biology)

► Show Figures

Figure 1

12 pages, 1569 KiB

Open AccessArticle

A Novel Aminoacyl-tRNA Synthetase Appended Domain Can Supply the Core Synthetase with Its Amino Acid Substrate

by Marc Muraski, Emil Nilsson, Benjamin Weekley, Sandhya Bharti Sharma and Rebecca W. Alexander

Genes 2020, 11(11), 1320; https://doi.org/10.3390/genes11111320 - 07 Nov 2020

Viewed by 2475

Abstract

The structural organization and functionality of aminoacyl-tRNA synthetases have been expanded through polypeptide additions to their core aminoacylation domain. We have identified a novel domain appended to the methionyl-tRNA synthetase (MetRS) of the intracellular pathogen Mycoplasma penetrans. Sequence analysis of this N-terminal [...] Read more.

The structural organization and functionality of aminoacyl-tRNA synthetases have been expanded through polypeptide additions to their core aminoacylation domain. We have identified a novel domain appended to the methionyl-tRNA synthetase (MetRS) of the intracellular pathogen Mycoplasma penetrans. Sequence analysis of this N-terminal region suggests the appended domain is an aminotransferase, which we demonstrate here. The aminotransferase domain of MpMetRS is capable of generating methionine from its α-keto acid analog, 2-keto-4-methylthiobutyrate (KMTB). The methionine thus produced can be subsequently attached to cognate tRNA^Met in the MpMetRS aminoacylation domain. Genomic erosion in the Mycoplasma species has impaired many canonical biosynthetic pathways, causing them to rely on their host for numerous metabolites. It is still unclear if this bifunctional MetRS is a key part of pathogen life cycle or is a neutral consequence of the reductive evolution experienced by Mycoplasma species. Full article

(This article belongs to the Special Issue tRNAs in Biology)

► Show Figures

Figure 1

17 pages, 2265 KiB

Open AccessArticle

Fine-Tuning of Alanyl-tRNA Synthetase Quality Control Alleviates Global Dysregulation of the Proteome

by Paul Kelly, Arundhati Kavoor and Michael Ibba

Genes 2020, 11(10), 1222; https://doi.org/10.3390/genes11101222 - 18 Oct 2020

Cited by 2 | Viewed by 2581

Abstract

One integral step in the transition from a nucleic acid encoded-genome to functional proteins is the aminoacylation of tRNA molecules. To perform this activity, aminoacyl-tRNA synthetases (aaRSs) activate free amino acids in the cell forming an aminoacyl-adenylate before transferring the amino acid on [...] Read more.

One integral step in the transition from a nucleic acid encoded-genome to functional proteins is the aminoacylation of tRNA molecules. To perform this activity, aminoacyl-tRNA synthetases (aaRSs) activate free amino acids in the cell forming an aminoacyl-adenylate before transferring the amino acid on to its cognate tRNA. These newly formed aminoacyl-tRNA (aa-tRNA) can then be used by the ribosome during mRNA decoding. In Escherichia coli, there are twenty aaRSs encoded in the genome, each of which corresponds to one of the twenty proteinogenic amino acids used in translation. Given the shared chemicophysical properties of many amino acids, aaRSs have evolved mechanisms to prevent erroneous aa-tRNA formation with non-cognate amino acid substrates. Of particular interest is the post-transfer proofreading activity of alanyl-tRNA synthetase (AlaRS) which prevents the accumulation of Ser-tRNA^Ala and Gly-tRNA^Ala in the cell. We have previously shown that defects in AlaRS proofreading of Ser-tRNA^Ala lead to global dysregulation of the E. coli proteome, subsequently causing defects in growth, motility, and antibiotic sensitivity. Here we report second-site AlaRS suppressor mutations that alleviate the aforementioned phenotypes, revealing previously uncharacterized residues within the AlaRS proofreading domain that function in quality control. Full article

(This article belongs to the Special Issue tRNAs in Biology)

► Show Figures

Figure 1

15 pages, 1580 KiB

Open AccessArticle

A Label-Free Assay for Aminoacylation of tRNA

by Howard Gamper and Ya-Ming Hou

Genes 2020, 11(10), 1173; https://doi.org/10.3390/genes11101173 - 07 Oct 2020

Cited by 6 | Viewed by 5786

Abstract

Aminoacylation of tRNA generates an aminoacyl-tRNA (aa-tRNA) that is active for protein synthesis on the ribosome. Quantification of aminoacylation of tRNA is critical to understand the mechanism of specificity and the flux of the aa-tRNA into the protein synthesis machinery, which determines the [...] Read more.

