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Herbert C, Valesyan S, Kist J, Limbach PA. Analysis of RNA and Its Modifications. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2024; 17:47-68. [PMID: 38594935 DOI: 10.1146/annurev-anchem-061622-125954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Ribonucleic acids (RNAs) are key biomolecules responsible for the transmission of genetic information, the synthesis of proteins, and modulation of many biochemical processes. They are also often the key components of viruses. Synthetic RNAs or oligoribonucleotides are becoming more widely used as therapeutics. In many cases, RNAs will be chemically modified, either naturally via enzymatic systems within a cell or intentionally during their synthesis. Analytical methods to detect, sequence, identify, and quantify RNA and its modifications have demands that far exceed requirements found in the DNA realm. Two complementary platforms have demonstrated their value and utility for the characterization of RNA and its modifications: mass spectrometry and next-generation sequencing. This review highlights recent advances in both platforms, examines their relative strengths and weaknesses, and explores some alternative approaches that lie at the horizon.
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Affiliation(s)
- Cassandra Herbert
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA;
| | - Satenik Valesyan
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA;
| | - Jennifer Kist
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA;
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA;
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Jaroch M, Sun G, Tsui HCT, Reed C, Sun J, Jörg M, Winkler ME, Rice KC, Dziergowska A, Stich TA, Dedon PC, Dos Santos PC, de Crécy-Lagard V. Alternate routes to mnm 5s 2U synthesis in Gram-positive bacteria. J Bacteriol 2024; 206:e0045223. [PMID: 38551342 PMCID: PMC11025329 DOI: 10.1128/jb.00452-23] [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: 12/27/2023] [Accepted: 03/09/2024] [Indexed: 04/09/2024] Open
Abstract
The wobble bases of tRNAs that decode split codons are often heavily modified. In bacteria, tRNAGlu, Gln, Asp contains a variety of xnm5s2U derivatives. The synthesis pathway for these modifications is complex and fully elucidated only in a handful of organisms, including the Gram-negative Escherichia coli K12 model. Despite the ubiquitous presence of mnm5s2U modification, genomic analysis shows the absence of mnmC orthologous genes, suggesting the occurrence of alternate biosynthetic schemes for the conversion of cmnm5s2U to mnm5s2U. Using a combination of comparative genomics and genetic studies, a member of the YtqA subgroup of the radical Sam superfamily was found to be involved in the synthesis of mnm5s2U in both Bacillus subtilis and Streptococcus mutans. This protein, renamed MnmL, is encoded in an operon with the recently discovered MnmM methylase involved in the methylation of the pathway intermediate nm5s2U into mnm5s2U in B. subtilis. Analysis of tRNA modifications of both S. mutans and Streptococcus pneumoniae shows that growth conditions and genetic backgrounds influence the ratios of pathway intermediates owing to regulatory loops that are not yet understood. The MnmLM pathway is widespread along the bacterial tree, with some phyla, such as Bacilli, relying exclusively on these two enzymes. Although mechanistic details of these newly discovered components are not fully resolved, the occurrence of fusion proteins, alternate arrangements of biosynthetic components, and loss of biosynthetic branches provide examples of biosynthetic diversity to retain a conserved tRNA modification in Nature.IMPORTANCEThe xnm5s2U modifications found in several tRNAs at the wobble base position are widespread in bacteria where they have an important role in decoding efficiency and accuracy. This work identifies a novel enzyme (MnmL) that is a member of a subgroup of the very versatile radical SAM superfamily and is involved in the synthesis of mnm5s2U in several Gram-positive bacteria, including human pathogens. This is another novel example of a non-orthologous displacement in the field of tRNA modification synthesis, showing how different solutions evolve to retain U34 tRNA modifications.
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Affiliation(s)
- Marshall Jaroch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Guangxin Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Singapore-MIT Alliance for Research and Technology, CREATE Tower, Singapore
| | | | - Colbie Reed
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Jingjing Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Singapore-MIT Alliance for Research and Technology, CREATE Tower, Singapore
| | - Marko Jörg
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Malcolm E. Winkler
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Kelly C. Rice
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | | | - Troy A. Stich
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Singapore-MIT Alliance for Research and Technology, CREATE Tower, Singapore
| | | | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
- University of Florida Genetics Institute, Gainesville, Florida, USA
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de Crécy-Lagard V, Hutinet G, Cediel-Becerra JDD, Yuan Y, Zallot R, Chevrette MG, Ratnayake RMMN, Jaroch M, Quaiyum S, Bruner S. Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages. Microbiol Mol Biol Rev 2024; 88:e0019923. [PMID: 38421302 PMCID: PMC10966956 DOI: 10.1128/mmbr.00199-23] [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] [Indexed: 03/02/2024] Open
Abstract
SUMMARYDeazaguanine modifications play multifaceted roles in the molecular biology of DNA and tRNA, shaping diverse yet essential biological processes, including the nuanced fine-tuning of translation efficiency and the intricate modulation of codon-anticodon interactions. Beyond their roles in translation, deazaguanine modifications contribute to cellular stress resistance, self-nonself discrimination mechanisms, and host evasion defenses, directly modulating the adaptability of living organisms. Deazaguanine moieties extend beyond nucleic acid modifications, manifesting in the structural diversity of biologically active natural products. Their roles in fundamental cellular processes and their presence in biologically active natural products underscore their versatility and pivotal contributions to the intricate web of molecular interactions within living organisms. Here, we discuss the current understanding of the biosynthesis and multifaceted functions of deazaguanines, shedding light on their diverse and dynamic roles in the molecular landscape of life.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
- University of Florida Genetics Institute, Gainesville, Florida, USA
| | - Geoffrey Hutinet
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | | | - Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Rémi Zallot
- Department of Life Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Marc G. Chevrette
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | | | - Marshall Jaroch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Steven Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
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Deng L, Kumar J, Rose R, McIntyre W, Fabris D. Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code. MASS SPECTROMETRY REVIEWS 2024; 43:5-38. [PMID: 36052666 DOI: 10.1002/mas.21798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
The discovery of RNA silencing has revealed that non-protein-coding sequences (ncRNAs) can cover essential roles in regulatory networks and their malfunction may result in severe consequences on human health. These findings have prompted a general reassessment of the significance of RNA as a key player in cellular processes. This reassessment, however, will not be complete without a greater understanding of the distribution and function of the over 170 variants of the canonical ribonucleotides, which contribute to the breathtaking structural diversity of natural RNA. This review surveys the analytical approaches employed for the identification, characterization, and detection of RNA posttranscriptional modifications (rPTMs). The merits of analyzing individual units after exhaustive hydrolysis of the initial biopolymer are outlined together with those of identifying their position in the sequence of parent strands. Approaches based on next generation sequencing and mass spectrometry technologies are covered in depth to provide a comprehensive view of their respective merits. Deciphering the epitranscriptomic code will require not only mapping the location of rPTMs in the various classes of RNAs, but also assessing the variations of expression levels under different experimental conditions. The fact that no individual platform is currently capable of meeting all such demands implies that it will be essential to capitalize on complementary approaches to obtain the desired information. For this reason, the review strived to cover the broadest possible range of techniques to provide readers with the fundamental elements necessary to make informed choices and design the most effective possible strategy to accomplish the task at hand.
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Affiliation(s)
- L Deng
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - J Kumar
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - R Rose
- Department of Advanced Research Technologies, New York University Langone Health Center, New York, USA
| | - W McIntyre
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Daniele Fabris
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
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Jaroch M, Sun G, Tsui HCT, Reed C, Sun J, Jörg M, Winkler ME, Rice KC, Stich TA, Dedon PC, Dos Santos PC, de Crécy-Lagard V. Alternate routes to mnm 5 s 2 U synthesis in Gram-positive bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.21.572861. [PMID: 38187551 PMCID: PMC10769405 DOI: 10.1101/2023.12.21.572861] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The wobble bases of tRNAs that decode split codons are often heavily modified. In Bacteria tRNA Glu, Gln, Asp contain a variety of xnm 5 s 2 U derivatives. The synthesis pathway for these modifications is complex and fully elucidated only in a handful of organisms, including the Gram-negative Escherichia coli K12 model. Despite the ubiquitous presence of mnm 5 s 2 U modification, genomic analysis shows the absence of mnmC orthologous genes, suggesting the occurrence of alternate biosynthetic schemes for the installation of this modification. Using a combination of comparative genomics and genetic studies, a member of the YtqA subgroup of the Radical Sam superfamily was found to be involved in the synthesis of mnm 5 s 2 U in both Bacillus subtilis and Streptococcus mutans . This protein, renamed MnmL, is encoded in an operon with the recently discovered MnmM methylase involved in the methylation of the pathway intermediate nm 5 s 2 U into mnm 5 s 2 U in B. subtilis . Analysis of tRNA modifications of both S. mutans and Streptococcus pneumoniae shows that growth conditions and genetic backgrounds influence the ratios of pathways intermediates in regulatory loops that are not yet understood. The MnmLM pathway is widespread along the bacterial tree, with some phyla, such as Bacilli, relying exclusively on these two enzymes. The occurrence of fusion proteins, alternate arrangements of biosynthetic components, and loss of biosynthetic branches provide examples of biosynthetic diversity to retain a conserved tRNA modification in nature. Importance The xnm 5 s 2 U modifications found in several tRNAs at the wobble base position are widespread in Bacteria where they have an important role in decoding efficiency and accuracy. This work identifies a novel enzyme (MnmL) that is a member of a subgroup of the very versatile Radical SAM superfamily and is involved in the synthesis of mnm 5 s 2 U in several Gram-positive bacteria, including human pathogens. This is another novel example of a non-orthologous displacement in the field of tRNA modification synthesis, showing how different solutions evolve to retain U34 tRNA modifications.
