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Biela A, Hammermeister A, Kaczmarczyk I, Walczak M, Koziej L, Lin TY, Glatt S. The diverse structural modes of tRNA binding and recognition. J Biol Chem 2023; 299:104966. [PMID: 37380076 PMCID: PMC10424219 DOI: 10.1016/j.jbc.2023.104966] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 06/30/2023] Open
Abstract
tRNAs are short noncoding RNAs responsible for decoding mRNA codon triplets, delivering correct amino acids to the ribosome, and mediating polypeptide chain formation. Due to their key roles during translation, tRNAs have a highly conserved shape and large sets of tRNAs are present in all living organisms. Regardless of sequence variability, all tRNAs fold into a relatively rigid three-dimensional L-shaped structure. The conserved tertiary organization of canonical tRNA arises through the formation of two orthogonal helices, consisting of the acceptor and anticodon domains. Both elements fold independently to stabilize the overall structure of tRNAs through intramolecular interactions between the D- and T-arm. During tRNA maturation, different modifying enzymes posttranscriptionally attach chemical groups to specific nucleotides, which not only affect translation elongation rates but also restrict local folding processes and confer local flexibility when required. The characteristic structural features of tRNAs are also employed by various maturation factors and modification enzymes to assure the selection, recognition, and positioning of specific sites within the substrate tRNAs. The cellular functional repertoire of tRNAs continues to extend well beyond their role in translation, partly, due to the expanding pool of tRNA-derived fragments. Here, we aim to summarize the most recent developments in the field to understand how three-dimensional structure affects the canonical and noncanonical functions of tRNA.
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Affiliation(s)
- Anna Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Igor Kaczmarczyk
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Marta Walczak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - Lukasz Koziej
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Ting-Yu Lin
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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2
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Kwak Y. An Update on Trichoderma Mitogenomes: Complete De Novo Mitochondrial Genome of the Fungal Biocontrol Agent Trichoderma harzianum (Hypocreales, Sordariomycetes), an Ex-Neotype Strain CBS 226.95, and Tracing the Evolutionary Divergences of Mitogenomes in Trichoderma. Microorganisms 2021; 9:1564. [PMID: 34442643 PMCID: PMC8401334 DOI: 10.3390/microorganisms9081564] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022] Open
Abstract
Members of the genus Trichoderma (Hypocreales), widely used as biofungicides, biofertilizers, and as model fungi for the industrial production of CAZymes, have actively been studied for the applications of their biological functions. Recently, the study of the nuclear genomes of Trichoderma has expanded in the directions of adaptation and evolution to gain a better understanding of their ecological traits. However, Trichoderma's mitochondria have received much less attention despite mitochondria being the most necessary element for sustaining cell life. In this study, a mitogenome of the fungus Trichoderma harzianum CBS 226.95 was assembled de novo. A 27,632 bp circular DNA molecule was revealed with specific features, such as the intronless of all core PCGs, one homing endonuclease, and a putative overlapping tRNA, on a closer phylogenetic relationship with T. reesei among hypocrealean fungi. Interestingly, the mitogenome of T. harzianum CBS 226.95 was predicted to have evolved earlier than those of other Trichoderma species and also assumed with a selection pressure in the cox3. Considering the bioavailability, both for the ex-neotype strain of the T. harzianum species complex and the most globally representative commercial fungal biocontrol agent, our results on the T. harzianum CBS 226.95 mitogenome provide crucial information which will be helpful criteria in future studies on Trichoderma.
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Affiliation(s)
- Yunyoung Kwak
- Écologie, Systématique et Évolution, CNRS, Université Paris Sud (Paris XI), Université Paris Saclay, AgroParisTech, 91400 Orsay, France;
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea
- Institute for Quality and Safety Assessment of Agricultural Products, Kyungpook National University, Daegu 41566, Korea
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3
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Berg MD, Brandl CJ. Transfer RNAs: diversity in form and function. RNA Biol 2021; 18:316-339. [PMID: 32900285 PMCID: PMC7954030 DOI: 10.1080/15476286.2020.1809197] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/31/2020] [Accepted: 08/08/2020] [Indexed: 12/11/2022] Open
Abstract
As the adaptor that decodes mRNA sequence into protein, the basic aspects of tRNA structure and function are central to all studies of biology. Yet the complexities of their properties and cellular roles go beyond the view of tRNAs as static participants in protein synthesis. Detailed analyses through more than 60 years of study have revealed tRNAs to be a fascinatingly diverse group of molecules in form and function, impacting cell biology, physiology, disease and synthetic biology. This review analyzes tRNA structure, biosynthesis and function, and includes topics that demonstrate their diversity and growing importance.
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Affiliation(s)
- Matthew D. Berg
- Department of Biochemistry, The University of Western Ontario, London, Canada
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4
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Kwak Y. Complete Mitochondrial Genome of the Fungal Biocontrol Agent Trichoderma atroviride: Genomic Features, Comparative Analysis and Insight Into the Mitochondrial Evolution in Trichoderma. Front Microbiol 2020; 11:785. [PMID: 32457712 PMCID: PMC7228111 DOI: 10.3389/fmicb.2020.00785] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 04/01/2020] [Indexed: 12/19/2022] Open
Abstract
The improvement of biopesticides for use in the agriculture industry requires an understanding of the biological- and ecological principles underlying their behavior in natural environments. The nuclear genomes of members of the genus Trichoderma, which are representative fungal biocontrol agents, have been actively studied in relation to the unique characteristics of these species as effective producers of CAZymes/secondary metabolites and biopesticides, but their mitochondrial genomes have received much less attention. In this study, the mitochondrial genome of Trichoderma atroviride (Hypocreales, Sordariomycetes), which targets wood-decaying fungal pathogens and has the ability to degrade chemical fungicides, was assembled de novo. A 32,758 bp circular DNA molecule was revealed with specific features, such as a few more protein CDS and trn genes, two homing endonucleases (LAGLIDADG-/GIY-YIG-type), and even a putative overlapping tRNA gene, on a closer phylogenetic relationship with T. gamsii among hypocrealean fungi. Particularly, introns were observed with several footprints likely to be evolutionarily associated with the intron dynamics of the Trichoderma mitochondrial genomes. This study is the first to report the complete de novo mitochondrial genome of T. atroviride, while comparative analyses of Trichoderma mitochondrial genomes were also conducted from the perspective of mitochondrial evolution for the first time.
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Affiliation(s)
- Yunyoung Kwak
- Écologie, Systématique et Évolution, CNRS, Université Paris Sud (Paris XI), Université Paris Saclay, AgroParisTech, Orsay, France
- School of Applied Biosciences, Kyungpook National University, Daegu, South Korea
- Institute for Quality and Safety Assessment of Agricultural Products, Kyungpook National University, Daegu, South Korea
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5
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Tamaki S, Tomita M, Suzuki H, Kanai A. Systematic Analysis of the Binding Surfaces between tRNAs and Their Respective Aminoacyl tRNA Synthetase Based on Structural and Evolutionary Data. Front Genet 2018; 8:227. [PMID: 29358943 PMCID: PMC5766645 DOI: 10.3389/fgene.2017.00227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/15/2017] [Indexed: 12/23/2022] Open
Abstract
To determine the mechanism underlying the flow of genetic information, it is important to understand the relationship between a tRNA and its binding enzyme, a member of the aminoacyl-tRNA synthetase (aaRS) family. We have developed a novel method to project the interacting regions of tRNA-aaRS complexes, obtained from their three-dimensional structures, onto two-dimensional space. The interacting surface between each tRNA and its aaRS was successfully identified by determining these interactions with an atomic distance threshold of 3.3 Å. We analyzed their interactions, using 60 mainly bacterial and eukaryotic tRNA-aaRS complexes, and showed that the tRNA sequence regions that interacted most strongly with each aaRS are the anticodon loop and the CCA terminal region, followed by the D-stem. A sequence conservation analysis of the canonical tRNAs was conducted in 83 bacterial, 182 archaeal, and 150 eukaryotic species. Our results show that the three tRNA regions that interact with the aaRS and two additional loop regions (D-loop and TΨC-loop) known to be important for formation of the tRNA L-shaped structure are broadly conserved. We also found sequence conservations near the tRNA discriminator in the Bacteria and Archaea, and an enormous number of noncanonical tRNAs in the Eukaryotes. This is the first global view of tRNA evolution based on its structure and an unprecedented number of sequence data.
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Affiliation(s)
- Satoshi Tamaki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Haruo Suzuki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Akio Kanai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
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6
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Nagata S, Imai J, Makino G, Tomita M, Kanai A. Evolutionary Analysis of HIV-1 Pol Proteins Reveals Representative Residues for Viral Subtype Differentiation. Front Microbiol 2017; 8:2151. [PMID: 29163435 PMCID: PMC5666293 DOI: 10.3389/fmicb.2017.02151] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/20/2017] [Indexed: 11/15/2022] Open
Abstract
RNA viruses have been used as model systems to understand the patterns and processes of molecular evolution because they have high mutation rates and are genetically diverse. Human immunodeficiency virus 1 (HIV-1), the etiological agent of acquired immune deficiency syndrome, is highly genetically diverse, and is classified into several groups and subtypes. However, it has been difficult to use its diverse sequences to establish the overall phylogenetic relationships of different strains or the trends in sequence conservation with the construction of phylogenetic trees. Our aims were to systematically characterize HIV-1 subtype evolution and to identify the regions responsible for HIV-1 subtype differentiation at the amino acid level in the Pol protein, which is often used to classify the HIV-1 subtypes. In this study, we systematically characterized the mutation sites in 2,052 Pol proteins from HIV-1 group M (144 subtype A; 1,528 subtype B; 380 subtype C), using sequence similarity networks. We also used spectral clustering to group the sequences based on the network graph structures. A stepwise analysis of the cluster hierarchies allowed us to estimate a possible evolutionary pathway for the Pol proteins. The subtype A sequences also clustered according to when and where the viruses were isolated, whereas both the subtype B and C sequences remained as single clusters. Because the Pol protein has several functional domains, we identified the regions that are discriminative by comparing the structures of the domain-based networks. Our results suggest that sequence changes in the RNase H domain and the reverse transcriptase (RT) connection domain are responsible for the subtype classification. By analyzing the different amino acid compositions at each site in both domain sequences, we found that a few specific amino acid residues (i.e., M357 in the RT connection domain and Q480, Y483, and L491 in the RNase H domain) represent the differences among the subtypes. These residues were located on the surface of the RT structure and in the vicinity of the amino acid sites responsible for RT enzymatic activity or function.
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Affiliation(s)
- Shohei Nagata
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Junnosuke Imai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Gakuto Makino
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Akio Kanai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
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7
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Mukai T, Vargas-Rodriguez O, Englert M, Tripp HJ, Ivanova NN, Rubin EM, Kyrpides NC, Söll D. Transfer RNAs with novel cloverleaf structures. Nucleic Acids Res 2017; 45:2776-2785. [PMID: 28076288 PMCID: PMC5389517 DOI: 10.1093/nar/gkw898] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/30/2016] [Indexed: 01/16/2023] Open
Abstract
We report the identification of novel tRNA species with 12-base pair amino-acid acceptor branches composed of longer acceptor stem and shorter T-stem. While canonical tRNAs have a 7/5 configuration of the branch, the novel tRNAs have either 8/4 or 9/3 structure. They were found during the search for selenocysteine tRNAs in terabytes of genome, metagenome and metatranscriptome sequences. Certain bacteria and their phages employ the 8/4 structure for serine and histidine tRNAs, while minor cysteine and selenocysteine tRNA species may have a modified 8/4 structure with one bulge nucleotide. In Acidobacteria, tRNAs with 8/4 and 9/3 structures may function as missense and nonsense suppressor tRNAs and/or regulatory noncoding RNAs. In δ-proteobacteria, an additional cysteine tRNA with an 8/4 structure mimics selenocysteine tRNA and may function as opal suppressor. We examined the potential translation function of suppressor tRNA species in Escherichia coli; tRNAs with 8/4 or 9/3 structures efficiently inserted serine, alanine and cysteine in response to stop and sense codons, depending on the identity element and anticodon sequence of the tRNA. These findings expand our view of how tRNA, and possibly the genetic code, is diversified in nature.
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Affiliation(s)
- Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, New Haven, CT 06520, USA
| | | | - Markus Englert
- Department of Molecular Biophysics and Biochemistry, New Haven, CT 06520, USA
| | - H James Tripp
- Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA 94598, USA
| | - Natalia N Ivanova
- Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA 94598, USA
| | - Edward M Rubin
- Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA 94598, USA
| | - Nikos C Kyrpides
- Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA 94598, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, New Haven, CT 06520, USA.,Department of Chemistry, Yale University, New Haven, CT 06520, USA
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8
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Santesmasses D, Mariotti M, Guigó R. Computational identification of the selenocysteine tRNA (tRNASec) in genomes. PLoS Comput Biol 2017; 13:e1005383. [PMID: 28192430 PMCID: PMC5330540 DOI: 10.1371/journal.pcbi.1005383] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 02/28/2017] [Accepted: 01/26/2017] [Indexed: 12/11/2022] Open
Abstract
Selenocysteine (Sec) is known as the 21st amino acid, a cysteine analogue with selenium replacing sulphur. Sec is inserted co-translationally in a small fraction of proteins called selenoproteins. In selenoprotein genes, the Sec specific tRNA (tRNASec) drives the recoding of highly specific UGA codons from stop signals to Sec. Although found in organisms from the three domains of life, Sec is not universal. Many species are completely devoid of selenoprotein genes and lack the ability to synthesize Sec. Since tRNASec is a key component in selenoprotein biosynthesis, its efficient identification in genomes is instrumental to characterize the utilization of Sec across lineages. Available tRNA prediction methods fail to accurately predict tRNASec, due to its unusual structural fold. Here, we present Secmarker, a method based on manually curated covariance models capturing the specific tRNASec structure in archaea, bacteria and eukaryotes. We exploited the non-universality of Sec to build a proper benchmark set for tRNASec predictions, which is not possible for the predictions of other tRNAs. We show that Secmarker greatly improves the accuracy of previously existing methods constituting a valuable tool to identify tRNASec genes, and to efficiently determine whether a genome contains selenoproteins. We used Secmarker to analyze a large set of fully sequenced genomes, and the results revealed new insights in the biology of tRNASec, led to the discovery of a novel bacterial selenoprotein family, and shed additional light on the phylogenetic distribution of selenoprotein containing genomes. Secmarker is freely accessible for download, or online analysis through a web server at http://secmarker.crg.cat. Most proteins are made of twenty amino acids. However, there is a small group of proteins that incorporate a 21st amino acid, Selenocysteine (Sec). These proteins are called selenoproteins and are present in some, but not all, species from the three domains of life. Sec is inserted in selenoproteins in response to the UGA codon, normally a stop codon. A Sec specific tRNA (tRNASec), which only exists in the organisms that synthesize selenoproteins recognizes the UGA codon. tRNASec is not only indispensable for Sec incorporation into selenoproteins, but also for Sec synthesis, since Sec is synthesized on its own tRNA. The structure of tRNASec differs from that of canonical tRNAs, and general tRNA detection methods fail to accurately predict it. We developed Secmarker, a tRNASec specific identification tool based on the characteristic structural features of the tRNASec. Our benchmark shows that Secmarker produces nearly flawless tRNASec predictions. We used Secmarker to scan all currently available genome sequences. The analysis of the highly accurate predictions obtained revealed new insights into the biology of tRNASec.
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Affiliation(s)
- Didac Santesmasses
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Barcelona, Spain
- * E-mail: (DS); (MM)
| | - Marco Mariotti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Barcelona, Spain
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (DS); (MM)
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Barcelona, Spain
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9
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Mitra S, Samadder A, Das P, Das S, Dasgupta M, Chakrabarti J. Decrypting ENCODEd epigenetic marks of human tRN-A-RS genes in normal, stem and cancer cell lines. J Biomol Struct Dyn 2016; 35:2759-2771. [PMID: 27659686 DOI: 10.1080/07391102.2016.1240107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Screening large-scale ENCODE data of 625 cytoplasmic transfer RNA (tRNAs) and 37 aminoacyl tRNA synthetase (AARSs) human genes, we deconstruct the array of relations between 10 histone marks affecting 15 chromatin states; their tissue specificity and variations and interchange amongst normal, cancerous and stem cells. The histone marks of RNA Pol II transcribed AARS genes share, but also contrast with that on RNA Pol III transcribed tRNA genes. tRNAs with identical/similar sequences may be in significantly varying states even within the same cell line; the chromatin scaffold, where the tRNA gene resides, is the key determinant. Hepatocellular carcinoma cell line has dominant H3K27me3, and singular clustering of other marks. Leukaemic cell line has hyperactive genes. The quiescence of the stem cells is encoded in the markers. Leaving aside the important exceptions in stem cells and elsewhere, tRNAs with cove scores above 50 have active markers and precise sets of transcription factors, and are usually well conserved compared to the low-scoring ones. Pseudo tRNAs are in heterochromatin/repressed state with anomalous exceptions in cancer cells. We motivate that Epigenetic-Phishing hacks the translation apparatus through the chromatin states governed by the histone marks of tRNA and AARS genes, and speculate on their therapeutic implications in cancer and on stem cells.
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Affiliation(s)
- Sanga Mitra
- a Computational Biology Group , Indian Association for the Cultivation of Science , Jadavpur , Kolkata 700032 , India
| | - Arpa Samadder
- b Computational & Systems Biology, Cancer Genomics, & Molecular Biophysics , University of Massachusetts , Boston , MA 02125 , USA
| | - Pijush Das
- c Structural Biology & Bioinformatics Division , Indian Institute of Chemical Biology , Kolkata 700032 , India
| | - Smarajit Das
- d Department of Genetics , University of Georgia , Athens , GA 30602 , USA
| | - Medhanjali Dasgupta
- e Department of Biochemistry , University of Nebraska-Lincoln , Lincoln , NE 68588 , USA
| | - Jayprokas Chakrabarti
- a Computational Biology Group , Indian Association for the Cultivation of Science , Jadavpur , Kolkata 700032 , India.,f Gyanxet , BF 286 Salt Lake, Kolkata 700064 , India
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