Aminoacylation of tRNA generates an aminoacyl-tRNA (aa-tRNA) that is active for protein synthesis on the ribosome. Quantification of aminoacylation of tRNA is critical to understand the mechanism of specificity and the flux of the aa-tRNA into the protein synthesis machinery, which determines the rate of cell growth. Traditional assays for the quantification of tRNA aminoacylation involve radioactivity, either with a radioactive amino acid or with a [3′-³²P]-labeled tRNA. We describe here a label-free assay that monitors aminoacylation by biotinylation-streptavidin (SA) conjugation to the α-amine or the α-imine of the aminoacyl group on the aa-tRNA. The conjugated aa-tRNA product is readily separated from the unreacted tRNA by a denaturing polyacrylamide gel, allowing for quantitative measurement of aminoacylation. This label-free assay is applicable to a wide range of amino acids and tRNA sequences and to both classes of aminoacylation. It is more sensitive and robust than the assay with a radioactive amino acid and has the potential to explore a wider range of tRNA than the assay with a [3′-³²P]-labeled tRNA. This label-free assay reports kinetic parameters of aminoacylation quantitatively similar to those reported by using a radioactive amino acid, suggesting its broad applicability to research relevant to human health and disease. Full article

(This article belongs to the Special Issue tRNAs in Biology)

► Show Figures

Figure 1

13 pages, 3597 KiB

Open AccessArticle

Plant-Specific Domains and Fragmented Sequences Imply Non-Canonical Functions in Plant Aminoacyl-tRNA Synthetases

by Yusuke Saga, Moeka Kawashima, Shiho Sakai, Kaori Yamazaki, Misato Kaneko, Moeka Takahashi, Natsuko Sato, Yohei Toyoda, Shohei Takase, Takeshi Nakano, Naoto Kawakami and Tetsuo Kushiro

Genes 2020, 11(9), 1056; https://doi.org/10.3390/genes11091056 - 07 Sep 2020

Cited by 2 | Viewed by 2698

Abstract

Aminoacyl-tRNA synthetases (aaRSs) play essential roles in protein translation. In addition, numerous aaRSs (mostly in vertebrates) have also been discovered to possess a range of non-canonical functions. Very few studies have been conducted to elucidate or characterize non-canonical functions of plant aaRSs. A [...] Read more.

Aminoacyl-tRNA synthetases (aaRSs) play essential roles in protein translation. In addition, numerous aaRSs (mostly in vertebrates) have also been discovered to possess a range of non-canonical functions. Very few studies have been conducted to elucidate or characterize non-canonical functions of plant aaRSs. A genome-wide search for aaRS genes in Arabidopsis thaliana revealed a total of 59 aaRS genes. Among them, asparaginyl-tRNA synthetase (AsnRS) was found to possess a WHEP domain inserted into the catalytic domain in a plant-specific manner. This insertion was observed only in the cytosolic isoform. In addition, a long stretch of sequence that exhibited weak homology with histidine ammonia lyase (HAL) was found at the N-terminus of histidyl-tRNA synthetase (HisRS). This HAL-like domain has only been seen in plant HisRS, and only in cytosolic isoforms. Additionally, a number of genes lacking minor or major portions of the full-length aaRS sequence were found. These genes encode 14 aaRS fragments that lack key active site sequences and are likely catalytically null. These identified genes that encode plant-specific additional domains or aaRS fragment sequences are candidates for aaRSs possessing non-canonical functions. Full article

(This article belongs to the Special Issue tRNAs in Biology)

► Show Figures

Graphical abstract

Review

Jump to: Research

20 pages, 2044 KiB

Open AccessReview

Drosophila Models for Charcot–Marie–Tooth Neuropathy Related to Aminoacyl-tRNA Synthetases

by Laura Morant, Maria-Luise Erfurth and Albena Jordanova

Genes 2021, 12(10), 1519; https://doi.org/10.3390/genes12101519 - 27 Sep 2021

Cited by 6 | Viewed by 3087

Abstract

Aminoacyl-tRNA synthetases (aaRS) represent the largest cluster of proteins implicated in Charcot–Marie–Tooth neuropathy (CMT), the most common neuromuscular disorder. Dominant mutations in six aaRS cause different axonal CMT subtypes with common clinical characteristics, including progressive distal muscle weakness and wasting, impaired sensory modalities, [...] Read more.