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Jones JD, Simcox KM, Kennedy RT, Koutmou KS. Direct sequencing of total Saccharomyces cerevisiae tRNAs by LC-MS/MS. RNA (NEW YORK, N.Y.) 2023; 29:1201-1214. [PMID: 37169396 PMCID: PMC10351886 DOI: 10.1261/rna.079656.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 04/23/2023] [Indexed: 05/13/2023]
Abstract
Among RNAs, transfer RNAs (tRNAs) contain the widest variety of abundant posttranscriptional chemical modifications. These modifications are crucial for tRNAs to participate in protein synthesis, promoting proper tRNA structure and aminoacylation, facilitating anticodon:codon recognition, and ensuring the reading frame maintenance of the ribosome. While tRNA modifications were long thought to be stoichiometric, it is becoming increasingly apparent that these modifications can change dynamically in response to the cellular environment. The ability to broadly characterize the fluctuating tRNA modification landscape will be essential for establishing the molecular level contributions of individual sites of tRNA modification. The locations of modifications within individual tRNA sequences can be mapped using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). In this approach, a single tRNA species is purified, treated with ribonucleases, and the resulting single-stranded RNA products are subject to LC-MS/MS analysis. The application of LC-MS/MS to study tRNAs is limited by the necessity of analyzing one tRNA at a time, because the digestion of total tRNA mixtures by commercially available ribonucleases produces many short digestion products unable to be uniquely mapped back to a single site within a tRNA. We overcame these limitations by taking advantage of the highly structured nature of tRNAs to prevent the full digestion by single-stranded RNA-specific ribonucleases. Folding total tRNA prior to digestion allowed us to sequence Saccharomyces cerevisiae tRNAs with up to 97% sequence coverage for individual tRNA species by LC-MS/MS. This method presents a robust avenue for directly detecting the distribution of modifications in total tRNAs.
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Affiliation(s)
- Joshua D Jones
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Kaley M Simcox
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Kristin S Koutmou
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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Huang G, Zhang F, Xie D, Ma Y, Wang P, Cao G, Chen L, Lin S, Zhao Z, Cai Z. High-throughput profiling of RNA modifications by ultra-performance liquid chromatography coupled to complementary mass spectrometry: Methods, quality control, and applications. Talanta 2023; 263:124697. [PMID: 37262985 DOI: 10.1016/j.talanta.2023.124697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/17/2023] [Accepted: 05/20/2023] [Indexed: 06/03/2023]
Abstract
Although next-generation sequencing technology has been used to delineate RNA modifications in recent years, the paucity of appropriate converting reactions or specific antibodies impedes the accurate characterization and quantification of numerous RNA modifications, especially when these modifications demonstrate wide variations across developmental stages and cell types. In this study, we developed a high-throughput analytical platform coupling ultra-performance liquid chromatograph (UPLC) with complementary mass spectrometry (MS) to identify and quantify RNA modifications in both synthetic and biological samples. Sixty-four types of RNA modifications, including positional isomers and hypermodified ribonucleosides, were successfully monitored within a 16-min single run of UPLC-MS. Two independent methods to cross-validate the purity of RNA extracted from Caenorhabditis elegans (C. elegans) were developed using the coexisting C. elegans and Escherichia coli (E. coli) as a surveillance system. To test the validity of the method, we investigated the RNA modification landscape of three model organisms, C. elegans, E. coli, and Arabidopsis thaliana (A. thaliana). Both the identity and molarity of modified ribonucleosides markedly varied among the species. Moreover, our platform is not only useful for exploring the dynamics of RNA modifications in response to environmental cues (e.g., cold shock) but can also help with the identification of RNA-modifying enzymes in genetic studies. Cumulatively, our method presents a novel platform for the comprehensive analysis of RNA modifications, which will be of benefit to both analytical chemists involved in biomarker discovery and biologists conducting functional studies of RNA modifications.
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Affiliation(s)
- Gefei Huang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Feng Zhang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Dongying Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Yiming Ma
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Pengxi Wang
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Guodong Cao
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Leijian Chen
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Siyi Lin
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China.
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China.
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8
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Detection technologies for RNA modifications. Exp Mol Med 2022; 54:1601-1616. [PMID: 36266445 PMCID: PMC9636272 DOI: 10.1038/s12276-022-00821-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/21/2022] [Accepted: 05/18/2022] [Indexed: 12/29/2022] Open
Abstract
To date, more than 170 chemical modifications have been characterized in RNA, providing a new layer of gene expression regulation termed the 'epitranscriptome'. RNA modification detection methods and tools advance the functional studies of the epitranscriptome. According to the detection throughput and principles, existing RNA modification detection technologies can be categorized into four classes, including quantification methods, locus-specific detection methods, next-generation sequencing-based detection technologies and nanopore direct RNA sequencing-based technologies. In this review, we summarize the current knowledge about these RNA modification detection technologies and discuss the challenges for the existing detection tools, providing information for a comprehensive understanding of the epitranscriptome.
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Miller JB, Meurs TE, Hodgman MW, Song B, Miller KN, Ebbert MTW, Kauwe JSK, Ridge PG. The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface. NAR Genom Bioinform 2022; 4:lqac039. [PMID: 35664804 PMCID: PMC9155233 DOI: 10.1093/nargab/lqac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/01/2022] [Accepted: 05/24/2022] [Indexed: 11/14/2022] Open
Abstract
Ramp sequences occur when the average translational efficiency of codons near the 5′ end of highly expressed genes is significantly lower than the rest of the gene sequence, which counterintuitively increases translational efficiency by decreasing downstream ribosomal collisions. Here, we show that the relative codon adaptiveness within different tissues changes the existence of a ramp sequence without altering the underlying genetic code. We present the first comprehensive analysis of tissue and cell type-specific ramp sequences and report 3108 genes with ramp sequences that change between tissues and cell types, which corresponds with increased gene expression within those tissues and cells. The Ramp Atlas (https://ramps.byu.edu/) allows researchers to query precomputed ramp sequences in 18 388 genes across 62 tissues and 66 cell types and calculate tissue-specific ramp sequences from user-uploaded FASTA files through an intuitive web interface. We used The Ramp Atlas to identify seven SARS-CoV-2 genes and seven human SARS-CoV-2 entry factor genes with tissue-specific ramp sequences that may help explain viral proliferation within those tissues. We anticipate that The Ramp Atlas will facilitate personalized and creative tissue-specific ramp sequence analyses for both human and viral genes that will increase our ability to utilize this often-overlooked regulatory region.
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Affiliation(s)
- Justin B Miller
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40504, USA
| | - Taylor E Meurs
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Matthew W Hodgman
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40504, USA
| | - Benjamin Song
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Kyle N Miller
- Department of Computer Science, Utah Valley University, Orem, UT 84058, USA
| | - Mark T W Ebbert
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40504, USA
| | - John S K Kauwe
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Perry G Ridge
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
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Anastasiou R, Kazou M, Georgalaki M, Aktypis A, Zoumpopoulou G, Tsakalidou E. Omics Approaches to Assess Flavor Development in Cheese. Foods 2022; 11:188. [PMID: 35053920 PMCID: PMC8775153 DOI: 10.3390/foods11020188] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/03/2022] [Accepted: 01/09/2022] [Indexed: 12/27/2022] Open
Abstract
Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.
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Affiliation(s)
- Rania Anastasiou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece; (M.K.); (M.G.); (A.A.); (G.Z.); (E.T.)
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11
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Espadas G, Morales-Sanfrutos J, Medina R, Lucas MC, Novoa EM, Sabidó E. High-performance nano-flow liquid chromatography column combined with high- and low-collision energy data-independent acquisition enables targeted and discovery identification of modified ribonucleotides by mass spectrometry. J Chromatogr A 2022; 1665:462803. [PMID: 35042139 DOI: 10.1016/j.chroma.2022.462803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/29/2021] [Accepted: 01/01/2022] [Indexed: 01/10/2023]
Abstract
Over 170 post-transcriptional RNA modifications have been described and are common in all kingdoms of life. These modifications range from methylation to complex chemical structures, with methylation being the most abundant. RNA modifications play a key role in RNA folding and function and their dysregulation in humans has been linked to several diseases such as cancer, metabolic diseases or neurological disorder. Nowadays, liquid chromatography-tandem mass spectrometry is considered the gold standard method for the identification and quantification of these modifications due to its sensitivity and accuracy. However, the analysis of modified ribonucleosides by mass spectrometry is complex due to the presence of positional isomers. In this scenario, optimal separation of these compounds by highly sensitive liquid chromatography combined with the generation of high-information spectra is critical to unequivocally identify them, especially in high-complex mixtures. Here we present an analytical method that comprises a new type of mixed-mode nano-flow liquid chromatography column combined with high- and low-collision energy data-independent mass spectrometric acquisition for the identification and quantitation of modified ribonucleosides. The method produces content-rich spectra and combines targeted and screening capabilities thus enabling the identification of a variety of modified nucleosides in biological matrices by single-shot liquid chromatographic analysis coupled to mass spectrometry.
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Affiliation(s)
- Guadalupe Espadas
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain; Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Julia Morales-Sanfrutos
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain; Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Rebeca Medina
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
| | - Morghan C Lucas
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain; Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Eva Maria Novoa
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain; Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Eduard Sabidó
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain; Universitat Pompeu Fabra, 08003, Barcelona, Spain.
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12
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Huang G, Ding Q, Xie D, Cai Z, Zhao Z. Technical challenges in defining RNA modifications. Semin Cell Dev Biol 2021; 127:155-165. [PMID: 34838434 DOI: 10.1016/j.semcdb.2021.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/28/2021] [Accepted: 11/10/2021] [Indexed: 01/27/2023]
Abstract
It is well established that DNA base modifications play a key role in gene regulation during development and in response to environmental stress. This type of epigenetic control of development and environmental responses has been intensively studied over the past few decades. Similar to DNA, various RNA species also undergo modifications that play important roles in, for example, RNA splicing, protein translation, and the avoidance of immune surveillance by host. More than 160 different types of RNA modifications have been identified. In addition to base modifications, RNA modification also involves splicing of pre-mRNAs, leading to as many as tens of transcript isoforms from a single pre-RNA, especially in higher organisms. However, the function, prevalence and distribution of RNA modifications are poorly understood. The lack of a suitable method for the reliable identification of RNA modifications constitutes a significant challenge to studying their functions. This review focuses on the technologies that enable de novo identification of RNA base modifications and the alternatively spliced mRNA transcripts.
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Affiliation(s)
- Gefei Huang
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China; State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
| | - Qiutao Ding
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Dongying Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Zongwei Cai
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China; State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China.
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, China; State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China.
