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Wang K, Liu CY, Fang B, Li B, Li YH, Xia QQ, Zhao Y, Cheng XL, Yang SM, Zhang MH, Wang K. The function and therapeutic potential of transfer RNA-derived small RNAs in cardiovascular diseases: A review. Pharmacol Res 2024; 206:107279. [PMID: 38942340 DOI: 10.1016/j.phrs.2024.107279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 06/20/2024] [Accepted: 06/20/2024] [Indexed: 06/30/2024]
Abstract
Transfer RNA-derived small RNAs (tsRNAs) are a class of small non-coding RNA (sncRNA) molecules derived from tRNA, including tRNA derived fragments (tRFs) and tRNA halfs (tiRNAs). tsRNAs can affect cell functions by participating in gene expression regulation, translation regulation, intercellular signal transduction, and immune response. They have been shown to play an important role in various human diseases, including cardiovascular diseases (CVDs). Targeted regulation of tsRNAs expression can affect the progression of CVDs. The tsRNAs induced by pathological conditions can be detected when released into the extracellular, giving them enormous potential as disease biomarkers. Here, we review the biogenesis, degradation process and related functional mechanisms of tsRNAs, and discuss the research progress and application prospects of tsRNAs in different CVDs, to provide a new perspective on the treatment of CVDs.
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Affiliation(s)
- Kai Wang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao University, Jinan 250014, China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Cui-Yun Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Bo Fang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Bo Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Ying-Hui Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Qian-Qian Xia
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Yan Zhao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Xue-Li Cheng
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Su-Min Yang
- Department of Cardiovascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266003, China.
| | - Mei-Hua Zhang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao University, Jinan 250014, China.
| | - Kun Wang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao University, Jinan 250014, China; Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China.
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Çiftçi YC, Yurtsever Y, Akgül B. Long non-coding RNA-mediated modulation of endoplasmic reticulum stress under pathological conditions. J Cell Mol Med 2024; 28:e18561. [PMID: 39072992 DOI: 10.1111/jcmm.18561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 06/12/2024] [Accepted: 06/27/2024] [Indexed: 07/30/2024] Open
Abstract
Endoplasmic reticulum (ER) stress, which ensues from an overwhelming protein folding capacity, activates the unfolded protein response (UPR) in an effort to restore cellular homeostasis. As ER stress is associated with numerous diseases, it is highly important to delineate the molecular mechanisms governing the ER stress to gain insight into the disease pathology. Long non-coding RNAs, transcripts with a length of over 200 nucleotides that do not code for proteins, interact with proteins and nucleic acids, fine-tuning the UPR to restore ER homeostasis via various modes of actions. Dysregulation of specific lncRNAs is implicated in the progression of ER stress-related diseases, presenting these molecules as promising therapeutic targets. The comprehensive analysis underscores the importance of understanding the nuanced interplay between lncRNAs and ER stress for insights into disease mechanisms. Overall, this review consolidates current knowledge, identifies research gaps and offers a roadmap for future investigations into the multifaceted roles of lncRNAs in ER stress and associated diseases to shed light on their pivotal roles in the pathogenesis of related diseases.
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Affiliation(s)
- Yusuf Cem Çiftçi
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey
| | - Yiğit Yurtsever
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey
| | - Bünyamin Akgül
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey
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Hou J, Li Q, Wang J, Lu W. tRFs and tRNA Halves: Novel Cellular Defenders in Multiple Biological Processes. Curr Issues Mol Biol 2022; 44:5949-5962. [PMID: 36547066 PMCID: PMC9777342 DOI: 10.3390/cimb44120405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
tRNA fragments derived from angiogenin or Dicer cleavage are referred to as tRNA-derived fragments (tRFs) and tRNA halves. tRFs and tRNA halves have been identified in both eukaryotes and prokaryotes and are precisely cleaved at specific sites on either precursor or mature tRNA transcripts rather than via random degradation. tRFs and tRNA halves are highly involved in regulating transcription and translation in a canonical or non-canonical manner in response to cellular stress. In this review, we summarize the biogenesis and types of tRFs and tRNA halves, clarify the biological functions and molecular mechanisms of tRNA fragments in both physiological and pathological processes with a particular focus on their cytoprotective roles in defending against oxidation and apoptosis, and highlight their potential application as biomarkers in determining cell fate.
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Affiliation(s)
- Jiani Hou
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Qianqing Li
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Jun Wang
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (J.W.); (W.L.); Tel.: +86-0431-84533525; Fax: +861-0431-84533525
| | - Wenfa Lu
- Jilin Provincial International Joint Research Center of Animal Breeding & Reproduction Technology, Jilin Agricultural University, Changchun 130118, China
- Key Lab of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (J.W.); (W.L.); Tel.: +86-0431-84533525; Fax: +861-0431-84533525
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Tian Q, Wang J, Cui L, Zeng W, Qiu G, Hu Q, Peng A, Zhang D, Shen L. Longitudinal physiological and transcriptomic analyses reveal the short term and long term response of Synechocystis sp. PCC6803 to cadmium stress. CHEMOSPHERE 2022; 303:134727. [PMID: 35513082 DOI: 10.1016/j.chemosphere.2022.134727] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Due to the bioaccumulation and non-biodegradability of cadmium, Cd can pose a serious threat to ecosystem even at low concentration. Microalgae is widely distributed photosynthetic organisms in nature, which is a promising heavy metal remover and an effective industrial sewage cleaner. However, there are few detailed reports on the short-term and long-term molecular mechanisms of microalgae under Cd stress. In this study, the adsorption behavior (growth curve, Cd removal efficiency, scanning electron microscope, Fourier transform infrared spectroscopy, and dynamic change of extracellular polymeric substances), cytotoxicity (photosynthetic pigment, MDA, GSH, H2O2, O2-) and stress response mechanism of microalgae were discussed under EC50. RNA-seq detected 1413 DEGs in 4 treatment groups. These genes were related to ribosome, nitrogen metabolism, sulfur transporter, and photosynthesis, and which been proved to be Cd-responsive DEGs. WGCNA (weighted gene co-expression network analysis) revealed two main gene expression patterns, short-term stress (381 genes) and long-term stress (364 genes). The enrichment analysis of DEGs showed that the expression of genes involved in N metabolism, sulfur transporter, and aminoacyl-tRNA biosynthesis were significantly up-regulated. This provided raw material for the synthesis of the important component (cysteine) of metal chelate protein, resistant metalloprotein and transporter (ABC transporter) in the initial stage, which was also the short-term response mechanism. Cd adsorption of the first 15 min was primary dependent on membrane transporter and beforehand accumulated EPS. Simultaneously, the up-regulated glutathione S-transferase (GSTs) family proteins played a role in the initial resistance to exogenous Cd. The damaged photosynthetic system was repaired at the later stage, the expressions of glycolysis and gluconeogenesis were up-regulated, to meet the energy and substances of physiological metabolic activities. The study is the first to provide detailed short-term and long-term genomic information on microalgae responding to Cd stress. Meanwhile, the key genes in this study can be used as potential targets for algae-mediated genetic engineering.
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Affiliation(s)
- Qinghua Tian
- School of Metallurgy and Environment, Central South University, Changsha, Hunan, 410083, China
| | - Junjun Wang
- School of Metallurgy and Environment, Central South University, Changsha, Hunan, 410083, China
| | - Linlin Cui
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, 410083, China
| | - Weimin Zeng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, 410083, China
| | - Guanzhou Qiu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, 410083, China
| | - Qi Hu
- Department of Bioinformatics Center, NEOMICS Institute, Shenzhen, Guangdong, 518118, China
| | - Anan Peng
- School of Environmental and Chemical Engineering, Foshan University, Foshan, 528000, China
| | - Du Zhang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China.
| | - Li Shen
- School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, 410083, China.
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Abstract
Transfer RNAs (tRNAs) are intermediate-sized non-coding RNAs found in all organisms that help translate messenger RNA into protein. Recently, the number of sequenced plant genomes has increased dramatically. The availability of this extensive data greatly accelerates the study of tRNAs on a large scale. Here, 8,768,261 scaffolds/chromosomes containing 229,093 giga-base pairs representing whole-genome sequences of 256 plant species were analyzed to identify tRNA genes. As a result, 331,242 nuclear, 3,216 chloroplast, and 1,467 mitochondrial tRNA genes were identified. The nuclear tRNA genes include 275,134 tRNAs decoding 20 standard amino acids, 1,325 suppressor tRNAs, 6,273 tRNAs with unknown isotypes, 48,475 predicted pseudogenes, and 37,873 tRNAs with introns. Efforts also extended to the creation of PltRNAdb (https://bioinformatics.um6p.ma/PltRNAdb/index.php), a data source for tRNA genes from 256 plant species. PltRNAdb website allows researchers to search, browse, visualize, BLAST, and download predicted tRNA genes. PltRNAdb will help improve our understanding of plant tRNAs and open the door to discovering the unknown regulatory roles of tRNAs in plant genomes.
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Affiliation(s)
- Morad M. Mokhtar
- African Genome Center, University Mohammed VI Polytechnic, Benguerir, Morocco
| | - Achraf EL Allali
- African Genome Center, University Mohammed VI Polytechnic, Benguerir, Morocco
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Proteomic Response of Deinococcus radiodurans to Short-Term Real Microgravity during Parabolic Flight Reveals Altered Abundance of Proteins Involved in Stress Response and Cell Envelope Functions. Life (Basel) 2021; 12:life12010023. [PMID: 35054415 PMCID: PMC8779699 DOI: 10.3390/life12010023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/22/2022] Open
Abstract
Rapidly evolving space exploration makes understanding the short- and long- term effects of microgravity on humans, plants, and microorganisms an important task. The ubiquitous presence of the gravitational force has had an influence on the development of all living entities on Earth, and short- and long-term changes in perceived gravitational force can induce notable changes within cells. Deinococcus radiodurans is the Gram-positive bacterium that is best known for its extreme resistance to UV-C and gamma radiation, oxidation stress, and desiccation. Thus increased interest has been placed on this species in the context of space research. The present study aims to elucidate the short-term proteomic response of this species to real microgravity during parabolic flight. Overnight cultures of D. radiodurans were subjected to microgravity during a single parabola, and metabolic activity was quenched using methanol. Proteins were extracted and subsequently measured using HPLC nESI MS/MS. The results, such as the enrichment of the peptidoglycan biosynthesis pathway with differentially abundant proteins and altered S-layer protein abundance, suggested molecular rearrangements in the cell envelope of D. radiodurans. Altered abundance of proteins involved in energy metabolism and DNA repair could be linked with increased endogenous ROS production that contributes to the stress response. Moreover, changes in protein abundance in response to microgravity show similarities with previously reported stress responses. Thus, the present results could be used to further investigate the complex regulation of the remarkable stress management of this bacterium.
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Zhang J, Li L, Luo L, Yang X, Zhang J, Xie Y, Liang R, Wang W, Lu S. Screening and potential role of tRFs and tiRNAs derived from tRNAs in the carcinogenesis and development of lung adenocarcinoma. Oncol Lett 2021; 22:506. [PMID: 33986867 PMCID: PMC8114470 DOI: 10.3892/ol.2021.12767] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 04/06/2021] [Indexed: 12/11/2022] Open
Abstract
Accumulating evidence has indicated that a group of novel molecules, known as transfer RNA (tRNA)-derived fragments (tRFs) and tRNA halves (tiRNAs), which are derived from tRNAs, serve an essential role in numerous types of human disease, in particular solid tumors. However, to the best of our knowledge, the underlying mechanisms of the effect of tRFs and tiRNAs in lung adenocarcinoma have not been reported. The present study aimed to determine the differential expression levels of tRFs and tiRNAs in lung adenocarcinoma and adjacent tissues using a NextSeq system, and further investigated their potential target genes via bioinformatics analysis. Kyoto Encyclopedia of Genes and Genomes signaling pathway and Gene Ontology functional term enrichment analyses were performed to investigate the function of these target genes in the occurrence and development of lung adenocarcinoma. In patients with lung adenocarcinoma, 338 types of tRFs and tiRNAs were detected via sequencing, 284 of which were not previously reported in the tRF database. Compared with the adjacent tissues, 17 types of tRFs and tiRNAs comprising 34 subtypes were found to be abnormally expressed in lung adenocarcinoma tissues, 20 of which were upregulated and 14 downregulated. Reverse transcription-quantitative PCR verification revealed that the expression levels of tiRNA-Lys-CTT-002, tRF-Val-CAC-010 and tRF-Val-CAC-011 were significantly upregulated, while those of tRF-Ser-TGA-005 were downregulated in lung adenocarcinoma tissues. Bioinformatics analysis identified that tRF-Ser-TGA-005 participated in the 'cellular response to transforming growth factor β stimulus' and tRF-Val-CAC-010 and tRF-Val-CAC-011 participated in the 'Hedgehog signaling pathway'. In conclusion, the results of the present study suggested that tRFs and tiRNAs may be closely associated with the pathogenesis and development of lung adenocarcinoma, providing a novel insight for further studies into lung adenocarcinoma.
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Affiliation(s)
- Jinhua Zhang
- Department of Pathology, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan 650032, P.R. China
| | - Linhui Li
- Department of Pathology, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan 650032, P.R. China
| | - Lilin Luo
- Department of Pathology, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan 650032, P.R. China
| | - Xuantao Yang
- Department of Pathology, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan 650032, P.R. China
| | - Juanjuan Zhang
- Department of Pathology, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan 650032, P.R. China
| | - Yuxin Xie
- Department of Pathology, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan 650032, P.R. China
| | - Rui Liang
- Department of Pathology, The Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China
| | - Wanpu Wang
- Department of Pathology, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan 650032, P.R. China
| | - Shuaiyao Lu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan 650118, P.R. China
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Fabres PJ, Anand L, Sai N, Pederson S, Zheng F, Stewart AA, Clements B, Lampugnani ER, Breen J, Gilliham M, Tricker P, Rodríguez López CM, David R. Tissue and regional expression patterns of dicistronic tRNA-mRNA transcripts in grapevine (Vitis vinifera) and their evolutionary co-appearance with vasculature in land plants. HORTICULTURE RESEARCH 2021; 8:137. [PMID: 34059643 PMCID: PMC8166872 DOI: 10.1038/s41438-021-00572-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 06/02/2023]
Abstract
Transfer RNAs (tRNA) are crucial adaptor molecules between messenger RNA (mRNA) and amino acids. Recent evidence in plants suggests that dicistronic tRNA-like structures also act as mobile signals for mRNA transcripts to move between distant tissues. Co-transcription is not a common feature in the plant nuclear genome and, in the few cases where polycistronic transcripts have been found, they include non-coding RNA species, such as small nucleolar RNAs and microRNAs. It is not known, however, the extent to which dicistronic transcripts of tRNA and mRNAs are expressed in field-grown plants, or the factors contributing to their expression. We analysed tRNA-mRNA dicistronic transcripts in the major horticultural crop grapevine (Vitis vinifera) using a novel pipeline developed to identify dicistronic transcripts from high-throughput RNA-sequencing data. We identified dicistronic tRNA-mRNA in leaf and berry samples from 22 commercial vineyards. Of the 124 tRNA genes that were expressed in both tissues, 18 tRNA were expressed forming part of 19 dicistronic tRNA-mRNAs. The presence and abundance of dicistronic molecules was tissue and geographic sub-region specific. In leaves, the expression patterns of dicistronic tRNA-mRNAs significantly correlated with tRNA expression, suggesting that their transcriptional regulation might be linked. We also found evidence of syntenic genomic arrangements of tRNAs and protein-coding genes between grapevine and Arabidopsis thaliana, and widespread prevalence of dicistronic tRNA-mRNA transcripts among vascular land plants but no evidence of these transcripts in non-vascular lineages. This suggests that the appearance of plant vasculature and tRNA-mRNA occurred concurrently during the evolution of land plants.
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Affiliation(s)
- Pastor Jullian Fabres
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Lakshay Anand
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Na Sai
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute & School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Stephen Pederson
- Bioinformatics Hub, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Fei Zheng
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute & School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Alexander A Stewart
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Benjamin Clements
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Edwin R Lampugnani
- School of Biosciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - James Breen
- Bioinformatics Hub, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Matthew Gilliham
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute & School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- ARC Industrial Transformation Training Centre in Innovative Wine Production, Waite Research Institute & School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Penny Tricker
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Carlos M Rodríguez López
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA.
| | - Rakesh David
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
- ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute & School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
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He J, Wu F, Han Z, Hu M, Lin W, Li Y, Cao M. Biomarkers (mRNAs and Non-Coding RNAs) for the Diagnosis and Prognosis of Colorectal Cancer - From the Body Fluid to Tissue Level. Front Oncol 2021; 11:632834. [PMID: 33996548 PMCID: PMC8118670 DOI: 10.3389/fonc.2021.632834] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/09/2021] [Indexed: 12/24/2022] Open
Abstract
In recent years, the diagnosis and treatment of colorectal cancer (CRC) have been continuously improved, but the mortality rate continues to be high, especially in advanced patients. CRC patients usually have no obvious symptoms in the early stage and are already in the advanced stage when they are diagnosed. The 5-year survival rate is only 10%. The blood markers currently used to screen for CRC, such as carcinoembryonic antigen and carbohydrate antigen 19-9, have low sensitivity and specificity, whereas other methods are invasive or too expensive. As a result, recent research has shifted to the development of minimally invasive or noninvasive biomarkers in the form of body fluid biopsies. Non-coding RNA molecules are composed of microRNAs, long non-coding RNAs, small nucleolar RNAs, and circular RNAs, which have important roles in the occurrence and development of diseases and can be utilized for the early diagnosis and prognosis of tumors. In this review, we focus on the latest findings of mRNA-ncRNA as biomarkers for the diagnosis and prognosis of CRC, from fluid to tissue level.
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Affiliation(s)
- Jinhua He
- Department of Laboratory Medicine, Central Hospital of Panyu District, Guangzhou, China
| | - Feifeng Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Zeping Han
- Department of Laboratory Medicine, Central Hospital of Panyu District, Guangzhou, China
| | - Min Hu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Weida Lin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yuguang Li
- Department of Laboratory Medicine, Central Hospital of Panyu District, Guangzhou, China
| | - Mingrong Cao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
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Li HM, Tan X, Zhang S, Yao J, Li HG. Transfer- or 'transmission'-RNA fragments? The roles of tsRNAs in the reproductive system. Mol Hum Reprod 2021; 27:6218776. [PMID: 33837423 DOI: 10.1093/molehr/gaab026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/25/2021] [Indexed: 12/13/2022] Open
Abstract
Transfer-RNAs (tRNAs) help ribosomes decode mRNAs and synthesize proteins; however, tRNA fragments produced under certain conditions, known as tRNA-derived small RNAs (tsRNAs), have been found to play important roles in pathophysiological processes. In the reproductive system, tsRNAs are abundant in gametes and embryos and at the maternal-fetal interface, as well as in microvesicles like epididymosomes, seminal plasma exosomes, and syncytiotrophoblast-derived extracellular vesicles. tsRNAs can affect gamete cell maturation, zygote activation, and early embryonic development. tsRNAs can transmit epigenetic information to later generations. In particular, exposure to environmental factors such as nutrition, isoproterenol, and poly(I:C) may allow tsRNAs to transfer information to the gametes or placenta to alter offspring phenotype. The underlying mechanisms of tsRNAs action include transposon silencing, translation regulation, and target mRNA degradation. Herein, we review the currently reported tsRNAs in the reproductive system, their validated functions, and potential roles. A better understanding of this field may help to provide useful recommendations or develop strategies to increase fertility and conception of healthy babies.
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Affiliation(s)
- Hui-Min Li
- Guilin Medical University, Guilin, P.R. China
| | - Xia Tan
- Center of Reproductive Medicine, Wuhan Union Hospital, Wuhan, P.R. China
| | - Shun Zhang
- Guilin Medical University Affiliated Hospital, Guilin, P.R. China
| | - Jun Yao
- Guilin Medical University Affiliated Hospital, Guilin, P.R. China
| | - Hong-Gang Li
- Institute of Reproductive Health/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China.,Genetic Laboratory, Wuhan Tongji Reproductive Medicine Hospital, Wuhan, P.R. China
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11
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Warren JM, Salinas-Giegé T, Hummel G, Coots NL, Svendsen JM, Brown KC, Drouard L, Sloan DB. Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification. RNA Biol 2021; 18:64-78. [PMID: 32715941 PMCID: PMC7834048 DOI: 10.1080/15476286.2020.1792089] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 06/18/2020] [Accepted: 06/30/2020] [Indexed: 12/27/2022] Open
Abstract
Differences in tRNA expression have been implicated in a remarkable number of biological processes. There is growing evidence that tRNA genes can play dramatically different roles depending on both expression and post-transcriptional modification, yet sequencing tRNAs to measure abundance and detect modifications remains challenging. Their secondary structure and extensive post-transcriptional modifications interfere with RNA-seq library preparation methods and have limited the utility of high-throughput sequencing technologies. Here, we combine two modifications to standard RNA-seq methods by treating with the demethylating enzyme AlkB and ligating with tRNA-specific adapters in order to sequence tRNAs from four species of flowering plants, a group that has been shown to have some of the most extensive rates of post-transcriptional tRNA modifications. This protocol has the advantage of detecting full-length tRNAs and sequence variants that can be used to infer many post-transcriptional modifications. We used the resulting data to produce a modification index of almost all unique reference tRNAs in Arabidopsis thaliana, which exhibited many anciently conserved similarities with humans but also positions that appear to be 'hot spots' for modifications in angiosperm tRNAs. We also found evidence based on northern blot analysis and droplet digital PCR that, even after demethylation treatment, tRNA-seq can produce highly biased estimates of absolute expression levels most likely due to biased reverse transcription. Nevertheless, the generation of full-length tRNA sequences with modification data is still promising for assessing differences in relative tRNA expression across treatments, tissues or subcellular fractions and help elucidate the functional roles of tRNA modifications.
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Affiliation(s)
- Jessica M. Warren
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Thalia Salinas-Giegé
- Institut De Biologie Moléculaire Des plantes-CNRS, Université De Strasbourg, Strasbourg, France
| | - Guillaume Hummel
- Institut De Biologie Moléculaire Des plantes-CNRS, Université De Strasbourg, Strasbourg, France
| | - Nicole L. Coots
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Kristen C. Brown
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Laurence Drouard
- Department of Biology, Colorado State University, Fort Collins, CO, USA
- Institut De Biologie Moléculaire Des plantes-CNRS, Université De Strasbourg, Strasbourg, France
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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12
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Catala M, Gato A, Tisné C, Barraud P. 1H, 15N chemical shift assignments of the imino groups of yeast tRNA Phe: influence of the post-transcriptional modifications. BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:169-174. [PMID: 32239363 DOI: 10.1007/s12104-020-09939-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/26/2020] [Indexed: 06/11/2023]
Abstract
Transfer RNAs (tRNAs) are heavily decorated with post-transcriptional modifications during their biosynthesis. To fulfil their functions within cells, tRNAs undergo a tightly controlled biogenesis process leading to the formation of mature tRNAs. In particular, the introduction of post-transcriptional modifications in tRNAs is controlled and influenced by multiple factors. In turn, tRNA biological functions are often modulated by their modifications. Although modifications play essential roles in tRNA biology, methods to directly detect their introduction during tRNA maturation are rare and do not easily provide information on the temporality of modification events. To obtain information on the tRNA maturation process, we have developed a methodology, using NMR as a tool to monitor tRNA maturation in a non-disruptive and continuous fashion in cellular extracts. Here we report the 1H,15N chemical shift assignments of imino groups in three forms of the yeast tRNAPhe differing in their modification content. These assignments are a prerequisite for the time-resolved NMR monitoring of yeast tRNAPhe maturation in yeast extracts.
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Affiliation(s)
- Marjorie Catala
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Alexandre Gato
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Carine Tisné
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Pierre Barraud
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 13 rue Pierre et Marie Curie, 75005, Paris, France.
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13
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Chen M, Kuhle B, Diedrich J, Liu Z, Moresco JJ, Yates Iii JR, Pan T, Yang XL. Cross-editing by a tRNA synthetase allows vertebrates to abundantly express mischargeable tRNA without causing mistranslation. Nucleic Acids Res 2020; 48:6445-6457. [PMID: 32484512 PMCID: PMC7337962 DOI: 10.1093/nar/gkaa469] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/19/2020] [Accepted: 05/31/2020] [Indexed: 01/18/2023] Open
Abstract
The accuracy in pairing tRNAs with correct amino acids by aminoacyl-tRNA synthetases (aaRSs) dictates the fidelity of translation. To ensure fidelity, multiple aaRSs developed editing functions that remove a wrong amino acid from tRNA before it reaches the ribosome. However, no specific mechanism within an aaRS is known to handle the scenario where a cognate amino acid is mischarged onto a wrong tRNA, as exemplified by AlaRS mischarging alanine to G4:U69-containing tRNAThr. Here, we report that the mischargeable G4:U69-containing tRNAThr are strictly conserved in vertebrates and are ubiquitously and abundantly expressed in mammalian cells and tissues. Although these tRNAs are efficiently mischarged, no corresponding Thr-to-Ala mistranslation is detectable. Mistranslation is prevented by a robust proofreading activity of ThrRS towards Ala-tRNAThr. Therefore, while wrong amino acids are corrected within an aaRS, a wrong tRNA is handled in trans by an aaRS cognate to the mischarged tRNA species. Interestingly, although Ala-tRNAThr mischarging is not known to occur in bacteria, Escherichia coli ThrRS also possesses robust cross-editing ability. We propose that the cross-editing activity of ThrRS is evolutionarily conserved and that this intrinsic activity allows G4:U69-containing tRNAThr to emerge and be preserved in vertebrates to have alternative functions without compromising translational fidelity.
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Affiliation(s)
- Meirong Chen
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA.,College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Bernhard Kuhle
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jolene Diedrich
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ze Liu
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - James J Moresco
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates Iii
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Xiang-Lei Yang
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
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14
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Warren JM, Sloan DB. Interchangeable parts: The evolutionarily dynamic tRNA population in plant mitochondria. Mitochondrion 2020; 52:144-156. [PMID: 32184120 DOI: 10.1016/j.mito.2020.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 01/31/2023]
Abstract
Transfer RNAs (tRNAs) remain one of the very few classes of genes still encoded in the mitochondrial genome. These key components of the protein translation system must interact with a large enzymatic network of nuclear-encoded gene products to maintain mitochondrial function. Plants have an evolutionarily dynamic mitochondrial tRNA population, including ongoing tRNA gene loss and replacement by both horizontal gene transfer from diverse sources and import of nuclear-expressed tRNAs from the cytosol. Thus, plant mitochondria represent an excellent model for understanding how anciently divergent genes can act as "interchangeable parts" during the evolution of complex molecular systems. In particular, understanding the integration of the mitochondrial translation system with elements of the corresponding machinery used in cytosolic protein synthesis is a key area for eukaryotic cellular evolution. Here, we review the increasingly detailed phylogenetic data about the evolutionary history of mitochondrial tRNA gene loss, transfer, and functional replacement that has created extreme variation in mitochondrial tRNA populations across plant species. We describe emerging tRNA-seq methods with promise for refining our understanding of the expression and subcellular localization of tRNAs. Finally, we summarize current evidence and identify open questions related to coevolutionary changes in nuclear-encoded enzymes that have accompanied turnover in mitochondrial tRNA populations.
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Affiliation(s)
- Jessica M Warren
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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15
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Cosio C, Renault D. Effects of cadmium, inorganic mercury and methyl-mercury on the physiology and metabolomic profiles of shoots of the macrophyte Elodea nuttallii. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 257:113557. [PMID: 31733966 DOI: 10.1016/j.envpol.2019.113557] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/31/2019] [Accepted: 10/31/2019] [Indexed: 05/28/2023]
Abstract
Macrophytes are known to bioaccumulate metals, but a thorough understanding of tolerance strategies and molecular impact of metals in aquatic plants is still lacking. The present study aimed to compare Hg and Cd effects in a representative macrophyte, Elodea nuttallii using physiological endpoints and metabolite profiles in shoots and cytosol. Exposure 24 h to methyl-Hg (30 ng L-1), inorganic Hg (70 ng L-1) and Cd (280 μg L-1) did not affect photosynthesis, or antioxidant enzymes despite the significant accumulation of metals, confirming a sublethal stress level. In shoots, Cd resulted in a higher level of regulation of metabolites than MeHg, while MeHg resulted in the largest number of regulated metabolites and IHg treatment regulated no metabolites significantly. In cytosol, Cd regulated more metabolites than IHg and only arginine, histidine and mannose were reduced by MeHg exposure. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of data suggested that exposure to MeHg resulted in biochemical changes including aminoacyl-tRNA biosynthesis, glycine, serine and threonine metabolism, nitrogen metabolism, arginine and proline metabolism, cyanoamino acid metabolism, while the treatment of Cd stress caused significant variations in aminoacyl-tRNA biosynthesis and branched-chain amino acids pathways. Data supports an impact of MeHg on N homeostasis, while Cd resulted in an osmotic stress-like pattern and IHg had a low impact. Marked differences in the responses to MeHg and IHg exposure were evidenced, supporting different molecular toxicity pathways and main impact of MeHg on non-soluble compartment, while main impact of IHg was on soluble compartment. Metabolomics was used for the first time in this species and proved to be very useful to confirm and complement recent knowledge gained by transcriptomics and proteomics, highlighting the high interest of multi-omics approaches to identify early impact of environmental pollution.
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Affiliation(s)
- Claudia Cosio
- Université de Reims Champagne-Ardenne, UMR-I 02 INERIS-URCA-ULH SEBIO, F-51687 Reims, France.
| | - David Renault
- Université de Rennes 1, UMR 6553 EcoBio CNRS, F-35042 Rennes, France; Institut Universitaire de France, 1 rue Descartes, 75231 Paris CEDEX 05, France
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16
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Leonardi A, Evke S, Lee M, Melendez JA, Begley TJ. Epitranscriptomic systems regulate the translation of reactive oxygen species detoxifying and disease linked selenoproteins. Free Radic Biol Med 2019; 143:573-593. [PMID: 31476365 PMCID: PMC7650020 DOI: 10.1016/j.freeradbiomed.2019.08.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 02/07/2023]
Abstract
Here we highlight the role of epitranscriptomic systems in post-transcriptional regulation, with a specific focus on RNA modifying writers required for the incorporation of the 21st amino acid selenocysteine during translation, and the pathologies linked to epitranscriptomic and selenoprotein defects. Epitranscriptomic marks in the form of enzyme-catalyzed modifications to RNA have been shown to be important signals regulating translation, with defects linked to altered development, intellectual impairment, and cancer. Modifications to rRNA, mRNA and tRNA can affect their structure and function, while the levels of these dynamic tRNA-specific epitranscriptomic marks are stress-regulated to control translation. The tRNA for selenocysteine contains five distinct epitranscriptomic marks and the ALKBH8 writer for the wobble uridine (U) has been shown to be vital for the translation of the glutathione peroxidase (GPX) and thioredoxin reductase (TRXR) family of selenoproteins. The reactive oxygen species (ROS) detoxifying selenocysteine containing proteins are a prime examples of how specialized translation can be regulated by specific tRNA modifications working in conjunction with distinct codon usage patterns, RNA binding proteins and specific 3' untranslated region (UTR) signals. We highlight the important role of selenoproteins in detoxifying ROS and provide details on how epitranscriptomic marks and selenoproteins can play key roles in and maintaining mitochondrial function and preventing disease.
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Affiliation(s)
- Andrea Leonardi
- Colleges of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY, USA
| | - Sara Evke
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA
| | - May Lee
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA
| | - J Andres Melendez
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA.
| | - Thomas J Begley
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA; RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
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17
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Ott E, Kawaguchi Y, Özgen N, Yamagishi A, Rabbow E, Rettberg P, Weckwerth W, Milojevic T. Proteomic and Metabolomic Profiling of Deinococcus radiodurans Recovering After Exposure to Simulated Low Earth Orbit Vacuum Conditions. Front Microbiol 2019; 10:909. [PMID: 31110498 PMCID: PMC6501615 DOI: 10.3389/fmicb.2019.00909] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/10/2019] [Indexed: 01/26/2023] Open
Abstract
The polyextremophile, gram-positive bacterium Deinococcus radiodurans can withstand harsh conditions of real and simulated outer space environment, e.g., UV and ionizing radiation. A long-term space exposure of D. radiodurans has been performed in Low Earth Orbit (LEO) in frames of the Tanpopo orbital mission aiming to investigate the possibility of interplanetary life transfer. Space vacuum (10-4–10-7 Pa) is a harmful factor, which induces dehydration and affects microbial integrity, severely damaging cellular components: lipids, carbohydrates, proteins, and nucleic acids. However, the molecular strategies by which microorganisms protect their integrity on molecular and cellular levels against vacuum damage are not yet understood. In a simulation experiment, we exposed dried D. radiodurans cells to vacuum (10-4–10-7 Pa), which resembles vacuum pressure present outside the International Space Station in LEO. After 90 days of high vacuum exposure, survival of D. radiodurans cells was 2.5-fold lower compared to control cells. To trigger molecular repair mechanisms, vacuum exposed cells of D. radiodurans were recovered in complex medium for 3 and 6 h. The combined approach of analyzing primary metabolites and proteins revealed important molecular activities during early recovery after vacuum exposure. In total, 1939 proteins covering 63% of D. radiodurans annotated protein sequences were detected. Proteases, tRNA ligases, reactive oxygen species (ROS) scavenging proteins, nucleic acid repair proteins, TCA cycle proteins, and S-layer proteins are highly abundant after vacuum exposure. The overall abundance of amino acids and TCA cycle intermediates is reduced during the recovery phase of D. radiodurans as they are needed as carbon source. Furthermore, vacuum exposure induces an upregulation of Type III histidine kinases, which trigger the expression of S-layer related proteins. Along with the highly abundant transcriptional regulator of FNR/CRP family, specific histidine kinases might be involved in the regulation of vacuum stress response. After repair processes are finished, D. radiodurans switches off the connected repair machinery and focuses on proliferation. Combined comparative analysis of alterations in the proteome and metabolome helps to identify molecular key players in the stress response of D. radiodurans, thus elucidating the mechanisms behind its extraordinary regenerative abilities and enabling this microorganism to withstand vacuum stress.
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Affiliation(s)
- Emanuel Ott
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Yuko Kawaguchi
- Planetary Exploration Research Center (PERC), Chiba Institute of Technology (CIT), Chiba, Japan
| | - Natalie Özgen
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Akihiko Yamagishi
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta, Yokohama, Japan
| | - Elke Rabbow
- Department of Radiation Biology, Institute of Aerospace Medicine, German Aerospace Center, Cologne, Germany
| | - Petra Rettberg
- Department of Radiation Biology, Institute of Aerospace Medicine, German Aerospace Center, Cologne, Germany
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Tetyana Milojevic
- Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
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18
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The Versatile Roles of the tRNA Epitranscriptome during Cellular Responses to Toxic Exposures and Environmental Stress. TOXICS 2019; 7:toxics7010017. [PMID: 30934574 PMCID: PMC6468425 DOI: 10.3390/toxics7010017] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/19/2019] [Accepted: 03/21/2019] [Indexed: 12/11/2022]
Abstract
Living organisms respond to environmental changes and xenobiotic exposures by regulating gene expression. While heat shock, unfolded protein, and DNA damage stress responses are well-studied at the levels of the transcriptome and proteome, tRNA-mediated mechanisms are only recently emerging as important modulators of cellular stress responses. Regulation of the stress response by tRNA shows a high functional diversity, ranging from the control of tRNA maturation and translation initiation, to translational enhancement through modification-mediated codon-biased translation of mRNAs encoding stress response proteins, and translational repression by stress-induced tRNA fragments. tRNAs need to be heavily modified post-transcriptionally for full activity, and it is becoming increasingly clear that many aspects of tRNA metabolism and function are regulated through the dynamic introduction and removal of modifications. This review will discuss the many ways that nucleoside modifications confer high functional diversity to tRNAs, with a focus on tRNA modification-mediated regulation of the eukaryotic response to environmental stress and toxicant exposures. Additionally, the potential applications of tRNA modification biology in the development of early biomarkers of pathology will be highlighted.
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19
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Chen H, Xu Z, Liu D. Small non-coding RNA and colorectal cancer. J Cell Mol Med 2019; 23:3050-3057. [PMID: 30801950 PMCID: PMC6484298 DOI: 10.1111/jcmm.14209] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/07/2019] [Accepted: 01/18/2019] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common malignance. Although great efforts have been made to understand the pathogenesis of CRC, the underlying mechanisms are still unclear. It is now clear that more than 90% of the total genome is actively transcribed, but lack of protein‐coding potential. The massive amount of RNA can be classified as housekeeping RNAs (such as ribosomal RNAs, transfer RNAs) and regulatory RNAs (such as microRNAs [miRNAs], PIWI‐interacting RNA [piRNAs], tRNA‐derived stress‐induced RNA, tRNA‐derived small RNA [tRFs] and long non‐coding RNAs [lncRNAs]). Small non‐coding RNAs are a group of ncRNAs with the length no more than 200 nt and they have been found to exert important regulatory functions under many pathological conditions. In this review, we summarize the biogenesis and functions of regulatory sncRNAs, such as miRNAs, piRNA and tRFs, and highlight their involvements in cancers, particularly in CRC.
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Affiliation(s)
- Hui Chen
- Department of Gastroenterology, People's Hospital of Taizhou, Taizhou, Jiangsu, China
| | - Zhiying Xu
- Department of Gastroenterology, People's Hospital of Taizhou, Taizhou, Jiangsu, China
| | - Deliang Liu
- Department of Gastroenterology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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20
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Zheng L, Shu C, Zhang M, Yang M, Zhou E. Molecular Characterization of a Novel Endornavirus Conferring Hypovirulence in Rice Sheath Blight Fungus Rhizoctonia solani AG-1 IA Strain GD-2. Viruses 2019; 11:v11020178. [PMID: 30791630 PMCID: PMC6409856 DOI: 10.3390/v11020178] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/17/2019] [Accepted: 02/18/2019] [Indexed: 01/09/2023] Open
Abstract
The complete sequence and genome organization of a novel Endornavirus from the hypovirulent strain GD-2 of Rhizoctonia solani AG-1 IA, the causal agent of rice sheath blight, were identified using a deep sequencing approach and it was tentatively named as Rhizoctonia solani endornavirus 1 (RsEV1). It was composed of only one segment that was 19,936 bp in length and was found to be the longest endornavirus genome that has been reported so far. The RsEV1 genome contained two open reading frames (ORFs): ORF1 and ORF2. ORF1 contained a glycosyltransferase 1 domain and a conserved RNA-dependent RNA polymerase domain, whereas ORF2 encoded a conserved hypothetical protein. Phylogenetic analysis revealed that RsEV1 was phylogenetically a new endogenous RNA virus. A horizontal transmission experiment indicated that RsEV1 could be transmitted from the host fungal strain GD-2 to a virulent strain GD-118P and resulted in hypovirulence in the derivative isogenic strain GD-118P-V1. Metabolomic analysis showed that 32 metabolites were differentially expressed between GD-118P and its isogenic hypovirulent strain GD-118P-V1. The differential metabolites were mainly classified as organic acids, amino acids, carbohydrates, and the intermediate products of energy metabolism. Pathway annotation revealed that these 32 metabolites were mainly involved in pentose and glucuronate interconversions and glyoxylate, dicarboxylate, starch, and sucrose metabolism, and so on. Taken together, our results showed that RsEV1 is a novel Endornavirus, and the infection of virulent strain GD-118P by RsEV1 caused metabolic disorders and resulted in hypovirulence. The results of this study lay a foundation for the biocontrol of rice sheath blight caused by R. solani AG1-IA.
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Affiliation(s)
- Li Zheng
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China.
- College of Plant Protection, Hainan University/Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Haikou 570228, China.
| | - Canwei Shu
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China.
| | - Meiling Zhang
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China.
| | - Mei Yang
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China.
| | - Erxun Zhou
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China.
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21
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Oberbauer V, Schaefer MR. tRNA-Derived Small RNAs: Biogenesis, Modification, Function and Potential Impact on Human Disease Development. Genes (Basel) 2018; 9:genes9120607. [PMID: 30563140 PMCID: PMC6315542 DOI: 10.3390/genes9120607] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 11/27/2018] [Accepted: 11/29/2018] [Indexed: 12/11/2022] Open
Abstract
Transfer RNAs (tRNAs) are abundant small non-coding RNAs that are crucially important for decoding genetic information. Besides fulfilling canonical roles as adaptor molecules during protein synthesis, tRNAs are also the source of a heterogeneous class of small RNAs, tRNA-derived small RNAs (tsRNAs). Occurrence and the relatively high abundance of tsRNAs has been noted in many high-throughput sequencing data sets, leading to largely correlative assumptions about their potential as biologically active entities. tRNAs are also the most modified RNAs in any cell type. Mutations in tRNA biogenesis factors including tRNA modification enzymes correlate with a variety of human disease syndromes. However, whether it is the lack of tRNAs or the activity of functionally relevant tsRNAs that are causative for human disease development remains to be elucidated. Here, we review the current knowledge in regard to tsRNAs biogenesis, including the impact of RNA modifications on tRNA stability and discuss the existing experimental evidence in support for the seemingly large functional spectrum being proposed for tsRNAs. We also argue that improved methodology allowing exact quantification and specific manipulation of tsRNAs will be necessary before developing these small RNAs into diagnostic biomarkers and when aiming to harness them for therapeutic purposes.
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Affiliation(s)
- Vera Oberbauer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria.
| | - Matthias R Schaefer
- Division of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria.
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22
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Li S, Xu Z, Sheng J. tRNA-Derived Small RNA: A Novel Regulatory Small Non-Coding RNA. Genes (Basel) 2018; 9:E246. [PMID: 29748504 PMCID: PMC5977186 DOI: 10.3390/genes9050246] [Citation(s) in RCA: 199] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 05/06/2018] [Accepted: 05/06/2018] [Indexed: 01/15/2023] Open
Abstract
Deep analysis of next-generation sequencing data unveils numerous small non-coding RNAs with distinct functions. Recently, fragments derived from tRNA, named as tRNA-derived small RNA (tsRNA), have attracted broad attention. There are mainly two types of tsRNAs, including tRNA-derived stress-induced RNA (tiRNA) and tRNA-derived fragment (tRF), which differ in the cleavage position of the precursor or mature tRNA transcript. Emerging evidence has shown that tsRNAs are not merely tRNA degradation debris but have been recognized to play regulatory roles in many specific physiological and pathological processes. In this review, we summarize the biogeneses of various tsRNAs, present the emerging concepts regarding functions and mechanisms of action of tsRNAs, highlight the potential application of tsRNAs in human diseases, and put forward the current problems and future research directions.
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Affiliation(s)
- Siqi Li
- Institute of Environmental Health, School of Public Health, Zhejiang University, Hangzhou 310058, China.
| | - Zhengping Xu
- Institute of Environmental Health, School of Public Health, Zhejiang University, Hangzhou 310058, China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China.
- Program in Molecular and Cellular Biology, School of Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Jinghao Sheng
- Institute of Environmental Health, School of Public Health, Zhejiang University, Hangzhou 310058, China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310003, China.
- Program in Molecular and Cellular Biology, School of Medicine, Zhejiang University, Hangzhou 310058, China.
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23
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Moutiez M, Belin P, Gondry M. Aminoacyl-tRNA-Utilizing Enzymes in Natural Product Biosynthesis. Chem Rev 2017; 117:5578-5618. [DOI: 10.1021/acs.chemrev.6b00523] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Mireille Moutiez
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Pascal Belin
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Muriel Gondry
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
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24
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Nikić I, Estrada Girona G, Kang JH, Paci G, Mikhaleva S, Koehler C, Shymanska NV, Ventura Santos C, Spitz D, Lemke EA. Debugging Eukaryotic Genetic Code Expansion for Site-Specific Click-PAINT Super-Resolution Microscopy. Angew Chem Int Ed Engl 2016; 55:16172-16176. [PMID: 27804198 PMCID: PMC5215487 DOI: 10.1002/anie.201608284] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/20/2016] [Indexed: 01/29/2023]
Abstract
Super‐resolution microscopy (SRM) greatly benefits from the ability to install small photostable fluorescent labels into proteins. Genetic code expansion (GCE) technology addresses this demand, allowing the introduction of small labeling sites, in the form of uniquely reactive noncanonical amino acids (ncAAs), at any residue in a target protein. However, low incorporation efficiency of ncAAs and high background fluorescence limit its current SRM applications. Redirecting the subcellular localization of the pyrrolysine‐based GCE system for click chemistry, combined with DNA‐PAINT microscopy, enables the visualization of even low‐abundance proteins inside mammalian cells. This approach links a versatile, biocompatible, and potentially unbleachable labeling method with residue‐specific precision. Moreover, our reengineered GCE system eliminates untargeted background fluorescence and substantially boosts the expression yield, which is of general interest for enhanced protein engineering in eukaryotes using GCE.
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Affiliation(s)
- Ivana Nikić
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Present address: Werner Reichardt Centre for Integrative, Neuroscience, University of Tübingen, Tübingen, 72076, Germany
| | - Gemma Estrada Girona
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Jun Hee Kang
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Giulia Paci
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Sofya Mikhaleva
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Christine Koehler
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Nataliia V Shymanska
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Camilla Ventura Santos
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Daniel Spitz
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
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25
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Nikić I, Estrada Girona G, Kang JH, Paci G, Mikhaleva S, Koehler C, Shymanska NV, Ventura Santos C, Spitz D, Lemke EA. Verbesserte Erweiterung des eukaryotischen genetischen Codes für seitenspezifische, hochauflösende Click-PAINT-Mikroskopie. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608284] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ivana Nikić
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
- Aktuelle Adresse: Werner Reichardt Zentrum für integrative Neurowissenschaften; Universität Tübingen; 72076 Tübingen Deutschland
| | - Gemma Estrada Girona
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Jun Hee Kang
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Giulia Paci
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Sofya Mikhaleva
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Christine Koehler
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Nataliia V. Shymanska
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Camilla Ventura Santos
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Daniel Spitz
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
| | - Edward A. Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit; EMBL; Meyerhofstraße 1 69117 Heidelberg Deutschland
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26
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Duechler M, Leszczyńska G, Sochacka E, Nawrot B. Nucleoside modifications in the regulation of gene expression: focus on tRNA. Cell Mol Life Sci 2016; 73:3075-95. [PMID: 27094388 PMCID: PMC4951516 DOI: 10.1007/s00018-016-2217-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 03/25/2016] [Accepted: 04/04/2016] [Indexed: 01/10/2023]
Abstract
Both, DNA and RNA nucleoside modifications contribute to the complex multi-level regulation of gene expression. Modified bases in tRNAs modulate protein translation rates in a highly dynamic manner. Synonymous codons, which differ by the third nucleoside in the triplet but code for the same amino acid, may be utilized at different rates according to codon-anticodon affinity. Nucleoside modifications in the tRNA anticodon loop can favor the interaction with selected codons by stabilizing specific base pairs. Similarly, weakening of base pairing can discriminate against binding to near-cognate codons. mRNAs enriched in favored codons are translated in higher rates constituting a fine-tuning mechanism for protein synthesis. This so-called codon bias establishes a basic protein level, but sometimes it is necessary to further adjust the production rate of a particular protein to actual requirements, brought by, e.g., stages in circadian rhythms, cell cycle progression or exposure to stress. Such an adjustment is realized by the dynamic change of tRNA modifications resulting in the preferential translation of mRNAs coding for example for stress proteins to facilitate cell survival. Furthermore, tRNAs contribute in an entirely different way to another, less specific stress response consisting in modification-dependent tRNA cleavage that contributes to the general down-regulation of protein synthesis. In this review, we summarize control functions of nucleoside modifications in gene regulation with a focus on recent findings on protein synthesis control by tRNA base modifications.
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Affiliation(s)
- Markus Duechler
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland.
| | - Grażyna Leszczyńska
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
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27
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Katz A, Elgamal S, Rajkovic A, Ibba M. Non-canonical roles of tRNAs and tRNA mimics in bacterial cell biology. Mol Microbiol 2016; 101:545-58. [PMID: 27169680 DOI: 10.1111/mmi.13419] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2016] [Indexed: 12/27/2022]
Abstract
Transfer RNAs (tRNAs) are the macromolecules that transfer activated amino acids from aminoacyl-tRNA synthetases to the ribosome, where they are used for the mRNA guided synthesis of proteins. Transfer RNAs are ancient molecules, perhaps even predating the existence of the translation machinery. Albeit old, these molecules are tremendously conserved, a characteristic that is well illustrated by the fact that some bacterial tRNAs are efficient and specific substrates of eukaryotic aminoacyl-tRNA synthetases and ribosomes. Considering their ancient origin and high structural conservation, it is not surprising that tRNAs have been hijacked during evolution for functions outside of translation. These roles beyond translation include synthetic, regulatory and information functions within the cell. Here we provide an overview of the non-canonical roles of tRNAs and their mimics in bacteria, and discuss some of the common themes that arise when comparing these different functions.
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Affiliation(s)
- Assaf Katz
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, 8380453, Chile
| | - Sara Elgamal
- Department of Microbiology and The Center for RNA Biology, Ohio State University, Columbus, Ohio, 43210, USA
| | - Andrei Rajkovic
- Department of Microbiology and The Center for RNA Biology, Ohio State University, Columbus, Ohio, 43210, USA
| | - Michael Ibba
- Department of Microbiology and The Center for RNA Biology, Ohio State University, Columbus, Ohio, 43210, USA
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28
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Abstract
Aminoacyl-tRNA synthetases (aaRSs) are modular enzymes globally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation. Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g., in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show huge structural plasticity related to function and limited idiosyncrasies that are kingdom or even species specific (e.g., the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS). Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably between distant groups such as Gram-positive and Gram-negative Bacteria. The review focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation, and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulated in last two decades is reviewed, showing how the field moved from essentially reductionist biology towards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRS paralogs (e.g., during cell wall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointed throughout the review and distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Mathias Springer
- Université Paris Diderot, Sorbonne Cité, UPR9073 CNRS, IBPC, 75005 Paris, France
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29
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Translation quality control is critical for bacterial responses to amino acid stress. Proc Natl Acad Sci U S A 2016; 113:2252-7. [PMID: 26858451 DOI: 10.1073/pnas.1525206113] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gene expression relies on quality control for accurate transmission of genetic information. One mechanism that prevents amino acid misincorporation errors during translation is editing of misacylated tRNAs by aminoacyl-tRNA synthetases. In the absence of editing, growth is limited upon exposure to excess noncognate amino acid substrates and other stresses, but whether these physiological effects result solely from mistranslation remains unclear. To explore if translation quality control influences cellular processes other than protein synthesis, an Escherichia coli strain defective in Tyr-tRNA(Phe) editing was used. In the absence of editing, cellular levels of aminoacylated tRNA(Phe) were elevated during amino acid stress, whereas in the wild-type strain these levels declined under the same growth conditions. In the editing-defective strain, increased levels of aminoacylated tRNA(Phe) led to continued synthesis of the PheL leader peptide and attenuation of pheA transcription under amino acid stress. Consequently, in the absence of editing, activation of the phenylalanine biosynthetic operon becomes less responsive to phenylalanine limitation. In addition to raising aminoacylated tRNA levels, the absence of editing lowered the amount of deacylated tRNA(Phe) in the cell. This reduction in deacylated tRNA was accompanied by decreased synthesis of the second messenger guanosine tetraphosphate and limited induction of stringent response-dependent gene expression in editing-defective cells during amino acid stress. These data show that a single quality-control mechanism, the editing of misacylated aminoacyl-tRNAs, provides a critical checkpoint both for maintaining the accuracy of translation and for determining the sensitivity of transcriptional responses to amino acid stress.
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30
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Structural Insights into tRNA Dynamics on the Ribosome. Int J Mol Sci 2015; 16:9866-95. [PMID: 25941930 PMCID: PMC4463622 DOI: 10.3390/ijms16059866] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 04/21/2015] [Accepted: 04/22/2015] [Indexed: 11/17/2022] Open
Abstract
High-resolution structures at different stages, as well as biochemical, single molecule and computational approaches have highlighted the elasticity of tRNA molecules when bound to the ribosome. It is well acknowledged that the inherent structural flexibility of the tRNA lies at the heart of the protein synthesis process. Here, we review the recent advances and describe considerations that the conformational changes of the tRNA molecules offer about the mechanisms grounded in translation.
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31
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Shepherd J, Ibba M. Bacterial transfer RNAs. FEMS Microbiol Rev 2015; 39:280-300. [PMID: 25796611 DOI: 10.1093/femsre/fuv004] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/21/2015] [Indexed: 11/14/2022] Open
Abstract
Transfer RNA is an essential adapter molecule that is found across all three domains of life. The primary role of transfer RNA resides in its critical involvement in the accurate translation of messenger RNA codons during protein synthesis and, therefore, ultimately in the determination of cellular gene expression. This review aims to bring together the results of intensive investigations into the synthesis, maturation, modification, aminoacylation, editing and recycling of bacterial transfer RNAs. Codon recognition at the ribosome as well as the ever-increasing number of alternative roles for transfer RNA outside of translation will be discussed in the specific context of bacterial cells.
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Affiliation(s)
- Jennifer Shepherd
- Department of Microbiology and the Center for RNA Biology, Ohio State University, Columbus, Ohio 43210, USA
| | - Michael Ibba
- Department of Microbiology and the Center for RNA Biology, Ohio State University, Columbus, Ohio 43210, USA
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32
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Fung AWS, Leung CCY, Fahlman RP. The determination of tRNALeu recognition nucleotides for Escherichia coli L/F transferase. RNA (NEW YORK, N.Y.) 2014; 20:1210-1222. [PMID: 24935875 PMCID: PMC4105747 DOI: 10.1261/rna.044529.114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/28/2014] [Indexed: 06/03/2023]
Abstract
Escherichia coli leucyl/phenylalanyl-tRNA protein transferase catalyzes the tRNA-dependent post-translational addition of amino acids onto the N-terminus of a protein polypeptide substrate. Based on biochemical and structural studies, the current tRNA recognition model by L/F transferase involves the identity of the 3' aminoacyl adenosine and the sequence-independent docking of the D-stem of an aminoacyl-tRNA to the positively charged cluster on L/F transferase. However, this model does not explain the isoacceptor preference observed 40 yr ago. Using in vitro-transcribed tRNA and quantitative MALDI-ToF MS enzyme activity assays, we have confirmed that, indeed, there is a strong preference for the most abundant leucyl-tRNA, tRNA(Leu) (anticodon 5'-CAG-3') isoacceptor for L/F transferase activity. We further investigate the molecular mechanism for this preference using hybrid tRNA constructs. We identified two independent sequence elements in the acceptor stem of tRNA(Leu) (CAG)-a G₃:C₇₀ base pair and a set of 4 nt (C₇₂, A₄:U₆₉, C₆₈)-that are important for the optimal binding and catalysis by L/F transferase. This maps a more specific, sequence-dependent tRNA recognition model of L/F transferase than previously proposed.
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Affiliation(s)
- Angela Wai Shan Fung
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | | | - Richard Peter Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7 Department of Oncology, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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33
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Abstract
Transfer RNAs (tRNA) are best known for their role as adaptors during translation of the genetic code. Beyond their canonical role during protein biosynthesis, tRNAs also perform additional functions in both prokaryotes and eukaryotes for example in regulating gene expression. Aminoacylated tRNAs have also been implicated as substrates for non-ribosomal peptide bond formation, post-translational protein labeling, modification of phospholipids in the cell membrane, and antibiotic biosyntheses. Most recently tRNA fragments, or tRFs, have also been recognized to play regulatory roles. Here, we examine in more detail some of the new functions emerging for tRNA in a variety of cellular processes outside of protein synthesis.
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Affiliation(s)
- Medha Raina
- Department of Microbiology, The Ohio State Biochemistry Program, The Ohio State University Columbus, OH, USA ; Center for RNA Biology, The Ohio State University Columbus, OH, USA
| | - Michael Ibba
- Department of Microbiology, The Ohio State Biochemistry Program, The Ohio State University Columbus, OH, USA ; Center for RNA Biology, The Ohio State University Columbus, OH, USA
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34
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Mehta A, López-Maury L, Florencio FJ. Proteomic pattern alterations of the cyanobacterium Synechocystis sp. PCC 6803 in response to cadmium, nickel and cobalt. J Proteomics 2014; 102:98-112. [PMID: 24650429 DOI: 10.1016/j.jprot.2014.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 02/24/2014] [Accepted: 03/07/2014] [Indexed: 11/19/2022]
Abstract
UNLABELLED Cyanobacteria represent the largest and most diverse group of prokaryotes capable of performing oxygenic photosynthesis and are frequently found in environments contaminated with heavy metals. Several studies have been performed in these organisms in order to better understand the effects of metals such as Zn, Cd, Cu, Ni and Co. In Synechocystis sp. PCC 6803, genes involved in Ni, Co, Cu and Zn resistance have been reported. However, proteomic studies for the identification of proteins modulated by heavy metals have not been carried out. In the present work, we have analyzed the proteomic pattern alterations of the cyanobacterium Synechocystis sp. PCC 6803 in response to Ni, Co and Cd in order to identify the metabolic processes affected by these metals. We show that some proteins are commonly regulated in response to the different metal ions, including ribulose1,5-bisphosphate carboxylase and the periplasmic iron-binding protein FutA2, while others, such as chaperones, were specifically induced by each metal. We also show that the main processes affected by the metals are carbon metabolism and photosynthesis, since heavy metals affect proteins required for the correct functioning of these activities. BIOLOGICAL SIGNIFICANCE This is the first report on the proteomic profile of Synechocystis sp. PCC 6803 wild type and mutant strains for the identification of proteins affected by the heavy metals Ni, Co and Cd. We have identified proteins commonly responsive to all three metals and also chaperones specifically modulated by each metal. Our data also supports previous studies that suggest the existence of additional sensor systems for Co.
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Affiliation(s)
- Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, Av. W5 Norte (final), 70770-917 Brasília, DF, Brazil
| | - Luis López-Maury
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, E-41092 Seville, Spain
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, E-41092 Seville, Spain
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35
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Zhang J, Ferré-D'Amaré AR. A flexible, scalable method for preparation of homogeneous aminoacylated tRNAs. Methods Enzymol 2014; 549:105-13. [PMID: 25432746 DOI: 10.1016/b978-0-12-801122-5.00005-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Transfer RNAs (tRNAs) are cellular courier molecules that decipher the genetic code in messenger RNAs and enable the transfer of appropriate esterified amino acids to the growing peptide chain. The preparation of biophysical quantities of homogeneous aminoacylated tRNAs has remained a significant technical challenge. This is primarily due to the difficulty in removing contaminating nonaminoacylated tRNAs that are have very similar properties overall, as well as the hydrolytic instability of the aminoacyl linkage. We describe a flexible, scalable method to prepare homogeneous aminoacylated tRNAs that is also broadly compatible with mutant, misacylated, or otherwise aberrant tRNAs and other RNAs. This method combines ribozyme-mediated aminoacylation with reversible N-pentenoylation of the esterified amino acid, which not only protects against spontaneous deacylation but also provides a hydrophobic purification handle. This protocol makes it straightforward to produce biophysical quantities of natural and unnatural aminoacylated tRNAs and has proven essential for mechanistic investigations of the T-box riboswitches.
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Affiliation(s)
- Jinwei Zhang
- National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
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36
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Zhou X, Wang E. Transfer RNA: a dancer between charging and mis-charging for protein biosynthesis. SCIENCE CHINA-LIFE SCIENCES 2013; 56:921-32. [PMID: 23982864 DOI: 10.1007/s11427-013-4542-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/13/2013] [Indexed: 01/17/2023]
Abstract
Transfer RNA plays a fundamental role in the protein biosynthesis as an adaptor molecule by functioning as a biological link between the genetic nucleotide sequence in the mRNA and the amino acid sequence in the protein. To perform its role in protein biosynthesis, it has to be accurately recognized by aminoacyl-tRNA synthetases (aaRSs) to generate aminoacyl-tRNAs (aa-tRNAs). The correct pairing between an amino acid with its cognate tRNA is crucial for translational quality control. Production and utilization of mis-charged tRNAs are usually detrimental for all the species, resulting in cellular dysfunctions. Correct aa-tRNAs formation is collectively controlled by aaRSs with distinct mechanisms and/or other trans-factors. However, in very limited instances, mis-charged tRNAs are intermediate for specific pathways or essential components for the translational machinery. Here, from the point of accuracy in tRNA charging, we review our understanding about the mechanism ensuring correct aa-tRNA generation. In addition, some unique mis-charged tRNA species necessary for the organism are also briefly described.
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Affiliation(s)
- Xiaolong Zhou
- Center for RNA Research, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
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37
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Shepherd J, Ibba M. Direction of aminoacylated transfer RNAs into antibiotic synthesis and peptidoglycan-mediated antibiotic resistance. FEBS Lett 2013; 587:2895-904. [PMID: 23907010 DOI: 10.1016/j.febslet.2013.07.036] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 07/17/2013] [Indexed: 12/30/2022]
Abstract
Prokaryotic aminoacylated-transfer RNAs often need to be efficiently segregated between translation and other cellular biosynthetic pathways. Many clinically relevant bacteria, including Streptococcus pneumoniae, Staphylococcus aureus, Enterococcus faecalis and Pseudomonas aeruginosa direct some aminoacylated-tRNA species into peptidoglycan biosynthesis and/or membrane phospholipid modification. Subsequent indirect peptidoglycan cross-linkage or change in membrane permeability is often a prerequisite for high-level antibiotic resistance. In Streptomycetes, aminoacylated-tRNA species are used for antibiotic synthesis as well as antibiotic resistance. The direction of coding aminoacylated-tRNA molecules away from translation and into antibiotic resistance and synthesis pathways are discussed in this review.
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Affiliation(s)
- Jennifer Shepherd
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, OH 43210-1292, USA
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38
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Cognat V, Pawlak G, Duchêne AM, Daujat M, Gigant A, Salinas T, Michaud M, Gutmann B, Giegé P, Gobert A, Maréchal-Drouard L. PlantRNA, a database for tRNAs of photosynthetic eukaryotes. Nucleic Acids Res 2013; 41:D273-9. [PMID: 23066098 PMCID: PMC3531208 DOI: 10.1093/nar/gks935] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/06/2012] [Accepted: 09/16/2012] [Indexed: 12/17/2022] Open
Abstract
PlantRNA database (http://plantrna.ibmp.cnrs.fr/) compiles transfer RNA (tRNA) gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. The set of annotated tRNA gene sequences has been manually curated for maximum quality and confidence. The novelty of this database resides in the inclusion of biological information relevant to the function of all the tRNAs entered in the library. This includes 5'- and 3'-flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences, aminoacyl-tRNA synthetases and enzymes responsible for tRNA maturation and modification. Finally, data on mitochondrial import of nuclear-encoded tRNAs as well as the bibliome for the respective tRNAs and tRNA-binding proteins are also included. The current annotation concerns complete genomes from 11 organisms: five flowering plants (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Medicago truncatula and Brachypodium distachyon), a moss (Physcomitrella patens), two green algae (Chlamydomonas reinhardtii and Ostreococcus tauri), one glaucophyte (Cyanophora paradoxa), one brown alga (Ectocarpus siliculosus) and a pennate diatom (Phaeodactylum tricornutum). The database will be regularly updated and implemented with new plant genome annotations so as to provide extensive information on tRNA biology to the research community.
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MESH Headings
- Bryopsida/genetics
- Chlorophyta/genetics
- Cyanophora/genetics
- Databases, Nucleic Acid
- Diatoms/genetics
- Enzymes/genetics
- Enzymes/metabolism
- Genome, Mitochondrial
- Genome, Plant
- Genome, Plastid
- Internet
- Magnoliopsida/genetics
- Phaeophyceae/genetics
- Photosynthesis/genetics
- Plants/genetics
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Stramenopiles/genetics
- User-Computer Interface
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Laurence Maréchal-Drouard
- Institut de Biologie Moléculaire des Plantes, UPR 2357-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg Cedex, France
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39
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Abstract
Aminoacyl-tRNAsynthetases (aaRSs) are modular enzymesglobally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation.Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g.,in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show hugestructural plasticity related to function andlimited idiosyncrasies that are kingdom or even speciesspecific (e.g.,the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS).Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably betweendistant groups such as Gram-positive and Gram-negative Bacteria.Thereview focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation,and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulatedin last two decades is reviewed,showing how thefield moved from essentially reductionist biologytowards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRSparalogs (e.g., during cellwall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointedthroughout the reviewand distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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40
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Rogers TE, Ataide SF, Dare K, Katz A, Seveau S, Roy H, Ibba M. A pseudo-tRNA modulates antibiotic resistance in Bacillus cereus. PLoS One 2012; 7:e41248. [PMID: 22815980 PMCID: PMC3399842 DOI: 10.1371/journal.pone.0041248] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 06/19/2012] [Indexed: 01/18/2023] Open
Abstract
Bacterial genomic islands are often flanked by tRNA genes, which act as sites for the integration of foreign DNA into the host chromosome. For example, Bacillus cereus ATCC14579 contains a pathogenicity island flanked by a predicted pseudo-tRNA, tRNAOther, which does not function in translation. Deletion of tRNAOther led to significant changes in cell wall morphology and antibiotic resistance and was accompanied by changes in the expression of numerous genes involved in oxidative stress responses, several of which contain significant complementarities to sequences surrounding tRNAOther. This suggested that tRNAOther might be expressed as part of a larger RNA, and RACE analysis subsequently confirmed the existence of several RNA species that significantly extend both the 3′ and 5′-ends of tRNAOther. tRNAOther expression levels were found to be responsive to changes in extracellular iron concentration, consistent with the presence of three putative ferric uptake regulator (Fur) binding sites in the 5′ leader region of one of these larger RNAs. Taken together with previous data, this study now suggests that tRNAOther may function by providing a tRNA-like structural element within a larger regulatory RNA. These findings illustrate that while integration of genomic islands often leaves tRNA genes intact and functional, in other instances inactivation may generate tRNA-like elements that are then recruited to other functions in the cell.
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Affiliation(s)
- Theresa E. Rogers
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
| | - Sandro F. Ataide
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
| | - Kiley Dare
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
| | - Assaf Katz
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
| | - Stephanie Seveau
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
| | - Hervé Roy
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, United States of America
| | - Michael Ibba
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
- Ohio State Biochemistry Program, Ohio State University, Columbus, Ohio, United States of America
- Center for RNA Biology, Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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41
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Chang AT, Nikonowicz EP. Solution nuclear magnetic resonance analyses of the anticodon arms of proteinogenic and nonproteinogenic tRNA(Gly). Biochemistry 2012; 51:3662-74. [PMID: 22468768 DOI: 10.1021/bi201900j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Although the fate of most tRNA molecules in the cell is aminoacylation and delivery to the ribosome, some tRNAs are destined to fulfill other functional roles. In addition to their central role in translation, tRNA molecules participate in processes such as regulation of gene expression, bacterial cell wall biosynthesis, viral replication, antibiotic biosynthesis, and suppression of alternative splicing. In bacteria, glycyl-tRNA molecules with anticodon sequences GCC and UCC exhibit multiple extratranslational functions, including transcriptional regulation and cell wall biosynthesis. We have determined the high-resolution structures of three glycyl-tRNA anticodon arms with anticodon sequences GCC and UCC. Two of the tRNA molecules are proteinogenic (tRNA(Gly,GCC) and tRNA(Gly,UCC)), and the third is nonproteinogenic (np-tRNA(Gly,UCC)) and participates in cell wall biosynthesis. The UV-monitored thermal melting curves show that the anticodon arm of tRNA(Gly,UCC) with a loop-closing C-A(+) base pair melts at a temperature 10 °C lower than those of tRNA(Gly,GCC) and np-tRNA(Gly,UCC). U-A and C-G pairs close the loops of the latter two molecules and enhance stem stability. Mg(2+) stabilizes the tRNA(Gly,UCC) anticodon arm and reduces the T(m) differential. The structures of the three tRNA(Gly) anticodon arms exhibit small differences among one another, but none of them form the classical U-turn motif. The anticodon loop of tRNA(Gly,GCC) becomes more dynamic and disordered in the presence of multivalent cations, whereas metal ion coordination in the anticodon loops of tRNA(Gly,UCC) and np-tRNA(Gly,UCC) establishes conformational homogeneity. The conformational similarity of the molecules is greater than their functional differences might suggest. Because aminoacylation of full-length tRNA molecules is accomplished by one tRNA synthetase, the similar structural context of the loop may facilitate efficient recognition of each of the anticodon sequences.
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Affiliation(s)
- Andrew T Chang
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251-1892, United States
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42
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Dare K, Ibba M. Roles of tRNA in cell wall biosynthesis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2012; 3:247-64. [PMID: 22262511 PMCID: PMC3873719 DOI: 10.1002/wrna.1108] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Recent research into various aspects of bacterial metabolism such as cell wall and antibiotic synthesis, degradation pathways, cellular stress, and amino acid biosynthesis has elucidated roles of aminoacyl-transfer ribonucleic acid (aa-tRNA) outside of translation. Although the two enzyme families responsible for cell wall modifications, aminoacyl-phosphatidylglycerol synthases (aaPGSs) and Fem, were discovered some time ago, they have recently become of intense interest for their roles in the antimicrobial resistance of pathogenic microorganisms. The addition of positively charged amino acids to phosphatidylglycerol (PG) by aaPGSs neutralizes the lipid bilayer making the bacteria less susceptible to positively charged antimicrobial agents. Fem transferases utilize aa-tRNA to form peptide bridges that link strands of peptidoglycan. These bridges vary among the bacterial species in which they are present and play a role in resistance to antibiotics that target the cell wall. Additionally, the formation of truncated peptides results in shorter peptide bridges and loss of branched linkages which makes bacteria more susceptible to antimicrobials. A greater understanding of the structure and substrate specificity of this diverse enzymatic family is necessary to aid current efforts in designing potential bactericidal agents. These two enzyme families are linked only by the substrate with which they modify the cell wall, aa-tRNA; their structure, cell wall modification processes and the physiological changes they impart on the bacterium differ greatly.
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Affiliation(s)
- Kiley Dare
- Department of Microbiology, Ohio State University, Columbus, OH, USA
| | - Michael Ibba
- Department of Microbiology, Ohio State University, Columbus, OH, USA
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43
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Bhaskaran H, Rodriguez-Hernandez A, Perona JJ. Kinetics of tRNA folding monitored by aminoacylation. RNA (NEW YORK, N.Y.) 2012; 18:569-80. [PMID: 22286971 PMCID: PMC3285943 DOI: 10.1261/rna.030080.111] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 11/23/2011] [Indexed: 05/20/2023]
Abstract
We describe a strategy for tracking Mg²⁺-initiated folding of ³²P-labeled tRNA molecules to their native structures based on the capacity for aminoacylation by the cognate aminoacyl-tRNA synthetase enzyme. The approach directly links folding to function, paralleling a common strategy used to study the folding of catalytic RNAs. Incubation of unfolded tRNA with magnesium ions, followed by the addition of aminoacyl-tRNA synthetase and further incubation, yields a rapid burst of aminoacyl-tRNA formation corresponding to the prefolded tRNA fraction. A subsequent slower increase in product formation monitors continued folding in the presence of the enzyme. Further analysis reveals the presence of a parallel fraction of tRNA that folds more rapidly than the majority of the population. The application of the approach to study the influence of post-transcriptional modifications in folding of Escherichia coli tRNA₁(Gln) reveals that the modified bases increase the folding rate but do not affect either the equilibrium between properly folded and misfolded states or the folding pathway. This assay allows the use of ³²P-labeled tRNA in integrated studies combining folding, post-transcriptional processing, and aminoacylation reactions.
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Affiliation(s)
| | | | - John J. Perona
- Department of Chemistry and Biochemistry
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106-9510, USA
- Corresponding author.E-mail .
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44
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Janssen BD, Diner EJ, Hayes CS. Analysis of aminoacyl- and peptidyl-tRNAs by gel electrophoresis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2012; 905:291-309. [PMID: 22736012 DOI: 10.1007/978-1-61779-949-5_19] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
During protein synthesis, ribosomes translate the genetic information encoded within messenger RNAs into defined amino acid sequences. Transfer RNAs (tRNAs) are crucial adaptor molecules in this process, delivering amino acid residues to the ribosome and holding the nascent peptide chain as it is assembled. Here, we present methods for the analysis of aminoacyl- and peptidyl-tRNA species isolated from Escherichia coli. These approaches utilize denaturing gel electrophoresis at acidic pH to preserve the labile ester bonds that link amino acids to tRNA. Specific aminoacyl- and peptidyl-tRNAs are detected by Northern blot hybridization using probes for tRNA isoacceptors. Small peptidyl-tRNAs can be differentiated from aminoacyl-tRNA through selective deacylation of the latter with copper sulfate. Additionally, peptidyl-tRNAs can be detected through metabolic labeling of the nascent peptide. This approach is amenable to pulse-chase analysis to examine peptidyl-tRNA turnover in vivo. We have applied these methods to study programmed translational arrests and the kinetics of paused ribosome turnover.
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Affiliation(s)
- Brian D Janssen
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
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45
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Cherkasova V, Maury LL, Bacikova D, Pridham K, Bähler J, Maraia RJ. Altered nuclear tRNA metabolism in La-deleted Schizosaccharomyces pombe is accompanied by a nutritional stress response involving Atf1p and Pcr1p that is suppressible by Xpo-t/Los1p. Mol Biol Cell 2011; 23:480-91. [PMID: 22160596 PMCID: PMC3268726 DOI: 10.1091/mbc.e11-08-0732] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Deletion of the sla1(+) gene, which encodes a homologue of the human RNA-binding protein La in Schizosaccharomyces pombe, causes irregularities in tRNA processing, with altered distribution of pre-tRNA intermediates. We show, using mRNA profiling, that cells lacking sla1(+) have increased mRNAs from amino acid metabolism (AAM) genes and, furthermore, exhibit slow growth in Edinburgh minimal medium. A subset of these AAM genes is under control of the AP-1-like, stress-responsive transcription factors Atf1p and Pcr1p. Although S. pombe growth is resistant to rapamycin, sla1-Δ cells are sensitive, consistent with deficiency of leucine uptake, hypersensitivity to NH4, and genetic links to the target of rapamycin (TOR) pathway. Considering that perturbed intranuclear pre-tRNA metabolism and apparent deficiency in tRNA nuclear export in sla1-Δ cells may trigger the AAM response, we show that modest overexpression of S. pombe los1(+) (also known as Xpo-t), encoding the nuclear exportin for tRNA, suppresses the reduction in pre-tRNA levels, AAM gene up-regulation, and slow growth of sla1-Δ cells. The conclusion that emerges is that sla1(+) regulates AAM mRNA production in S. pombe through its effects on nuclear tRNA processing and probably nuclear export. Finally, the results are discussed in the context of stress response programs in Saccharomyces cerevisiae.
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Affiliation(s)
- Vera Cherkasova
- Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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46
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Olmedo-Verd E, Santamaría-Gómez J, Ochoa de Alda JAG, Ribas de Pouplana L, Luque I. Membrane anchoring of aminoacyl-tRNA synthetases by convergent acquisition of a novel protein domain. J Biol Chem 2011; 286:41057-68. [PMID: 21965654 DOI: 10.1074/jbc.m111.242461] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Four distinct aminoacyl-tRNA synthetases (aaRSs) found in some cyanobacterial species contain a novel protein domain that bears two putative transmembrane helices. This CAAD domain is present in glutamyl-, isoleucyl-, leucyl-, and valyl-tRNA synthetases, the latter of which has probably recruited the domain more than once during evolution. Deleting the CAAD domain from the valyl-tRNA synthetase of Anabaena sp. PCC 7120 did not significantly modify the catalytic properties of this enzyme, suggesting that it does not participate in its canonical tRNA-charging function. Multiple lines of evidence suggest that the function of the CAAD domain is structural, mediating the membrane anchorage of the enzyme, although membrane localization of aaRSs has not previously been described in any living organism. Synthetases containing the CAAD domain were localized in the intracytoplasmic thylakoid membranes of cyanobacteria and were largely absent from the plasma membrane. The CAAD domain was necessary and apparently sufficient for protein targeting to membranes. Moreover, localization of aaRSs in thylakoids was important under nitrogen limiting conditions. In Anabaena, a multicellular filamentous cyanobacterium often used as a model for prokaryotic cell differentiation, valyl-tRNA synthetase underwent subcellular relocation at the cell poles during heterocyst differentiation, a process also dependent on the CAAD domain.
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Affiliation(s)
- Elvira Olmedo-Verd
- Instituto de Bioquímica Vegetal y Fotosíntesis, C.S.I.C. and Universidad de Sevilla, Avda Américo Vespucio 49, E-41092 Seville, Spain
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47
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Giegé R, Jühling F, Pütz J, Stadler P, Sauter C, Florentz C. Structure of transfer RNAs: similarity and variability. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:37-61. [DOI: 10.1002/wrna.103] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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48
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Gilreath MS, Roy H, Bullwinkle TJ, Katz A, Navarre WW, Ibba M. β-Lysine discrimination by lysyl-tRNA synthetase. FEBS Lett 2011; 585:3284-8. [PMID: 21925499 DOI: 10.1016/j.febslet.2011.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 09/04/2011] [Accepted: 09/05/2011] [Indexed: 10/17/2022]
Abstract
Elongation factor P is modified with (R)-β-lysine by the lysyl-tRNA synthetase (LysRS) paralog PoxA. PoxA specificity is orthogonal to LysRS, despite their high similarity. To investigate α- and β-lysine recognition by LysRS and PoxA, amino acid replacements were made in the LysRS active site guided by the PoxA structure. A233S LysRS behaved as wild type with α-lysine, while the G469A and A233S/G469A variants decreased stable α-lysyl-adenylate formation. A233S LysRS recognized β-lysine better than wildtype, suggesting a role for this residue in discriminating α- and β-amino acids. Both enantiomers of β-lysine were substrates for tRNA aminoacylation by LysRS, which, together with the relaxed specificity of the A233S variant, suggest a possible means to develop systems for in vivo co-translational insertion of β-amino acids.
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Affiliation(s)
- Marla S Gilreath
- Ohio State Biochemistry Program, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
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49
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Sauguet L, Moutiez M, Li Y, Belin P, Seguin J, Le Du MH, Thai R, Masson C, Fonvielle M, Pernodet JL, Charbonnier JB, Gondry M. Cyclodipeptide synthases, a family of class-I aminoacyl-tRNA synthetase-like enzymes involved in non-ribosomal peptide synthesis. Nucleic Acids Res 2011; 39:4475-89. [PMID: 21296757 PMCID: PMC3105412 DOI: 10.1093/nar/gkr027] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cyclodipeptide synthases (CDPSs) belong to a newly defined family of enzymes that use aminoacyl-tRNAs (aa-tRNAs) as substrates to synthesize the two peptide bonds of various cyclodipeptides, which are the precursors of many natural products with noteworthy biological activities. Here, we describe the crystal structure of AlbC, a CDPS from Streptomyces noursei. The AlbC structure consists of a monomer containing a Rossmann-fold domain. Strikingly, it is highly similar to the catalytic domain of class-I aminoacyl-tRNA synthetases (aaRSs), especially class-Ic TyrRSs and TrpRSs. AlbC contains a deep pocket, highly conserved among CDPSs. Site-directed mutagenesis studies indicate that this pocket accommodates the aminoacyl moiety of the aa-tRNA substrate in a way similar to that used by TyrRSs to recognize their tyrosine substrates. These studies also suggest that the tRNA moiety of the aa-tRNA interacts with AlbC via at least one patch of basic residues, which is conserved among CDPSs but not present in class-Ic aaRSs. AlbC catalyses its two-substrate reaction via a ping-pong mechanism with a covalent intermediate in which l-Phe is shown to be transferred from Phe-tRNAPhe to an active serine. These findings provide insight into the molecular bases of the interactions between CDPSs and their aa-tRNAs substrates, and the catalytic mechanism used by CDPSs to achieve the non-ribosomal synthesis of cyclodipeptides.
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Affiliation(s)
- Ludovic Sauguet
- CEA, IBITECS, Service d'Ingénierie Moléculaire des Protéines, F-91191 Gif-sur-Yvette, France
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50
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Guo FB, Ning LW, Huang J, Lin H, Zhang HX. Chromosome translocation and its consequence in the genome of Burkholderia cenocepacia AU-1054. Biochem Biophys Res Commun 2010; 403:375-9. [DOI: 10.1016/j.bbrc.2010.11.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2010] [Accepted: 11/11/2010] [Indexed: 10/18/2022]
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