Aminoacyl-tRNA synthetases (aaRS) represent the largest cluster of proteins implicated in Charcot–Marie–Tooth neuropathy (CMT), the most common neuromuscular disorder. Dominant mutations in six aaRS cause different axonal CMT subtypes with common clinical characteristics, including progressive distal muscle weakness and wasting, impaired sensory modalities, gait problems and skeletal deformities. These clinical manifestations are caused by “dying back” axonal degeneration of the longest peripheral sensory and motor neurons. Surprisingly, loss of aminoacylation activity is not a prerequisite for CMT to occur, suggesting a gain-of-function disease mechanism. Here, we present the Drosophila melanogaster disease models that have been developed to understand the molecular pathway(s) underlying GARS1- and YARS1-associated CMT etiology. Expression of dominant CMT mutations in these aaRSs induced comparable neurodegenerative phenotypes, both in larvae and adult animals. Interestingly, recent data suggests that shared molecular pathways, such as dysregulation of global protein synthesis, might play a role in disease pathology. In addition, it has been demonstrated that the important function of nuclear YARS1 in transcriptional regulation and the binding properties of mutant GARS1 are also conserved and can be studied in D. melanogaster in the context of CMT. Taken together, the fly has emerged as a faithful companion model for cellular and molecular studies of aaRS-CMT that also enables in vivo investigation of candidate CMT drugs. Full article

(This article belongs to the Special Issue tRNAs in Biology)

► Show Figures

Figure 1

21 pages, 1852 KiB

Open AccessEditor’s ChoiceReview

Inosine in Biology and Disease

by Sundaramoorthy Srinivasan, Adrian Gabriel Torres and Lluís Ribas de Pouplana

Genes 2021, 12(4), 600; https://doi.org/10.3390/genes12040600 - 19 Apr 2021

Cited by 48 | Viewed by 9789

Abstract

The nucleoside inosine plays an important role in purine biosynthesis, gene translation, and modulation of the fate of RNAs. The editing of adenosine to inosine is a widespread post-transcriptional modification in transfer RNAs (tRNAs) and messenger RNAs (mRNAs). At the wobble position of [...] Read more.

The nucleoside inosine plays an important role in purine biosynthesis, gene translation, and modulation of the fate of RNAs. The editing of adenosine to inosine is a widespread post-transcriptional modification in transfer RNAs (tRNAs) and messenger RNAs (mRNAs). At the wobble position of tRNA anticodons, inosine profoundly modifies codon recognition, while in mRNA, inosines can modify the sequence of the translated polypeptide or modulate the stability, localization, and splicing of transcripts. Inosine is also found in non-coding and exogenous RNAs, where it plays key structural and functional roles. In addition, molecular inosine is an important secondary metabolite in purine metabolism that also acts as a molecular messenger in cell signaling pathways. Here, we review the functional roles of inosine in biology and their connections to human health. Full article

(This article belongs to the Special Issue tRNAs in Biology)

► Show Figures

Figure 1

14 pages, 976 KiB

Open AccessReview

Did Amino Acid Side Chain Reactivity Dictate the Composition and Timing of Aminoacyl-tRNA Synthetase Evolution?

by Tamara L. Hendrickson, Whitney N. Wood and Udumbara M. Rathnayake

Genes 2021, 12(3), 409; https://doi.org/10.3390/genes12030409 - 12 Mar 2021

Cited by 5 | Viewed by 2468

Abstract

The twenty amino acids in the standard genetic code were fixed prior to the last universal common ancestor (LUCA). Factors that guided this selection included establishment of pathways for their metabolic synthesis and the concomitant fixation of substrate specificities in the emerging aminoacyl-tRNA [...] Read more.