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13
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Santamaría-Gómez J, Rubio MÁ, López-Igual R, Romero-Losada AB, Delgado-Chaves FM, Bru-Martínez R, Romero-Campero FJ, Herrero A, Ibba M, Ochoa de Alda JAG, Luque I. Role of a cryptic tRNA gene operon in survival under translational stress. Nucleic Acids Res 2021; 49:8757-8776. [PMID: 34379789 PMCID: PMC8421152 DOI: 10.1093/nar/gkab661] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 07/12/2021] [Accepted: 07/22/2021] [Indexed: 01/08/2023] Open
Abstract
As compared to eukaryotes, bacteria have a reduced tRNA gene set encoding between 30 and 220 tRNAs. Although in most bacterial phyla tRNA genes are dispersed in the genome, many species from distinct phyla also show genes forming arrays. Here, we show that two types of arrays with distinct evolutionary origins exist. This work focuses on long tRNA gene arrays (L-arrays) that encompass up to 43 genes, which disseminate by horizontal gene transfer and contribute supernumerary tRNA genes to the host. Although in the few cases previously studied these arrays were reported to be poorly transcribed, here we show that the L-array of the model cyanobacterium Anabaena sp. PCC 7120, encoding 23 functional tRNAs, is largely induced upon impairment of the translation machinery. The cellular response to this challenge involves a global reprogramming of the transcriptome in two phases. tRNAs encoded in the array are induced in the second phase of the response, directly contributing to cell survival. Results presented here show that in some bacteria the tRNA gene set may be partitioned between a housekeeping subset, which constantly sustains translation, and an inducible subset that is generally silent but can provide functionality under particular conditions.
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Affiliation(s)
- Javier Santamaría-Gómez
- Instituto de Bioquímica Vegetal y Fotosíntesis, C.S.I.C. and Universidad de Sevilla, Seville E-41092, Spain
| | - Miguel Ángel Rubio
- Instituto de Bioquímica Vegetal y Fotosíntesis, C.S.I.C. and Universidad de Sevilla, Seville E-41092, Spain.,Center for RNA Biology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA.,Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA
| | - Rocío López-Igual
- Instituto de Bioquímica Vegetal y Fotosíntesis, C.S.I.C. and Universidad de Sevilla, Seville E-41092, Spain
| | - Ana B Romero-Losada
- Instituto de Bioquímica Vegetal y Fotosíntesis, C.S.I.C. and Universidad de Sevilla, Seville E-41092, Spain.,Department of Computer Science and Artificial Intelligence, Universidad de Sevilla, Seville E-41012, Spain
| | - Fernando M Delgado-Chaves
- Instituto de Bioquímica Vegetal y Fotosíntesis, C.S.I.C. and Universidad de Sevilla, Seville E-41092, Spain
| | - Roque Bru-Martínez
- Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, Alicante E- 03690, Spain
| | - Francisco J Romero-Campero
- Instituto de Bioquímica Vegetal y Fotosíntesis, C.S.I.C. and Universidad de Sevilla, Seville E-41092, Spain.,Department of Computer Science and Artificial Intelligence, Universidad de Sevilla, Seville E-41012, Spain
| | - Antonia Herrero
- Instituto de Bioquímica Vegetal y Fotosíntesis, C.S.I.C. and Universidad de Sevilla, Seville E-41092, Spain
| | - Michael Ibba
- Center for RNA Biology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA.,Department of Microbiology, The Ohio State University, 318 West 12th Avenue, Columbus, OH 43210, USA.,Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA
| | - Jesús A G Ochoa de Alda
- Didáctica de las Ciencias Experimentales, Facultad de Formación del Profesorado, Universidad de Extremadura, Cáceres E-10003, Spain
| | - Ignacio Luque
- Instituto de Bioquímica Vegetal y Fotosíntesis, C.S.I.C. and Universidad de Sevilla, Seville E-41092, Spain
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14
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Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria. BMC Genomics 2021; 22:28. [PMID: 33413101 PMCID: PMC7788899 DOI: 10.1186/s12864-020-07338-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Psychrotrophic lactic acid bacteria (LAB) species are the dominant species in the microbiota of cold-stored modified-atmosphere-packaged food products and are the main cause of food spoilage. Despite the importance of psychrotrophic LAB, their response to cold or heat has not been studied. Here, we studied the transcriptome-level cold- and heat-shock response of spoilage lactic acid bacteria with time-series RNA-seq for Le. gelidum, Lc. piscium, and P. oligofermentans at 0 °C, 4 °C, 14 °C, 25 °C, and 28 °C. RESULTS We observed that the cold-shock protein A (cspA) gene was the main cold-shock protein gene in all three species. Our results indicated that DEAD-box RNA helicase genes (cshA, cshB) also play a critical role in cold-shock response in psychrotrophic LAB. In addition, several RNase genes were involved in cold-shock response in Lc. piscium and P. oligofermentans. Moreover, gene network inference analysis provided candidate genes involved in cold-shock response. Ribosomal proteins, tRNA modification, rRNA modification, and ABC and efflux MFS transporter genes clustered with cold-shock response genes in all three species, indicating that these genes could be part of the cold-shock response machinery. Heat-shock treatment caused upregulation of Clp protease and chaperone genes in all three species. We identified transcription binding site motifs for heat-shock response genes in Le. gelidum and Lc. piscium. Finally, we showed that food spoilage-related genes were upregulated at cold temperatures. CONCLUSIONS The results of this study provide new insights on the cold- and heat-shock response of psychrotrophic LAB. In addition, candidate genes involved in cold- and heat-shock response predicted using gene network inference analysis could be used as targets for future studies.
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15
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Galvanin A, Vogt LM, Grober A, Freund I, Ayadi L, Bourguignon-Igel V, Bessler L, Jacob D, Eigenbrod T, Marchand V, Dalpke A, Helm M, Motorin Y. Bacterial tRNA 2'-O-methylation is dynamically regulated under stress conditions and modulates innate immune response. Nucleic Acids Res 2020; 48:12833-12844. [PMID: 33275131 PMCID: PMC7736821 DOI: 10.1093/nar/gkaa1123] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/03/2020] [Indexed: 12/23/2022] Open
Abstract
RNA modifications are a well-recognized way of gene expression regulation at the post-transcriptional level. Despite the importance of this level of regulation, current knowledge on modulation of tRNA modification status in response to stress conditions is far from being complete. While it is widely accepted that tRNA modifications are rather dynamic, such variations are mostly assessed in terms of total tRNA, with only a few instances where changes could be traced to single isoacceptor species. Using Escherichia coli as a model system, we explored stress-induced modulation of 2'-O-methylations in tRNAs by RiboMethSeq. This analysis and orthogonal analytical measurements by LC-MS show substantial, but not uniform, increase of the Gm18 level in selected tRNAs under mild bacteriostatic antibiotic stress, while other Nm modifications remain relatively constant. The absence of Gm18 modification in tRNAs leads to moderate alterations in E. coli mRNA transcriptome, but does not affect polysomal association of mRNAs. Interestingly, the subset of motility/chemiotaxis genes is significantly overexpressed in ΔTrmH mutant, this corroborates with increased swarming motility of the mutant strain. The stress-induced increase of tRNA Gm18 level, in turn, reduced immunostimulation properties of bacterial tRNAs, which is concordant with the previous observation that Gm18 is a suppressor of Toll-like receptor 7 (TLR7)-mediated interferon release. This documents an effect of stress induced modulation of tRNA modification that acts outside protein translation.
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Affiliation(s)
- Adeline Galvanin
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
| | - Lea-Marie Vogt
- Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Antonia Grober
- Institute of Medical Microbiology and Hygiene, Technische Universität Dresden, 01307 Dresden, Germany
| | - Isabel Freund
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Ruprecht-Karls University Heidelberg, 69117 Heidelberg, Germany
| | - Lilia Ayadi
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
| | - Valerie Bourguignon-Igel
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
| | - Larissa Bessler
- Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Dominik Jacob
- Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Tatjana Eigenbrod
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Ruprecht-Karls University Heidelberg, 69117 Heidelberg, Germany
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
| | - Alexander Dalpke
- Institute of Medical Microbiology and Hygiene, Technische Universität Dresden, 01307 Dresden, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Science, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France
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16
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de Crécy-Lagard V, Jaroch M. Functions of Bacterial tRNA Modifications: From Ubiquity to Diversity. Trends Microbiol 2020; 29:41-53. [PMID: 32718697 DOI: 10.1016/j.tim.2020.06.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 01/21/2023]
Abstract
Modified nucleotides in tRNA are critical components of the translation apparatus, but their importance in the process of translational regulation had until recently been greatly overlooked. Two breakthroughs have recently allowed a fuller understanding of the importance of tRNA modifications in bacterial physiology. One is the identification of the full set of tRNA modification genes in model organisms such as Escherichia coli K12. The second is the improvement of available analytical tools to monitor tRNA modification patterns. The role of tRNA modifications varies greatly with the specific modification within a given tRNA and with the organism studied. The absence of these modifications or reductions can lead to cell death or pleiotropic phenotypes or may have no apparent visible effect. By linking translation through their decoding functions to metabolism through their biosynthetic pathways, tRNA modifications are emerging as important components of the bacterial regulatory toolbox.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Marshall Jaroch
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA
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17
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de Crécy-Lagard V, Ross RL, Jaroch M, Marchand V, Eisenhart C, Brégeon D, Motorin Y, Limbach PA. Survey and Validation of tRNA Modifications and Their Corresponding Genes in Bacillus subtilis sp Subtilis Strain 168. Biomolecules 2020; 10:E977. [PMID: 32629984 PMCID: PMC7408541 DOI: 10.3390/biom10070977] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 12/14/2022] Open
Abstract
Extensive knowledge of both the nature and position of tRNA modifications in all cellular tRNAs has been limited to two bacteria, Escherichia coli and Mycoplasma capricolum. Bacillus subtilis sp subtilis strain 168 is the model Gram-positive bacteria and the list of the genes involved in tRNA modifications in this organism is far from complete. Mass spectrometry analysis of bulk tRNA extracted from B. subtilis, combined with next generation sequencing technologies and comparative genomic analyses, led to the identification of 41 tRNA modification genes with associated confidence scores. Many differences were found in this model Gram-positive bacteria when compared to E. coli. In general, B. subtilis tRNAs are less modified than those in E. coli, even if some modifications, such as m1A22 or ms2t6A, are only found in the model Gram-positive bacteria. Many examples of non-orthologous displacements and of variations in the most complex pathways are described. Paralog issues make uncertain direct annotation transfer from E. coli to B. subtilis based on homology only without further experimental validation. This difficulty was shown with the identification of the B. subtilis enzyme that introduces ψ at positions 31/32 of the tRNAs. This work presents the most up to date list of tRNA modification genes in B. subtilis, identifies the gaps in knowledge, and lays the foundation for further work to decipher the physiological role of tRNA modifications in this important model organism and other bacteria.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA;
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Robert L. Ross
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45221, USA;
| | - Marshall Jaroch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA;
| | - Virginie Marchand
- UMR7365 IMoPA CNRS-UL and UMS2008 CNRS-UL-INSERM, Université de Lorraine, Biopôle UL, 54000 Nancy, France; (V.M.); (Y.M.)
| | - Christina Eisenhart
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (C.E.); (P.A.L.)
| | - Damien Brégeon
- IBPS, Biology of Aging and Adaptation, Sorbonne University, 7 Quai Saint Bernard, CEDEX 05, F-75252 Paris, France;
| | - Yuri Motorin
- UMR7365 IMoPA CNRS-UL and UMS2008 CNRS-UL-INSERM, Université de Lorraine, Biopôle UL, 54000 Nancy, France; (V.M.); (Y.M.)
| | - Patrick A. Limbach
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA; (C.E.); (P.A.L.)
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18
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Meyer B, Immer C, Kaiser S, Sharma S, Yang J, Watzinger P, Weiß L, Kotter A, Helm M, Seitz HM, Kötter P, Kellner S, Entian KD, Wöhnert J. Identification of the 3-amino-3-carboxypropyl (acp) transferase enzyme responsible for acp3U formation at position 47 in Escherichia coli tRNAs. Nucleic Acids Res 2020; 48:1435-1450. [PMID: 31863583 PMCID: PMC7026641 DOI: 10.1093/nar/gkz1191] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 02/06/2023] Open
Abstract
tRNAs from all domains of life contain modified nucleotides. However, even for the experimentally most thoroughly characterized model organism Escherichia coli not all tRNA modification enzymes are known. In particular, no enzyme has been found yet for introducing the acp3U modification at position 47 in the variable loop of eight E. coli tRNAs. Here we identify the so far functionally uncharacterized YfiP protein as the SAM-dependent 3-amino-3-carboxypropyl transferase catalyzing this modification and thereby extend the list of known tRNA modification enzymes in E. coli. Similar to the Tsr3 enzymes that introduce acp modifications at U or m1Ψ nucleotides in rRNAs this protein contains a DTW domain suggesting that acp transfer reactions to RNA nucleotides are a general function of DTW domain containing proteins. The introduction of the acp3U-47 modification in E. coli tRNAs is promoted by the presence of the m7G-46 modification as well as by growth in rich medium. However, a deletion of the enzymes responsible for the modifications at position 46 and 47 in the variable loop of E. coli tRNAs did not lead to a clearly discernible phenotype suggesting that these two modifications play only a minor role in ensuring the proper function of tRNAs in E. coli.
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Affiliation(s)
- Britta Meyer
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Carina Immer
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Steffen Kaiser
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 Munich, Germany
| | - Sunny Sharma
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany.,Department of Cell Biology and Neurosciences, Rutgers University, Piscataway, NJ 08854, USA
| | - Jun Yang
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany.,Department of Cell Biology and Neurosciences, Rutgers University, Piscataway, NJ 08854, USA
| | - Peter Watzinger
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Lena Weiß
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Annika Kotter
- Institute of Pharmacy and Biochemistry, Johannes-Gutenberg-Universität Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes-Gutenberg-Universität Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Hans-Michael Seitz
- Institute for Geosciences, Research Unit Mineralogy, and Frankfurt Isotope and Element Research Center (FIERCE), Goethe-Universität Frankfurt, Altenhöferallee 1, 60438 Frankfurt/M., Germany
| | - Peter Kötter
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Stefanie Kellner
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5, 81377 Munich, Germany
| | - Karl-Dieter Entian
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany.,Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt/M., Germany
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19
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Thakur P, Estevez M, Lobue PA, Limbach PA, Addepalli B. Improved RNA modification mapping of cellular non-coding RNAs using C- and U-specific RNases. Analyst 2020; 145:816-827. [PMID: 31825413 PMCID: PMC7002195 DOI: 10.1039/c9an02111f] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Locating ribonucleoside modifications within an RNA sequence requires digestion of the RNA into oligoribonucleotides of amenable size for subsequent analysis by LC-MS (liquid chromatography-mass spectrometry). This approach, widely referred to as RNA modification mapping, is facilitated through ribonucleases (RNases) such as T1 (guanosine-specific), U2 (purine-selective) and A (pyrimidine-specific) among others. Sequence coverage by these enzymes depends on positioning of the recognized nucleobase (such as guanine or purine or pyrimidine) in the sequence and its ribonucleotide composition. Using E. coli transfer RNA (tRNA) and ribosomal RNA (rRNA) as model samples, we demonstrate the ability of complementary nucleobase-specific ribonucleases cusativin (C-specific) and MC1 (U-specific) to generate digestion products that facilitate confident mapping of modifications in regions such as G-rich and pyrimidine-rich segments of RNA, and to distinguish C to U sequence differences. These enzymes also increase the number of oligonucleotide digestion products that are unique to a specific RNA sequence. Further, with these additional RNases, multiple modifications can be localized with high confidence in a single set of experiments with minimal dependence on the individual tRNA abundance in a mixture. The sequence overlaps observed with these complementary digestion products and that of RNase T1 improved sequence coverage to 75% or above. A similar level of sequence coverage was also observed for the 2904 nt long 23S rRNA indicating their utility has no dependence on RNA size. Wide-scale adoption of these additional modification mapping tools could help expedite the characterization of modified RNA sequences to understand their structural and functional role in various living systems.
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Affiliation(s)
- Priti Thakur
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA.
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20
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Boccaletto P, Machnicka MA, Purta E, Piatkowski P, Baginski B, Wirecki TK, de Crécy-Lagard V, Ross R, Limbach PA, Kotter A, Helm M, Bujnicki JM. MODOMICS: a database of RNA modification pathways. 2017 update. Nucleic Acids Res 2019; 46:D303-D307. [PMID: 29106616 PMCID: PMC5753262 DOI: 10.1093/nar/gkx1030] [Citation(s) in RCA: 1289] [Impact Index Per Article: 257.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/18/2017] [Indexed: 12/13/2022] Open
Abstract
MODOMICS is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA-modifying enzymes. In the current database version, we included the following new features and data: extended mass spectrometry and liquid chromatography data for modified nucleosides; links between human tRNA sequences and MINTbase - a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments; new, machine-friendly system of unified abbreviations for modified nucleoside names; sets of modified tRNA sequences for two bacterial species, updated collection of mammalian tRNA modifications, 19 newly identified modified ribonucleosides and 66 functionally characterized proteins involved in RNA modification. Data from MODOMICS have been linked to the RNAcentral database of RNA sequences. MODOMICS is available at http://modomics.genesilico.pl.
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Affiliation(s)
- Pietro Boccaletto
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Magdalena A Machnicka
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.,Institute of Informatics, University of Warsaw, Banacha 2, PL-02-097 Warsaw, Poland
| | - Elzbieta Purta
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Pawel Piatkowski
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Blazej Baginski
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Tomasz K Wirecki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | | | - Robert Ross
- Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Patrick A Limbach
- Department of Chemistry, Rieveschl Laboratories for Mass Spectrometry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Annika Kotter
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Mark Helm
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland.,Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, PL-61-614 Poznan, Poland
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21
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Barraud P, Tisné C. To be or not to be modified: Miscellaneous aspects influencing nucleotide modifications in tRNAs. IUBMB Life 2019; 71:1126-1140. [PMID: 30932315 PMCID: PMC6850298 DOI: 10.1002/iub.2041] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/10/2019] [Indexed: 12/12/2022]
Abstract
Transfer RNAs (tRNAs) are essential components of the cellular protein synthesis machineries, but are also implicated in many roles outside translation. To become functional, tRNAs, initially transcribed as longer precursor tRNAs, undergo a tightly controlled biogenesis process comprising the maturation of their extremities, removal of intronic sequences if present, addition of the 3'-CCA amino-acid accepting sequence, and aminoacylation. In addition, the most impressive feature of tRNA biogenesis consists in the incorporation of a large number of posttranscriptional chemical modifications along its sequence. The chemical nature of these modifications is highly diverse, with more than hundred different modifications identified in tRNAs to date. All functions of tRNAs in cells are controlled and modulated by modifications, making the understanding of the mechanisms that determine and influence nucleotide modifications in tRNAs an essential point in tRNA biology. This review describes the different aspects that determine whether a certain position in a tRNA molecule is modified or not. We describe how sequence and structural determinants, as well as the presence of prior modifications control modification processes. We also describe how environmental factors and cellular stresses influence the level and/or the nature of certain modifications introduced in tRNAs, and report situations where these dynamic modulations of tRNA modification levels are regulated by active demodification processes. © 2019 IUBMB Life, 71(8):1126-1140, 2019.
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Affiliation(s)
- Pierre Barraud
- Expression génétique microbienneInstitut de biologie physico‐chimique (IBPC), UMR 8261, CNRS, Université Paris DiderotParisFrance
| | - Carine Tisné
- Expression génétique microbienneInstitut de biologie physico‐chimique (IBPC), UMR 8261, CNRS, Université Paris DiderotParisFrance
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22
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Antoine L, Wolff P, Westhof E, Romby P, Marzi S. Mapping post-transcriptional modifications in Staphylococcus aureus tRNAs by nanoLC/MSMS. Biochimie 2019; 164:60-69. [PMID: 31295507 DOI: 10.1016/j.biochi.2019.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/03/2019] [Indexed: 02/06/2023]
Abstract
RNA modifications are involved in numerous biological processes. These modifications are constitutive or modulated in response to adaptive processes and can impact RNA base-pairing formation, protein recognition, RNA structure and stability. tRNAs are the most abundantly modified RNA molecules. Analysis of the roles of their modifications in response to stress, environmental changes, and infections caused by pathogens, has fueled new research areas. Nevertheless, the detection of modified nucleotides in RNAs is still a challenging task. We present here a reliable method to identify and localize tRNA modifications, which was applied to the human pathogenic bacteria, Staphyloccocus aureus. The method is based on a separation of tRNA species on a two-dimensional polyacrylamide gel electrophoresis followed by nano liquid chromatography-mass spectrometry. We provided a list of modifications mapped on 25 out of the 40 tRNA species (one isoacceptor for each amino acid). This method can be easily used to monitor the dynamics of tRNA modifications in S. aureus in response to stress adaptation and during infection of the host, a relatively unexplored field.
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Affiliation(s)
- Laura Antoine
- Université de Strasbourg, CNRS, Architecture et Réactivité de L'ARN, UPR 9002, F-67000, Strasbourg, France
| | - Philippe Wolff
- Université de Strasbourg, CNRS, Architecture et Réactivité de L'ARN, UPR 9002, F-67000, Strasbourg, France; Plateforme Protéomique Strasbourg Esplanade, CNRS, FR1589, F-67000, Strasbourg, France
| | - Eric Westhof
- Université de Strasbourg, CNRS, Architecture et Réactivité de L'ARN, UPR 9002, F-67000, Strasbourg, France
| | - Pascale Romby
- Université de Strasbourg, CNRS, Architecture et Réactivité de L'ARN, UPR 9002, F-67000, Strasbourg, France
| | - Stefano Marzi
- Université de Strasbourg, CNRS, Architecture et Réactivité de L'ARN, UPR 9002, F-67000, Strasbourg, France.
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23
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tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii. J Bacteriol 2019; 201:JB.00690-18. [PMID: 30745370 DOI: 10.1128/jb.00690-18] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/31/2019] [Indexed: 12/13/2022] Open
Abstract
tRNAs play a critical role in mRNA decoding, and posttranscriptional modifications within tRNAs drive decoding efficiency and accuracy. The types and positions of tRNA modifications in model bacteria have been extensively studied, and tRNA modifications in a few eukaryotic organisms have also been characterized and localized to particular tRNA sequences. However, far less is known regarding tRNA modifications in archaea. While the identities of modifications have been determined for multiple archaeal organisms, Haloferax volcanii is the only organism for which modifications have been extensively localized to specific tRNA sequences. To improve our understanding of archaeal tRNA modification patterns and codon-decoding strategies, we have used liquid chromatography and tandem mass spectrometry to characterize and then map posttranscriptional modifications on 34 of the 35 unique tRNA sequences of Methanocaldococcus jannaschii A new posttranscriptionally modified nucleoside, 5-cyanomethyl-2-thiouridine (cnm5s2U), was discovered and localized to position 34. Moreover, data consistent with wyosine pathway modifications were obtained beyond the canonical tRNAPhe as is typical for eukaryotes. The high-quality mapping of tRNA anticodon loops enriches our understanding of archaeal tRNA modification profiles and decoding strategies.IMPORTANCE While many posttranscriptional modifications in M. jannaschii tRNAs are also found in bacteria and eukaryotes, several that are unique to archaea were identified. By RNA modification mapping, the modification profiles of M. jannaschii tRNA anticodon loops were characterized, allowing a comparative analysis with H. volcanii modification profiles as well as a general comparison with bacterial and eukaryotic decoding strategies. This general comparison reveals that M. jannaschii, like H. volcanii, follows codon-decoding strategies similar to those used by bacteria, although position 37 appears to be modified to a greater extent than seen in H. volcanii.
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24
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Ayadi L, Galvanin A, Pichot F, Marchand V, Motorin Y. RNA ribose methylation (2'-O-methylation): Occurrence, biosynthesis and biological functions. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:253-269. [PMID: 30572123 DOI: 10.1016/j.bbagrm.2018.11.009] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/26/2018] [Accepted: 11/30/2018] [Indexed: 01/01/2023]
Abstract
Methylation of riboses at 2'-OH group is one of the most common RNA modifications found in number of cellular RNAs from almost any species which belong to all three life domains. This modification was extensively studied for decades in rRNAs and tRNAs, but recent data revealed the presence of 2'-O-methyl groups also in low abundant RNAs, like mRNAs. Ribose methylation is formed in RNA by two alternative enzymatic mechanisms: either by stand-alone protein enzymes or by complex assembly of proteins associated with snoRNA guides (sno(s)RNPs). In that case one catalytic subunit acts at various RNA sites, the specificity is provided by base pairing of the sno(s)RNA guide with the target RNA. In this review we compile available information on 2'-OH ribose methylation in different RNAs, enzymatic machineries involved in their biosynthesis and dynamics, as well as on the physiological functions of these modified residues.
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Affiliation(s)
- Lilia Ayadi
- UMR7365 IMoPA CNRS-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Adeline Galvanin
- UMR7365 IMoPA CNRS-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Florian Pichot
- UMS2008 IBSLor CNRS-INSERM-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Virginie Marchand
- UMS2008 IBSLor CNRS-INSERM-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Yuri Motorin
- UMR7365 IMoPA CNRS-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France.
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25
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Schwartz MH, Wang H, Pan JN, Clark WC, Cui S, Eckwahl MJ, Pan DW, Parisien M, Owens SM, Cheng BL, Martinez K, Xu J, Chang EB, Pan T, Eren AM. Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis. Nat Commun 2018; 9:5353. [PMID: 30559359 PMCID: PMC6297222 DOI: 10.1038/s41467-018-07675-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 11/09/2018] [Indexed: 12/13/2022] Open
Abstract
Advances in high-throughput sequencing have facilitated remarkable insights into the diversity and functioning of naturally occurring microbes; however, current sequencing strategies are insufficient to reveal physiological states of microbial communities associated with protein translation dynamics. Transfer RNAs (tRNAs) are core components of protein synthesis machinery, present in all living cells, and are phylogenetically tractable, which make them ideal targets to gain physiological insights into environmental microbes. Here we report a direct sequencing approach, tRNA-seq, and a software suite, tRNA-seq-tools, to recover sequences, abundance profiles, and post-transcriptional modifications of microbial tRNA transcripts. Our analysis of cecal samples using tRNA-seq distinguishes high-fat- and low-fat-fed mice in a comparable fashion to 16S ribosomal RNA gene amplicons, and reveals taxon- and diet-dependent variations in tRNA modifications. Our results provide taxon-specific in situ insights into the dynamics of tRNA gene expression and post-transcriptional modifications within complex environmental microbiomes.
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Affiliation(s)
- Michael H Schwartz
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.,Committee on Microbiology, University of Chicago, Chicago, IL, 60637, USA
| | - Haipeng Wang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.,School of Computer Science and Technology, Shandong University of Technology, Zibo, Shandong, China.,Toyota Technological Institute at Chicago, Chicago, IL, 60637, USA
| | - Jessica N Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Wesley C Clark
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Steven Cui
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Matthew J Eckwahl
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - David W Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Marc Parisien
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Sarah M Owens
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.,Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Brian L Cheng
- Committee on Microbiology, University of Chicago, Chicago, IL, 60637, USA
| | - Kristina Martinez
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Jinbo Xu
- Toyota Technological Institute at Chicago, Chicago, IL, 60637, USA
| | - Eugene B Chang
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA. .,Committee on Microbiology, University of Chicago, Chicago, IL, 60637, USA.
| | - A Murat Eren
- Committee on Microbiology, University of Chicago, Chicago, IL, 60637, USA. .,Department of Medicine, University of Chicago, Chicago, IL, 60637, USA. .,Marine Biological Laboratory, Woods Hole, MA, 02543, USA.
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26
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Solivio B, Yu N, Addepalli B, Limbach PA. Improving RNA modification mapping sequence coverage by LC-MS through a nonspecific RNase U2-E49A mutant. Anal Chim Acta 2018; 1036:73-79. [PMID: 30253839 PMCID: PMC6214470 DOI: 10.1016/j.aca.2018.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/31/2018] [Accepted: 08/03/2018] [Indexed: 11/21/2022]
Abstract
We report the identification and use of a mutant of the purine selective ribonuclease RNase U2 that randomly cleaves RNA in a manner that is directly compatible with RNA modification mapping by mass spectrometry. A number of RNase U2 mutants were generated using site-saturation mutagenesis. The enzyme activity and specificity were tested using oligonucleotide substrates, which revealed an RNase U2 E49A mutant with limited specificity and a tendency to undercut RNA. Using this mutant, RNA digestion conditions were optimized to yield long, overlapping digestion products, which improve sequence coverage in RNA modification mapping experiments. The analytical utility of this mutant was demonstrated by liquid chromatography tandem mass spectrometry (LC-MS/MS) mapping of several modified RNAs where 100% sequence coverage could be obtained using only a single enzymatic digestion. This new mutant facilitates more accurate and efficient RNA modification mapping than traditional highly base-specific RNases that are currently used.
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Affiliation(s)
- Beulah Solivio
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH, 45221-0172, United States
| | - Ningxi Yu
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH, 45221-0172, United States
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH, 45221-0172, United States
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH, 45221-0172, United States.
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27
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Detection of ribonucleoside modifications by liquid chromatography coupled with mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:280-290. [PMID: 30414470 DOI: 10.1016/j.bbagrm.2018.10.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/20/2018] [Accepted: 10/27/2018] [Indexed: 12/21/2022]
Abstract
A small set of ribonucleoside modifications have been found in different regions of mRNA including the open reading frame. Accurate detection of these specific modifications is critical to understanding their modulatory roles in facilitating mRNA maturation, translation and degradation. While transcriptome-wide next-generation sequencing (NGS) techniques could provide exhaustive information about the sites of one specific or class of modifications at a time, recent investigations strongly indicate cautionary interpretation due to the appearance of false positives. Therefore, it is suggested that NGS-based modification data can only be treated as predicted sites and their existence need to be validated by orthogonal methods. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is an analytical technique that can yield accurate and reproducible information about the qualitative and quantitative characteristics of ribonucleoside modifications. Here, we review the recent advancements in LC-MS/MS technology that could help in securing accurate, gold-standard quality information about the resident post-transcriptional modifications of mRNA.
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28
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Torrent M, Chalancon G, de Groot NS, Wuster A, Madan Babu M. Cells alter their tRNA abundance to selectively regulate protein synthesis during stress conditions. Sci Signal 2018; 11:11/546/eaat6409. [PMID: 30181241 PMCID: PMC6130803 DOI: 10.1126/scisignal.aat6409] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Decoding the information in mRNA during protein synthesis relies on tRNA adaptors, the abundance of which can affect the decoding rate and translation efficiency. To determine whether cells alter tRNA abundance to selectively regulate protein expression, we quantified changes in the abundance of individual tRNAs at different time points in response to diverse stress conditions in Saccharomyces cerevisiae. We found that the tRNA pool was dynamic and rearranged in a manner that facilitated selective translation of stress-related transcripts. Through genomic analysis of multiple data sets, stochastic simulations, and experiments with designed sequences of proteins with identical amino acids but altered codon usage, we showed that changes in tRNA abundance affected protein expression independently of factors such as mRNA abundance. We suggest that cells alter their tRNA abundance to selectively affect the translation rates of specific transcripts to increase the amounts of required proteins under diverse stress conditions.
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Affiliation(s)
- Marc Torrent
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK. .,Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Guilhem Chalancon
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Natalia S de Groot
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Arthur Wuster
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - M Madan Babu
- Laboratory of Molecular Biology, Medical Research Council, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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29
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Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis. Nat Chem Biol 2018; 14:1010-1020. [PMID: 30150682 DOI: 10.1038/s41589-018-0119-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 07/09/2018] [Indexed: 11/08/2022]
Abstract
Modification of tRNA anticodons plays a critical role in ensuring accurate translation. N4-acetylcytidine (ac4C) is present at the anticodon first position (position 34) of bacterial elongator tRNAMet. Herein, we identified Bacillus subtilis ylbM (renamed tmcAL) as a novel gene responsible for ac4C34 formation. Unlike general acetyltransferases that use acetyl-CoA, TmcAL activates an acetate ion to form acetyladenylate and then catalyzes ac4C34 formation through a mechanism similar to tRNA aminoacylation. The crystal structure of TmcAL with an ATP analog reveals the molecular basis of ac4C34 formation. The ΔtmcAL strain displayed a cold-sensitive phenotype and a strong genetic interaction with tilS that encodes the enzyme responsible for synthesizing lysidine (L) at position 34 of tRNAIle to facilitate AUA decoding. Mistranslation of the AUA codon as Met in the ΔtmcAL strain upon tilS repression suggests that ac4C34 modification of tRNAMet and L34 modification of tRNAIle act cooperatively to prevent misdecoding of the AUA codon.
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30
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Koh CS, Sarin LP. Transfer RNA modification and infection – Implications for pathogenicity and host responses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:419-432. [DOI: 10.1016/j.bbagrm.2018.01.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/04/2018] [Accepted: 01/19/2018] [Indexed: 12/19/2022]
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31
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van der Meulen SB, de Jong A, Kok J. Early Transcriptome Response of Lactococcus lactis to Environmental Stresses Reveals Differentially Expressed Small Regulatory RNAs and tRNAs. Front Microbiol 2017; 8:1704. [PMID: 28959239 PMCID: PMC5603721 DOI: 10.3389/fmicb.2017.01704] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/23/2017] [Indexed: 01/02/2023] Open
Abstract
Bacteria can deploy various mechanisms to combat environmental stresses. Many genes have previously been identified in Lactococcus lactis that are involved in sensing the stressors and those that are involved in regulating and mounting a defense against the stressful conditions. However, the expression of small regulatory RNAs (sRNAs) during industrially relevant stress conditions has not been assessed yet in L. lactis, while sRNAs have been shown to be involved in many stress responses in other bacteria. We have previously reported the presence of hundreds of putative regulatory RNAs in L. lactis, and have used high-throughput RNA sequencing (RNA-seq) in this study to assess their expression under six different stress conditions. The uniformly designed experimental set-up enabled a highly reliable comparison between the different stress responses and revealed that many sRNAs are differentially expressed under the conditions applied. The primary stress responses of L. lactis NCDO712 was benchmarked to earlier work and, for the first time, the differential expression was assessed of transfer RNAs (tRNAs) and the genes from the six recently sequenced plasmids of NCDO712. Although, we only applied stresses for 5 min, the majority of the well-known specific stress-induced genes are already differentially expressed. We find that most tRNAs decrease after all stresses applied, except for a small number, which are increased upon cold stress. Starvation was shown to induce the highest differential response, both in terms of number and expression level of genes. Our data pinpoints many novel stress-related uncharacterized genes and sRNAs, which calls for further assessment of their molecular and cellular function. These insights furthermore could impact the way parameters are designed for bacterial culture production and milk fermentation, as we find that very short stress conditions already greatly alter gene expression.
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Affiliation(s)
- Sjoerd B van der Meulen
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands.,Top Institute Food and NutritionWageningen, Netherlands
| | - Anne de Jong
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands.,Top Institute Food and NutritionWageningen, Netherlands
| | - Jan Kok
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands.,Top Institute Food and NutritionWageningen, Netherlands
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32
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Paulines MJ, Limbach PA. Stable Isotope Labeling for Improved Comparative Analysis of RNA Digests by Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:551-561. [PMID: 28105550 DOI: 10.1007/s13361-017-1593-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 01/02/2017] [Accepted: 01/03/2017] [Indexed: 06/06/2023]
Abstract
Even with the advent of high throughput methods to detect modified ribonucleic acids (RNAs), mass spectrometry remains a reliable method to detect, characterize, and place post-transcriptional modifications within an RNA sequence. Here we have developed a stable isotope labeling comparative analysis of RNA digests (SIL-CARD) approach, which improves upon the original 18O/16O labeling CARD method. Like the original, SIL-CARD allows sequence or modification information from a previously uncharacterized in vivo RNA sample to be obtained by direct comparison with a reference RNA, the sequence of which is known. This reference is in vitro transcribed using a 13C/15N isotopically enriched nucleoside triphosphate (NTP). The two RNAs are digested with an endonuclease, the specificity of which matches the labeled NTP used for transcription. As proof of concept, several transfer RNAs (tRNAs) were characterized by SIL-CARD, where labeled guanosine triphosphate was used for the reference in vitro transcription. RNase T1 digestion products from the in vitro transcript will be 15 Da higher in mass than the same digestion products from the in vivo tRNA that are unmodified, leading to a doublet in the mass spectrum. Singlets, rather than doublets, arise if a sequence variation or a post-transcriptional modification is present that results in a relative mass shift different from 15 Da. Moreover, the use of the in vitro synthesized tRNA transcript allows for quantitative measurement of RNA abundance. Overall, SIL-CARD simplifies data analysis and enhances quantitative RNA modification mapping by mass spectrometry. Graphical Abstract ᅟ.
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Affiliation(s)
- Mellie June Paulines
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH, 45221-0172, USA
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH, 45221-0172, USA.
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33
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Mapping Post-Transcriptional Modifications onto Transfer Ribonucleic Acid Sequences by Liquid Chromatography Tandem Mass Spectrometry. Biomolecules 2017; 7:biom7010021. [PMID: 28241457 PMCID: PMC5372733 DOI: 10.3390/biom7010021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 02/15/2017] [Indexed: 01/07/2023] Open
Abstract
Liquid chromatography, coupled with tandem mass spectrometry, has become one of the most popular methods for the analysis of post-transcriptionally modified transfer ribonucleic acids (tRNAs). Given that the information collected using this platform is entirely determined by the mass of the analyte, it has proven to be the gold standard for accurately assigning nucleobases to the sequence. For the past few decades many labs have worked to improve the analysis, contiguous to instrumentation manufacturers developing faster and more sensitive instruments. With biological discoveries relating to ribonucleic acid happening more frequently, mass spectrometry has been invaluable in helping to understand what is happening at the molecular level. Here we present a brief overview of the methods that have been developed and refined for the analysis of modified tRNAs by liquid chromatography tandem mass spectrometry.
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34
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Svenningsen SL, Kongstad M, Stenum TS, Muñoz-Gómez AJ, Sørensen MA. Transfer RNA is highly unstable during early amino acid starvation in Escherichia coli. Nucleic Acids Res 2017; 45:793-804. [PMID: 27903898 PMCID: PMC5314770 DOI: 10.1093/nar/gkw1169] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 11/02/2016] [Accepted: 11/09/2016] [Indexed: 11/17/2022] Open
Abstract
Due to its long half-life compared to messenger RNA, bacterial transfer RNA is known as stable RNA. Here, we show that tRNAs become highly unstable as part of Escherichia coli's response to amino acid starvation. Degradation of the majority of cellular tRNA occurs within twenty minutes of the onset of starvation for each of several amino acids. Both the non-cognate and cognate tRNA for the amino acid that the cell is starving for are degraded, and both charged and uncharged tRNA species are affected. The alarmone ppGpp orchestrates the stringent response to amino acid starvation. However, tRNA degradation occurs in a ppGpp-independent manner, as it occurs with similar kinetics in a relaxed mutant. Further, we also observe rapid tRNA degradation in response to rifampicin treatment, which does not induce the stringent response. We propose a unifying model for these observations, in which the surplus tRNA is degraded whenever the demand for protein synthesis is reduced. Thus, the tRNA pool is a highly regulated, dynamic entity. We propose that degradation of surplus tRNA could function to reduce mistranslation in the stressed cell, because it would reduce competition between cognate and near-cognate charged tRNAs at the ribosomal A-site.
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Affiliation(s)
| | - Mette Kongstad
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | | | - Ana J Muñoz-Gómez
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Michael A Sørensen
- Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
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36
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Limbach PA, June Paulines M. Going global: the new era of mapping modifications in RNA. WILEY INTERDISCIPLINARY REVIEWS. RNA 2017; 8:10.1002/wrna.1367. [PMID: 27251302 PMCID: PMC5133204 DOI: 10.1002/wrna.1367] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 04/22/2016] [Accepted: 04/28/2016] [Indexed: 12/30/2022]
Abstract
The post-transcriptional modification of RNA by the addition of one or more chemical groups has been known for over 50 years. These chemical modifications, once thought to be static, are now being discovered to play key regulatory roles in gene expression. The advent of massive parallel sequencing of RNA (RNA-seq) now allows us to probe the complexity of cellular RNA and how chemically altering RNA structure expands the RNA vocabulary. Here we present an overview of the various strategies and technologies that are available to profile RNA chemical modifications at the cellular level. These strategies can be characterized as targeted and untargeted approaches: targeted strategies are developed for one single chemical modification while untargeted strategies are more broadly applicable to a range of such chemical changes. Key for all of these approaches is the ability to locate modifications within the RNA sequence. While most of these methods are built upon an RNA-Seq pipeline, alternative approaches based on mass spectrometry or conventional DNA sequencing retain value in the overall analysis process. We also look forward toward future opportunities and technologies that may expand the types of modifications that can be globally profiled. Given the ever increasing recognition that these RNA chemical modifications play important biological roles, a variety of methods, preferably orthogonal approaches, will be required to globally identify, validate and quantify RNA chemical modifications found in the transcriptome. WIREs RNA 2017, 8:e1367. doi: 10.1002/wrna.1367 For further resources related to this article, please visit the WIREs website.
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37
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Abstract
We describe the comparative analysis of ribonucleic acid digests (CARD) approach for RNA modification analysis. This approach employs isotope labeling during RNase digestion, which allows the direct comparison of a tRNA of unknown modification status against a reference tRNA, whose sequence or modification status is known. The reference sample is labeled with 18O during RNase digestion while the candidate (unknown) sample is labeled with 16O. These RNase digestion products are combined and analyzed by mass spectrometry. Identical RNase digestion products will appear in the mass spectrum as characteristic doublets, separated by 2 Da due to the 16O/18O mass difference. Singlets arise in the mass spectrum when the sequence or modification status of a particular RNase digestion product from the reference is not matched in the candidate (unknown) sample. This CARD approach for RNA modification analysis simplifies the determination of differences between reference and candidate samples, providing a route for higher throughput screening of samples for modification profiles, including determination of tRNA methylation patterns.
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38
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Abstract
tRNAs are fundamental components of translation and emerging evidence places them more centrally in various other cellular processes. However, rather than being uniformly conserved, tRNA abundance is instead highly variable and adaptable. The amount of tRNA genes greatly differs among species. Moreover, even within the same genome, tRNA abundance shapes the proteome in a tissue- and cell-specific manner and is dynamically regulated in response to stress. Here, we review approaches for identification and quantification of tRNAs and their functional integrity. We discuss the resolution of each method and highlight new approaches with cell-wide resolution based on deep-sequencing technologies.
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39
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Gorgoni B, Ciandrini L, McFarland MR, Romano MC, Stansfield I. Identification of the mRNA targets of tRNA-specific regulation using genome-wide simulation of translation. Nucleic Acids Res 2016; 44:9231-9244. [PMID: 27407108 PMCID: PMC5100601 DOI: 10.1093/nar/gkw630] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/02/2016] [Indexed: 01/11/2023] Open
Abstract
tRNA gene copy number is a primary determinant of tRNA abundance and therefore the rate at which each tRNA delivers amino acids to the ribosome during translation. Low-abundance tRNAs decode rare codons slowly, but it is unclear which genes might be subject to tRNA-mediated regulation of expression. Here, those mRNA targets were identified via global simulation of translation. In-silico mRNA translation rates were compared for each mRNA in both wild-type and a \documentclass[12pt]{minimal}
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}{}${\rm{tRNA}}_{{\rm{CUG}}}^{{\rm{Gln}}}$\end{document}sup70-65 mutant, which exhibits a pseudohyphal growth phenotype and a 75% slower CAG codon translation rate. Of 4900 CAG-containing mRNAs, 300 showed significantly reduced in silico translation rates in a simulated tRNA mutant. Quantitative immunoassay confirmed that the reduced translation rates of sensitive mRNAs were \documentclass[12pt]{minimal}
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}{}${\rm{tRNA}}_{{\rm{CUG}}}^{{\rm{Gln}}}$\end{document} concentration-dependent. Translation simulations showed that reduced \documentclass[12pt]{minimal}
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}{}${\rm{tRNA}}_{{\rm{CUG}}}^{{\rm{Gln}}}$\end{document} concentrations triggered ribosome queues, which dissipated at reduced translation initiation rates. To validate this prediction experimentally, constitutive gcn2 kinase mutants were used to reduce in vivo translation initiation rates. This repaired the relative translational rate defect of target mRNAs in the sup70-65 background, and ameliorated sup70-65 pseudohyphal growth phenotypes. We thus validate global simulation of translation as a new tool to identify mRNA targets of tRNA-specific gene regulation.
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Affiliation(s)
- Barbara Gorgoni
- University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Luca Ciandrini
- DIMNP - UMR 5235 & CNRS, Université de Montpellier, 34095 Montpellier, France.,Laboratoire Charles Coulomb UMR5221 & CNRS, Université de Montpellier, 34095 Montpellier, France
| | - Matthew R McFarland
- University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - M Carmen Romano
- University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK.,University of Aberdeen, Institute for Complex Systems and Mathematical Biology, King's College, Aberdeen AB24 3UE, UK
| | - Ian Stansfield
- University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
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40
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tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs. Methods 2016; 107:34-41. [PMID: 27016142 DOI: 10.1016/j.ymeth.2016.03.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/19/2016] [Accepted: 03/21/2016] [Indexed: 11/20/2022] Open
Abstract
tRNA molecules contain numerous chemically altered nucleosides, which are formed by enzymatic modification of the primary transcripts during the complex tRNA maturation process. Some of the modifications are introduced by single reactions, while other require complex series of reactions carried out by several different enzymes. The location and distribution of various types of modifications vary greatly between different tRNA molecules, organisms and organelles. We have developed a computational method tRNAmodpred, for predicting modifications in tRNA sequences. Briefly, our method takes as an input one or more unmodified tRNA sequences and a set of protein sequences corresponding to a proteome of a cell. Subsequently it identifies homologs of known tRNA modification enzymes in the proteome, predicts tRNA modification activities and maps them onto known pathways of RNA modification from the MODOMICS database. Thereby, theoretically possible modification pathways are identified, and products of these modification reactions are proposed for query tRNAs. This method allows for predicting modification patterns for newly sequenced genomes as well as for checking tentative modification status of tRNAs from one species treated with enzymes from another source, e.g. to predict the possible modifications of eukaryotic tRNAs expressed in bacteria. tRNAmodpred is freely available as a web server at http://genesilico.pl/trnamodpred/.
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41
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Abstract
A common feature of ribonucleic acids (RNAs) is that they can undergo a variety of chemical modifications. As nearly all of these chemical modifications result in an increase in the mass of the canonical nucleoside, mass spectrometry has long been a powerful approach for identifying and characterizing modified RNAs. Over the past several years, significant advances have been made in method development and software for interpreting tandem mass spectra resulting in approaches that can yield qualitative and quantitative information on RNA modifications, often at the level of sequence specificity. We discuss these advances along with instrumentation developments that have increased our ability to extract such information from relatively complex biological samples. With the increasing interest in how these modifications impact the epitranscriptome, mass spectrometry will continue to play an important role in bioanalytical investigations revolving around RNA.
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Affiliation(s)
- Collin Wetzel
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172. and University of Cincinnati, Cincinnati, OH 45221-0172, USA.
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42
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Machnicka MA, Olchowik A, Grosjean H, Bujnicki JM. Distribution and frequencies of post-transcriptional modifications in tRNAs. RNA Biol 2015; 11:1619-29. [PMID: 25611331 DOI: 10.4161/15476286.2014.992273] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Functional tRNA molecules always contain a wide variety of post-transcriptionally modified nucleosides. These modifications stabilize tRNA structure, allow for proper interaction with other macromolecules and fine-tune the decoding of mRNAs during translation. Their presence in functionally important regions of tRNA is conserved in all domains of life. However, the identities of many of these modified residues depend much on the phylogeny of organisms the tRNAs are found in, attesting for domain-specific strategies of tRNA maturation. In this work we present a new tool, tRNAmodviz web server (http://genesilico.pl/trnamodviz) for easy comparative analysis and visualization of modification patterns in individual tRNAs, as well as in groups of selected tRNA sequences. We also present results of comparative analysis of tRNA sequences derived from 7 phylogenetically distinct groups of organisms: Gram-negative bacteria, Gram-positive bacteria, cytosol of eukaryotic single cell organisms, Fungi and Metazoa, cytosol of Viridiplantae, mitochondria, plastids and Euryarchaeota. These data update the study conducted 20 y ago with the tRNA sequences available at that time.
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43
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Gaston KW, Limbach PA. The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry. RNA Biol 2015; 11:1568-85. [PMID: 25616408 PMCID: PMC4615682 DOI: 10.4161/15476286.2014.992280] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The analysis of ribonucleic acids (RNA) by mass spectrometry has been a valuable analytical approach for more than 25 years. In fact, mass spectrometry has become a method of choice for the analysis of modified nucleosides from RNA isolated out of biological samples. This review summarizes recent progress that has been made in both nucleoside and oligonucleotide mass spectral analysis. Applications of mass spectrometry in the identification, characterization and quantification of modified nucleosides are discussed. At the oligonucleotide level, advances in modern mass spectrometry approaches combined with the standard RNA modification mapping protocol enable the characterization of RNAs of varying lengths ranging from low molecular weight short interfering RNAs (siRNAs) to the extremely large 23 S rRNAs. New variations and improvements to this protocol are reviewed, including top-down strategies, as these developments now enable qualitative and quantitative measurements of RNA modification patterns in a variety of biological systems.
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Affiliation(s)
- Kirk W Gaston
- a Rieveschl Laboratories for Mass Spectrometry; Department of Chemistry ; University of Cincinnati ; Cincinnati , OH USA
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44
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Thiaville PC, El Yacoubi B, Köhrer C, Thiaville JJ, Deutsch C, Iwata-Reuyl D, Bacusmo JM, Armengaud J, Bessho Y, Wetzel C, Cao X, Limbach PA, RajBhandary UL, de Crécy-Lagard V. Essentiality of threonylcarbamoyladenosine (t(6)A), a universal tRNA modification, in bacteria. Mol Microbiol 2015; 98:1199-221. [PMID: 26337258 DOI: 10.1111/mmi.13209] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2015] [Indexed: 02/06/2023]
Abstract
Threonylcarbamoyladenosine (t(6)A) is a modified nucleoside universally conserved in tRNAs in all three kingdoms of life. The recently discovered genes for t(6)A synthesis, including tsaC and tsaD, are essential in model prokaryotes but not essential in yeast. These genes had been identified as antibacterial targets even before their functions were known. However, the molecular basis for this prokaryotic-specific essentiality has remained a mystery. Here, we show that t(6)A is a strong positive determinant for aminoacylation of tRNA by bacterial-type but not by eukaryotic-type isoleucyl-tRNA synthetases and might also be a determinant for the essential enzyme tRNA(Ile)-lysidine synthetase. We confirm that t(6)A is essential in Escherichia coli and a survey of genome-wide essentiality studies shows that genes for t(6)A synthesis are essential in most prokaryotes. This essentiality phenotype is not universal in Bacteria as t(6)A is dispensable in Deinococcus radiodurans, Thermus thermophilus, Synechocystis PCC6803 and Streptococcus mutans. Proteomic analysis of t(6)A(-) D. radiodurans strains revealed an induction of the proteotoxic stress response and identified genes whose translation is most affected by the absence of t(6)A in tRNAs. Thus, although t(6)A is universally conserved in tRNAs, its role in translation might vary greatly between organisms.
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Affiliation(s)
- Patrick C Thiaville
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.,Genetics and Genomics Graduate Program, University of Florida, Gainesville, FL, 32610, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.,Institut de Génétique et Microbiologie, Université of Paris-Sud, Orsay, France
| | - Basma El Yacoubi
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Caroline Köhrer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jennifer J Thiaville
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Chris Deutsch
- Department of Chemistry, Portland State University, Portland, OR, 97297, USA
| | - Dirk Iwata-Reuyl
- Department of Chemistry, Portland State University, Portland, OR, 97297, USA
| | - Jo Marie Bacusmo
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Jean Armengaud
- CEA, DSV, IBiTec-S, SPI, Li2D, Laboratory 'Innovative technologies for Detection and Diagnostics', Bagnols-sur-Cèze, F-30200, France
| | - Yoshitaka Bessho
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.,Institute of Physics, Academia Sinica, 128 Sec. 2, Academia Rd., Nankang, Taipei, 11529, Taiwan
| | - Collin Wetzel
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, 45221, USA
| | - Xiaoyu Cao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, 45221, USA
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, 45221, USA
| | - Uttam L RajBhandary
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
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45
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Addepalli B, Lesner NP, Limbach PA. Detection of RNA nucleoside modifications with the uridine-specific ribonuclease MC1 from Momordica charantia. RNA (NEW YORK, N.Y.) 2015; 21:1746-1756. [PMID: 26221047 PMCID: PMC4574751 DOI: 10.1261/rna.052472.115] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/28/2015] [Indexed: 06/06/2023]
Abstract
A codon-optimized recombinant ribonuclease, MC1 is characterized for its uridine-specific cleavage ability to map nucleoside modifications in RNA. The published MC1 amino acid sequence, as noted in a previous study, was used as a template to construct a synthetic gene with a natural codon bias favoring expression in Escherichia coli. Following optimization of various expression conditions, the active recombinant ribonuclease was successfully purified as a C-terminal His-tag fusion protein from E. coli [Rosetta 2(DE3)] cells. The isolated protein was tested for its ribonuclease activity against oligoribonucleotides and commercially available E. coli tRNA(Tyr I). Analysis of MC1 digestion products by ion-pairing reverse phase liquid-chromatography coupled with mass spectrometry (IP-RP-LC-MS) revealed enzymatic cleavage of RNA at the 5'-termini of uridine and pseudouridine, but cleavage was absent if the uridine was chemically modified or preceded by a nucleoside with a bulky modification. Furthermore, the utility of this enzyme to generate complementary digestion products to other common endonucleases, such as RNase T1, which enables the unambiguous mapping of modified residues in RNA is demonstrated.
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Affiliation(s)
- Balasubrahmanym Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA
| | - Nicholas P Lesner
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA Department of Chemistry, The College of Wooster, Wooster, Ohio 44691-2393, USA
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA
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46
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Cao X, Limbach PA. Enhanced detection of post-transcriptional modifications using a mass-exclusion list strategy for RNA modification mapping by LC-MS/MS. Anal Chem 2015; 87:8433-40. [PMID: 26176336 PMCID: PMC4542202 DOI: 10.1021/acs.analchem.5b01826] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
There
has been a renewed appreciation for the dynamic nature of
ribonucleic acid (RNA) modifications and for the impact of modified
RNAs on organism health resulting in an increased emphasis on developing
analytical methods capable of detecting modifications within specific
RNA sequence contexts. Here we demonstrate that a DNA-based exclusion
list enhances data dependent liquid chromatography tandem mass spectrometry
(LC-MS/MS) detection of post-transcriptionally modified nucleosides
within specific RNA sequences. This approach is possible because all
post-transcriptional modifications of RNA, except pseudouridine, result
in a mass increase in the canonical nucleoside undergoing chemical
modification. Thus, DNA-based sequences reflect the state of the RNA
prior to or in the absence of modification. The utility of this exclusion
list strategy is demonstrated through the RNA modification mapping
of total tRNAs from the bacteria Escherichia coli, Lactococcus lactis, and Streptomyces griseus. Creation of a DNA-based exclusion list is shown to consistently
enhance the number of detected modified ribonuclease (RNase) digestion
products by ∼20%. All modified RNase digestion products that
were detected during standard data dependent acquisition (DDA) LC-MS/MS
were also detected when the DNA-based exclusion list was used. Consequently,
the increase in detected modified RNase digestion products is attributed
to new experimental information only obtained when using the exclusion
list. This exclusion list strategy should be broadly applicable to
any class of RNA and improves the utility of mass spectrometry approaches
for discovery-based analyses of RNA modifications, such as are required
for studies of the epitranscriptome.
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Affiliation(s)
- Xiaoyu Cao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, Ohio 45221-0172, United States
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47
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The importance of codon–anticodon interactions in translation elongation. Biochimie 2015; 114:72-9. [DOI: 10.1016/j.biochi.2015.04.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 04/16/2015] [Indexed: 11/16/2022]
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Zhong J, Xiao C, Gu W, Du G, Sun X, He QY, Zhang G. Transfer RNAs Mediate the Rapid Adaptation of Escherichia coli to Oxidative Stress. PLoS Genet 2015; 11:e1005302. [PMID: 26090660 PMCID: PMC4474833 DOI: 10.1371/journal.pgen.1005302] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 05/27/2015] [Indexed: 11/18/2022] Open
Abstract
Translational systems can respond promptly to sudden environmental changes to provide rapid adaptations to environmental stress. Unlike the well-studied translational responses to oxidative stress in eukaryotic systems, little is known regarding how prokaryotes respond rapidly to oxidative stress in terms of translation. In this study, we measured protein synthesis from the entire Escherichia coli proteome and found that protein synthesis was severely slowed down under oxidative stress. With unchanged translation initiation, this slowdown was caused by decreased translation elongation speed. We further confirmed by tRNA sequencing and qRT-PCR that this deceleration was caused by a global, enzymatic downregulation of almost all tRNA species shortly after exposure to oxidative agents. Elevation in tRNA levels accelerated translation and protected E. coli against oxidative stress caused by hydrogen peroxide and the antibiotic ciprofloxacin. Our results showed that the global regulation of tRNAs mediates the rapid adjustment of the E. coli translation system for prompt adaptation to oxidative stress. All organisms need to respond quickly to sudden environmental changes. Translational regulation can occur in response to environmental stresses within minutes, which is much faster than transcriptional regulation, and thus normally provides immediate adaptation. Eukaryotic cells can manipulate their tRNA molecules, mainly in a reversible manner, to suppress translation. Here, we showed for the first time that bacteria respond to oxidative stress by adjusting the translational system in a manner that differs from that of eukaryotes. The bacteria nonspecifically, irreversibly, and enzymatically degrade tRNAs to block protein synthesis. Interestingly, we showed that elevated tRNA concentrations lead to opposing effects by causing increased protein aggregation, which impairs fitness under normal conditions but facilitates adaptation under oxidative stress, including that caused by antibiotics. Our results provide a new understanding of the role of global adjustments to the entire translation system during stress adaptation in bacteria. This mechanism may also be involved in the development of antibiotic resistance in bacteria.
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Affiliation(s)
- Jiayong Zhong
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Chuanle Xiao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Wei Gu
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Gaofei Du
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Xuesong Sun
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
- * E-mail: (QYH); (GZ)
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
- * E-mail: (QYH); (GZ)
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Sample PJ, Gaston KW, Alfonzo JD, Limbach PA. RoboOligo: software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids. Nucleic Acids Res 2015; 43:e64. [PMID: 25820423 PMCID: PMC4446411 DOI: 10.1093/nar/gkv145] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 02/10/2015] [Accepted: 02/15/2015] [Indexed: 11/14/2022] Open
Abstract
Ribosomal ribonucleic acid (RNA), transfer RNA and other biological or synthetic RNA polymers can contain nucleotides that have been modified by the addition of chemical groups. Traditional Sanger sequencing methods cannot establish the chemical nature and sequence of these modified-nucleotide containing oligomers. Mass spectrometry (MS) has become the conventional approach for determining the nucleotide composition, modification status and sequence of modified RNAs. Modified RNAs are analyzed by MS using collision-induced dissociation tandem mass spectrometry (CID MS/MS), which produces a complex dataset of oligomeric fragments that must be interpreted to identify and place modified nucleosides within the RNA sequence. Here we report the development of RoboOligo, an interactive software program for the robust analysis of data generated by CID MS/MS of RNA oligomers. There are three main functions of RoboOligo: (i) automated de novo sequencing via the local search paradigm. (ii) Manual sequencing with real-time spectrum labeling and cumulative intensity scoring. (iii) A hybrid approach, coined 'variable sequencing', which combines the user intuition of manual sequencing with the high-throughput sampling of automated de novo sequencing.
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Affiliation(s)
- Paul J Sample
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Kirk W Gaston
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172, University of Cincinnati, Cincinnati, OH 45221-0172, USA
| | - Juan D Alfonzo
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, PO Box 210172, University of Cincinnati, Cincinnati, OH 45221-0172, USA
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50
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Hess AK, Saffert P, Liebeton K, Ignatova Z. Optimization of translation profiles enhances protein expression and solubility. PLoS One 2015; 10:e0127039. [PMID: 25965266 PMCID: PMC4428881 DOI: 10.1371/journal.pone.0127039] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/11/2015] [Indexed: 12/12/2022] Open
Abstract
mRNA is translated with a non-uniform speed that actively coordinates co-translational folding of protein domains. Using structure-based homology we identified the structural domains in epoxide hydrolases (EHs) and introduced slow-translating codons to delineate the translation of single domains. These changes in translation speed dramatically improved the solubility of two EHs of metagenomic origin in Escherichia coli. Conversely, the importance of transient attenuation for the folding, and consequently solubility, of EH was evidenced with a member of the EH family from Agrobacterium radiobacter, which partitions in the soluble fraction when expressed in E. coli. Synonymous substitutions of codons shaping the slow-transiting regions to fast-translating codons render this protein insoluble. Furthermore, we show that low protein yield can be enhanced by decreasing the free folding energy of the initial 5’-coding region, which can disrupt mRNA secondary structure and enhance ribosomal loading. This study provides direct experimental evidence that mRNA is not a mere messenger for translation of codons into amino acids but bears an additional layer of information for folding, solubility and expression level of the encoded protein. Furthermore, it provides a general frame on how to modulate and fine-tune gene expression of a target protein.
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Affiliation(s)
- Anne-Katrin Hess
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Paul Saffert
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Zoya Ignatova
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Biochemistry, Department of Chemistry and Biochemistry, University of Hamburg, Hamburg, Germany
- * E-mail: (ZI); (KL)
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