The twenty amino acids in the standard genetic code were fixed prior to the last universal common ancestor (LUCA). Factors that guided this selection included establishment of pathways for their metabolic synthesis and the concomitant fixation of substrate specificities in the emerging aminoacyl-tRNA synthetases (aaRSs). In this conceptual paper, we propose that the chemical reactivity of some amino acid side chains (e.g., lysine, cysteine, homocysteine, ornithine, homoserine, and selenocysteine) delayed or prohibited the emergence of the corresponding aaRSs and helped define the amino acids in the standard genetic code. We also consider the possibility that amino acid chemistry delayed the emergence of the glutaminyl- and asparaginyl-tRNA synthetases, neither of which are ubiquitous in extant organisms. We argue that fundamental chemical principles played critical roles in fixation of some aspects of the genetic code pre- and post-LUCA. Full article

(This article belongs to the Special Issue tRNAs in Biology)

► Show Figures

Figure 1

20 pages, 8662 KiB

Open AccessReview

Localization and RNA Binding of Mitochondrial Aminoacyl tRNA Synthetases

by Shahar Garin, Ofri Levi, Bar Cohen, Adi Golani-Armon and Yoav S. Arava

Genes 2020, 11(10), 1185; https://doi.org/10.3390/genes11101185 - 12 Oct 2020

Cited by 10 | Viewed by 4722

Abstract

Mitochondria contain a complete translation machinery that is used to translate its internally transcribed mRNAs. This machinery uses a distinct set of tRNAs that are charged with cognate amino acids inside the organelle. Interestingly, charging is executed by aminoacyl tRNA synthetases (aaRS) that [...] Read more.

Mitochondria contain a complete translation machinery that is used to translate its internally transcribed mRNAs. This machinery uses a distinct set of tRNAs that are charged with cognate amino acids inside the organelle. Interestingly, charging is executed by aminoacyl tRNA synthetases (aaRS) that are encoded by the nuclear genome, translated in the cytosol, and need to be imported into the mitochondria. Here, we review import mechanisms of these enzymes with emphasis on those that are localized to both mitochondria and cytosol. Furthermore, we describe RNA recognition features of these enzymes and their interaction with tRNA and non-tRNA molecules. The dual localization of mitochondria-destined aaRSs and their association with various RNA types impose diverse impacts on cellular physiology. Yet, the breadth and significance of these functions are not fully resolved. We highlight here possibilities for future explorations. Full article

(This article belongs to the Special Issue tRNAs in Biology)

► Show Figures

Graphical abstract

19 pages, 1573 KiB

Open AccessReview

Extracurricular Functions of tRNA Modifications in Microorganisms

by Ashley M. Edwards, Maame A. Addo and Patricia C. Dos Santos

Genes 2020, 11(8), 907; https://doi.org/10.3390/genes11080907 - 07 Aug 2020

Cited by 14 | Viewed by 4816

Abstract

Transfer RNAs (tRNAs) are essential adaptors that mediate translation of the genetic code. These molecules undergo a variety of post-transcriptional modifications, which expand their chemical reactivity while influencing their structure, stability, and functionality. Chemical modifications to tRNA ensure translational competency and promote cellular [...] Read more.

Transfer RNAs (tRNAs) are essential adaptors that mediate translation of the genetic code. These molecules undergo a variety of post-transcriptional modifications, which expand their chemical reactivity while influencing their structure, stability, and functionality. Chemical modifications to tRNA ensure translational competency and promote cellular viability. Hence, the placement and prevalence of tRNA modifications affects the efficiency of aminoacyl tRNA synthetase (aaRS) reactions, interactions with the ribosome, and transient pairing with messenger RNA (mRNA). The synthesis and abundance of tRNA modifications respond directly and indirectly to a range of environmental and nutritional factors involved in the maintenance of metabolic homeostasis. The dynamic landscape of the tRNA epitranscriptome suggests a role for tRNA modifications as markers of cellular status and regulators of translational capacity. This review discusses the non-canonical roles that tRNA modifications play in central metabolic processes and how their levels are modulated in response to a range of cellular demands. Full article

(This article belongs to the Special Issue tRNAs in Biology)

► Show Figures

Graphical abstract

Journal Menu

Journal Browser

tRNAs in Biology

Share This Special Issue

Special Issue Editors

Special Issue Information

Keywords

Published Papers (11 papers)

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI