1
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Jenne F, Berezkin I, Tempel F, Schmidt D, Popov R, Nesterov-Mueller A. Screening for Primordial RNA–Peptide Interactions Using High-Density Peptide Arrays. Life (Basel) 2023; 13:life13030796. [PMID: 36983951 PMCID: PMC10053474 DOI: 10.3390/life13030796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
RNA–peptide interactions are an important factor in the origin of the modern mechanism of translation and the genetic code. Despite great progress in the bioinformatics of RNA–peptide interactions due to the rapid growth in the number of known RNA–protein complexes, there is no comprehensive experimental method to take into account the influence of individual amino acids on non-covalent RNA–peptide bonds. First, we designed the combinatorial libraries of primordial peptides according to the combinatorial fusion rules based on Watson–Crick mutations. Next, we used high-density peptide arrays to investigate the interaction of primordial peptides with their cognate homo-oligonucleotides. We calculated the interaction scores of individual peptide fragments and evaluated the influence of the peptide length and its composition on the strength of RNA binding. The analysis shows that the amino acids phenylalanine, tyrosine, and proline contribute significantly to the strong binding between peptides and homo-oligonucleotides, while the sum charge of the peptide does not have a significant effect. We discuss the physicochemical implications of the combinatorial fusion cascade, a hypothesis that follows from the amino acid partition used in the work.
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Affiliation(s)
- Felix Jenne
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, DE-76344 Eggenstein-Leopoldshafen, Germany
| | - Ivan Berezkin
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, DE-76344 Eggenstein-Leopoldshafen, Germany
| | - Frank Tempel
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, DE-76344 Eggenstein-Leopoldshafen, Germany
| | - Dimitry Schmidt
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, DE-76344 Eggenstein-Leopoldshafen, Germany
| | | | - Alexander Nesterov-Mueller
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, DE-76344 Eggenstein-Leopoldshafen, Germany
- Correspondence: ; Tel.: +49-721-608-29253
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2
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Villarreal L, Witzany G. Self-empowerment of life through RNA networks, cells and viruses. F1000Res 2023; 12:138. [PMID: 36785664 PMCID: PMC9918806 DOI: 10.12688/f1000research.130300.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/20/2023] [Indexed: 01/05/2024] Open
Abstract
Our understanding of the key players in evolution and of the development of all organisms in all domains of life has been aided by current knowledge about RNA stem-loop groups, their proposed interaction motifs in an early RNA world and their regulative roles in all steps and substeps of nearly all cellular processes, such as replication, transcription, translation, repair, immunity and epigenetic marking. Cooperative evolution was enabled by promiscuous interactions between single-stranded regions in the loops of naturally forming stem-loop structures in RNAs. It was also shown that cooperative RNA stem-loops outcompete selfish ones and provide foundational self-constructive groups (ribosome, editosome, spliceosome, etc.). Self-empowerment from abiotic matter to biological behavior does not just occur at the beginning of biological evolution; it is also essential for all levels of socially interacting RNAs, cells and viruses.
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Affiliation(s)
- Luis Villarreal
- Center for Virus Research, University of California, Irvine, California, USA
| | - Guenther Witzany
- Telos - Philosophische Praxis, Buermoos, Salzburg, 5111, Austria
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3
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Villarreal L, Witzany G. Self-empowerment of life through RNA networks, cells and viruses. F1000Res 2023; 12:138. [PMID: 36785664 PMCID: PMC9918806 DOI: 10.12688/f1000research.130300.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 03/08/2023] Open
Abstract
Our understanding of the key players in evolution and of the development of all organisms in all domains of life has been aided by current knowledge about RNA stem-loop groups, their proposed interaction motifs in an early RNA world and their regulative roles in all steps and substeps of nearly all cellular processes, such as replication, transcription, translation, repair, immunity and epigenetic marking. Cooperative evolution was enabled by promiscuous interactions between single-stranded regions in the loops of naturally forming stem-loop structures in RNAs. It was also shown that cooperative RNA stem-loops outcompete selfish ones and provide foundational self-constructive groups (ribosome, editosome, spliceosome, etc.). Self-empowerment from abiotic matter to biological behavior does not just occur at the beginning of biological evolution; it is also essential for all levels of socially interacting RNAs, cells and viruses.
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Affiliation(s)
- Luis Villarreal
- Center for Virus Research, University of California, Irvine, California, USA
| | - Guenther Witzany
- Telos - Philosophische Praxis, Buermoos, Salzburg, 5111, Austria
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4
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Hayne CK, Lewis TA, Stanley RE. Recent insights into the structure, function, and regulation of the eukaryotic transfer RNA splicing endonuclease complex. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1717. [PMID: 35156311 PMCID: PMC9465713 DOI: 10.1002/wrna.1717] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 04/30/2023]
Abstract
The splicing of transfer RNA (tRNA) introns is a critical step of tRNA maturation, for intron-containing tRNAs. In eukaryotes, tRNA splicing is a multi-step process that relies on several RNA processing enzymes to facilitate intron removal and exon ligation. Splicing is initiated by the tRNA splicing endonuclease (TSEN) complex which catalyzes the excision of the intron through its two nuclease subunits. Mutations in all four subunits of the TSEN complex are linked to a family of neurodegenerative and neurodevelopmental diseases known as pontocerebellar hypoplasia (PCH). Recent studies provide molecular insights into the structure, function, and regulation of the eukaryotic TSEN complex and are beginning to illuminate how mutations in the TSEN complex lead to neurodegenerative disease. Using new advancements in the prediction of protein structure, we created a three-dimensional model of the human TSEN complex. We review functions of the TSEN complex beyond tRNA splicing by highlighting recently identified substrates of the eukaryotic TSEN complex and discuss mechanisms for the regulation of tRNA splicing, by enzymes that modify cleaved tRNA exons and introns. Finally, we review recent biochemical and animal models that have worked to address the mechanisms that drive PCH and synthesize these studies with previous studies to try to better understand PCH pathogenesis. This article is categorized under: RNA Processing > tRNA Processing RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition.
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Affiliation(s)
- Cassandra K Hayne
- Department of Health and Human Services, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Tanae A Lewis
- Department of Chemistry, North Carolina Agricultural and Technical State University, Greensboro, North Carolina, USA
| | - Robin E Stanley
- Department of Health and Human Services, Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
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5
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Chakrabarti A, Kaushik M, Khan J, Soota D, Ponnusamy K, Saini S, Manvati S, Singhal J, Ranganathan A, Pati S, Dhar PK, Singh S. tREPs-A New Class of Functional tRNA-Encoded Peptides. ACS OMEGA 2022; 7:18361-18373. [PMID: 35694484 PMCID: PMC9178612 DOI: 10.1021/acsomega.2c00661] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
We asked if transfer RNA (tRNA) ever got an opportunity of translating its own sequence during evolution, what would have been the function of such tRNA-encoded peptides (tREPs)? If not, could one artificially synthesize tREPs to study the corresponding functional outcomes? Here, we report a novel, first-in-the-class, chemically synthesized tREP-18 molecule originating from the Escherichia coli tRNA sequence showing potent antileishmanial property. As a first step, E. coli tRNAs were computationally translated into peptide sequence equivalents and a database of full-length hypothetical tREPs was created. The tREP sequences were sent into sequence, structure, and energy filters to narrow down potential peptides for experimental validation. Based on the functional predictions, tREPs were screened against antiparasitic targets, leading to the identification of tREP-18 as a potential antiparasitic peptide. The in vitro assay of chemically synthesized tREP-18 on the Ag83 strain of Leishmania donovani showed its potent antileishmanial property (IC50 value of 22.13 nM). The atomic force microscopy and scanning electron microscopy images indicated significant alteration in the cytoskeletal architecture of tREP-18-treated parasites. Also, tREP-18 seems to destabilize the mitochondrial membrane potential of parasites, disrupting their cellular integrity and leading to parasitic death. The cellular assays of the tREP-18 peptide on the BS12 strain, a clinical isolate of post-kala azar dermal leishmaniasis, demonstrated its significant efficacy at an IC50 value of 15 nM. The tREP-18 peptide showed a toxic effect on the amastigote stage of the parasite, showing macrophage pathogen clearance at a concentration of 22.5 nM. This study provides the proof of the concept of making a new class of functional peptides from tRNA sequences. It also opens a huge untapped tRNA-peptide space toward novel discoveries and applications. In the future, it would be interesting to perform tREP edits and redesign tREPs toward specific applications.
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Affiliation(s)
- Amrita Chakrabarti
- Department of Life Sciences, Shiv Nadar University, Greater Noida 201314, Uttar Pradesh, India
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Monika Kaushik
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Juveria Khan
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Deepanshu Soota
- National Centre for Biological Sciences, Bangalore 560065, India
| | | | - Sunil Saini
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Siddharth Manvati
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Jhalak Singhal
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Anand Ranganathan
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Soumya Pati
- Department of Life Sciences, Shiv Nadar University, Greater Noida 201314, Uttar Pradesh, India
| | - Pawan Kumar Dhar
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
- Special Centre for Systems Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
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6
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Tosar JP, Ivanov P, Ribas de Pouplana L, Torres AG. Editorial: Understanding the Importance of Non-Canonical tRNA Function. Front Mol Biosci 2021; 8:769784. [PMID: 34692774 PMCID: PMC8529061 DOI: 10.3389/fmolb.2021.769784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Juan Pablo Tosar
- Functional Genomics Unit, Institute Pasteur de Montevideo, Montevideo, Uruguay.,Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, United States.,Department of Medicine, Harvard Medical School, Boston, MA, United States.,The Broad Institute of Harvard and M.I.T., Cambridge, MA, United States
| | - Lluís Ribas de Pouplana
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain.,Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
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7
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Grigoriev A. Transfer RNA and Origins of RNA Interference. Front Mol Biosci 2021; 8:708984. [PMID: 34368233 PMCID: PMC8343393 DOI: 10.3389/fmolb.2021.708984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/08/2021] [Indexed: 01/21/2023] Open
Affiliation(s)
- Andrey Grigoriev
- Department of Biology, Center for Computational and Integrative Biology, Rutgers University, Camden, NY, Uinted States
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8
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Novel Structural Variation and Evolutionary Characteristics of Chloroplast tRNA in Gossypium Plants. Genes (Basel) 2021; 12:genes12060822. [PMID: 34071968 PMCID: PMC8228828 DOI: 10.3390/genes12060822] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/16/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022] Open
Abstract
Cotton is one of the most important fiber and oil crops in the world. Chloroplast genomes harbor their own genetic materials and are considered to be highly conserved. Transfer RNAs (tRNAs) act as "bridges" in protein synthesis by carrying amino acids. Currently, the variation and evolutionary characteristics of tRNAs in the cotton chloroplast genome are poorly understood. Here, we analyzed the structural variation and evolution of chloroplast tRNA (cp tRNA) based on eight diploid and two allotetraploid cotton species. We also investigated the nucleotide evolution of chloroplast genomes in cotton species. We found that cp tRNAs in cotton encoded 36 or 37 tRNAs, and 28 or 29 anti-codon types with lengths ranging from 60 to 93 nucleotides. Cotton chloroplast tRNA sequences possessed specific conservation and, in particular, the Ψ-loop contained the conserved U-U-C-X3-U. The cp tRNAs of Gossypium L. contained introns, and cp tRNAIle contained the anti-codon (C-A-U), which was generally the anti-codon of tRNAMet. The transition and transversion analyses showed that cp tRNAs in cotton species were iso-acceptor specific and had undergone unequal rates of evolution. The intergenic region was more variable than coding regions, and non-synonymous mutations have been fixed in cotton cp genomes. On the other hand, phylogeny analyses indicated that cp tRNAs of cotton were derived from several inferred ancestors with greater gene duplications. This study provides new insights into the structural variation and evolution of chloroplast tRNAs in cotton plants. Our findings could contribute to understanding the detailed characteristics and evolutionary variation of the tRNA family.
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9
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Zhong Q, Fu X, Zhang T, Zhou T, Yue M, Liu J, Li Z. Phylogeny and evolution of chloroplast tRNAs in Adoxaceae. Ecol Evol 2021; 11:1294-1309. [PMID: 33598131 PMCID: PMC7863635 DOI: 10.1002/ece3.7133] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 11/14/2020] [Accepted: 11/23/2020] [Indexed: 12/24/2022] Open
Abstract
Chloroplasts are semiautonomous organelles found in photosynthetic plants. The major functions of chloroplasts include photosynthesis and carbon fixation, which are mainly regulated by its circular genomes. In the highly conserved chloroplast genome, the chloroplast transfer RNA genes (cp tRNA) play important roles in protein translation within chloroplasts. However, the evolution of cp tRNAs remains unclear. Thus, in the present study, we investigated the evolutionary characteristics of chloroplast tRNAs in five Adoxaceae species using 185 tRNA gene sequences. In total, 37 tRNAs encoding 28 anticodons are found in the chloroplast genome in Adoxaceae species. Some consensus sequences are found within the Ψ-stem and anticodon loop of the tRNAs. Some putative novel structures were also identified, including a new stem located in the variable region of tRNATyr in a similar manner to the anticodon stem. Furthermore, phylogenetic and evolutionary analyses indicated that synonymous tRNAs may have evolved from multiple ancestors and frequent tRNA duplications during the evolutionary process may have been primarily caused by positive selection and adaptive evolution. The transition and transversion rates are uneven among different tRNA isotypes. For all tRNAs, the transition rate is greater with a transition/transversion bias of 3.13. Phylogenetic analysis of cp tRNA suggested that the type I introns in different taxa (including eukaryote organisms and cyanobacteria) share the conserved sequences "U-U-x2-C" and "U-x-G-x2-T," thereby indicating the diverse cyanobacterial origins of organelles. This detailed study of cp tRNAs in Adoxaceae may facilitate further investigations of the evolution, phylogeny, structure, and related functions of chloroplast tRNAs.
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Affiliation(s)
- Qiu‐Yi Zhong
- Shaanxi Key Laboratory for Animal ConservationKey Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunmingChina
| | - Xiao‐Gang Fu
- Shaanxi Key Laboratory for Animal ConservationKey Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Ting‐Ting Zhang
- Shaanxi Key Laboratory for Animal ConservationKey Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Tong Zhou
- Shaanxi Key Laboratory for Animal ConservationKey Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Ming Yue
- Shaanxi Key Laboratory for Animal ConservationKey Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Jian‐Ni Liu
- Department of GeologyState Key Laboratory of Continental DynamicsEarly Life InstituteNorthwest UniversityXi'anChina
| | - Zhong‐Hu Li
- Shaanxi Key Laboratory for Animal ConservationKey Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
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10
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Nesterov-Mueller A, Popov R, Seligmann H. Combinatorial Fusion Rules to Describe Codon Assignment in the Standard Genetic Code. Life (Basel) 2020; 11:life11010004. [PMID: 33374866 PMCID: PMC7824455 DOI: 10.3390/life11010004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/15/2020] [Accepted: 12/21/2020] [Indexed: 11/16/2022] Open
Abstract
We propose combinatorial fusion rules that describe the codon assignment in the standard genetic code simply and uniformly for all canonical amino acids. These rules become obvious if the origin of the standard genetic code is considered as a result of a fusion of four protocodes: Two dominant AU and GC protocodes and two recessive AU and GC protocodes. The biochemical meaning of the fusion rules consists of retaining the complementarity between cognate codons of the small hydrophobic amino acids and large charged or polar amino acids within the protocodes. The proto tRNAs were assembled in form of two kissing hairpins with 9-base and 10-base loops in the case of dominant protocodes and two 9-base loops in the case of recessive protocodes. The fusion rules reveal the connection between the stop codons, the non-canonical amino acids, pyrrolysine and selenocysteine, and deviations in the translation of mitochondria. Using fusion rules, we predicted the existence of additional amino acids that are essential for the development of the standard genetic code. The validity of the proposed partition of the genetic code into dominant and recessive protocodes is considered referring to state-of-the-art hypotheses. The formation of two aminoacyl-tRNA synthetase classes is compatible with four-protocode partition.
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Affiliation(s)
- Alexander Nesterov-Mueller
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany; (R.P.); (H.S.)
- Correspondence:
| | - Roman Popov
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany; (R.P.); (H.S.)
| | - Hervé Seligmann
- Institute of Microstructure Technology, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany; (R.P.); (H.S.)
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Laboratory AGEIS EA 7407, Team Tools for e-GnosisMedical & LabcomCNRS/UGA/OrangeLabs Telecoms4Health, Faculty of Medicine, Université Grenoble Alpes, F-38700 La Tronche, France
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11
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Zhang TT, Hou YK, Yang T, Zhang SY, Yue M, Liu J, Li Z. Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect. PeerJ 2020; 8:e10312. [PMID: 33304650 PMCID: PMC7698693 DOI: 10.7717/peerj.10312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 10/15/2020] [Indexed: 12/27/2022] Open
Abstract
Gymnosperms such as ginkgo, conifers, cycads, and gnetophytes are vital components of land ecosystems, and they have significant economic and ecologic value, as well as important roles as forest vegetation. In this study, we investigated the structural variation and evolution of chloroplast transfer RNAs (tRNAs) in gymnosperms. Chloroplasts are important organelles in photosynthetic plants. tRNAs are key participants in translation where they act as adapter molecules between the information level of nucleic acids and functional level of proteins. The basic structures of gymnosperm chloroplast tRNAs were found to have family-specific conserved sequences. The tRNAΨ -loop was observed to contain a conforming sequence, i.e., U-U-C-N-A-N2. In gymnosperms, tRNAIle was found to encode a "CAU" anticodon, which is usually encoded by tRNAMet. Phylogenetic analysis suggested that plastid tRNAs have a common polyphyletic evolutionary pattern, i.e., rooted in abundant common ancestors. Analyses of duplication and loss events in chloroplast tRNAs showed that gymnosperm tRNAs have experienced little more gene loss than gene duplication. Transition and transversion analysis showed that the tRNAs are iso-acceptor specific and they have experienced unequal evolutionary rates. These results provide new insights into the structural variation and evolution of gymnosperm chloroplast tRNAs, which may improve our comprehensive understanding of the biological characteristics of the tRNA family.
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Affiliation(s)
- Ting-Ting Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Yi-Kun Hou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Ting Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Shu-Ya Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Jianni Liu
- Early Life Institute, State Key Laboratory of Continental Dynamics, Department of Geology, Northwest University, Xi’an, China
| | - Zhonghu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
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12
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Abstract
Transfer RNA (tRNA) is the central intellectual property in the evolution of life on Earth. tRNA evolved from repeats and inverted repeats of known sequence. The anticodon and the T stem-loop-stems are homologs with significant conserved sequence identity. A number of models have been advanced to explain tRNA evolution. No 2-minihelix model or accretion model (built a stem at a time) can be correct, in part because of anticodon and T stem-loop-stem identity. Only a 3-minihelix model is adequate.
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13
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Tosar JP, Gámbaro F, Darré L, Pantano S, Westhof E, Cayota A. Dimerization confers increased stability to nucleases in 5' halves from glycine and glutamic acid tRNAs. Nucleic Acids Res 2019; 46:9081-9093. [PMID: 29893896 PMCID: PMC6158491 DOI: 10.1093/nar/gky495] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/22/2018] [Indexed: 11/22/2022] Open
Abstract
We have previously shown that 5′ halves from tRNAGlyGCC and tRNAGluCUC are the most enriched small RNAs in the extracellular space of human cell lines, and especially in the non-vesicular fraction. Extracellular RNAs are believed to require protection by either encapsulation in vesicles or ribonucleoprotein complex formation. However, deproteinization of non-vesicular tRNA halves does not affect their retention in size-exclusion chromatography. Thus, we considered alternative explanations for their extracellular stability. In-silico analysis of the sequence of these tRNA-derived fragments showed that tRNAGly 5′ halves can form homodimers or heterodimers with tRNAGlu 5′ halves. This capacity is virtually unique to glycine tRNAs. By analyzing synthetic oligonucleotides by size exclusion chromatography, we provide evidence that dimerization is possible in vitro. tRNA halves with single point substitutions preventing dimerization are degraded faster both in controlled nuclease digestion assays and after transfection in cells, showing that dimerization can stabilize tRNA halves against the action of cellular nucleases. Finally, we give evidence supporting dimerization of endogenous tRNAGlyGCC 5′ halves inside cells. Considering recent reports have shown that 5′ tRNA halves from Ala and Cys can form tetramers, our results highlight RNA intermolecular structures as a new layer of complexity in the biology of tRNA-derived fragments.
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Affiliation(s)
- Juan Pablo Tosar
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay.,Nuclear Research Center, Faculty of Science, Universidad de la República, Montevideo 11400, Uruguay
| | - Fabiana Gámbaro
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay.,Nuclear Research Center, Faculty of Science, Universidad de la República, Montevideo 11400, Uruguay
| | - Leonardo Darré
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay.,Group of Biomolecular Simulations, Institut Pasteur de Montevideo. Montevideo 11400, Uruguay
| | - Sergio Pantano
- Group of Biomolecular Simulations, Institut Pasteur de Montevideo. Montevideo 11400, Uruguay
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 rue René Descartes, 67084 Strasbourg, France
| | - Alfonso Cayota
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay.,Department of Medicine, Faculty of Medicine, Universidad de la República, Montevideo 11600, Uruguay
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14
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Taxis TM, Bauermann FV, Ridpath JF, Casas E. Analysis of tRNA halves (tsRNAs) in serum from cattle challenged with bovine viral diarrhea virus. Genet Mol Biol 2019; 42:374-379. [PMID: 31259361 PMCID: PMC6726165 DOI: 10.1590/1678-4685-gmb-2018-0019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 09/04/2018] [Indexed: 12/15/2022] Open
Abstract
Acute infections of bovine viral diarrhea virus (BVDV) lead to a range of
clinical presentations. Laboratory tests for detection depend on collection of
samples during a short viremia. Acutely infected animals remain largely
undiagnosed. Transfer RNA halves (tsRNAs) are hypothesized to function like
microRNAs to regulate gene expression during an immune response. The objective
of this study was to identify tsRNAs in cattle that had been challenged with a
non-cytopathic field strain of BVDV. Colostrum-deprived neonatal Holstein calves
were either challenged with BVDV (n=5) or mock challenged (n=4). Sera was
collected prior to challenge and days 4, 9, and 16 post challenge. RNA was
extracted and read counts of small non-coding RNAs were assessed using
next-generation sequencing. A total of 87,838,207 reads identified 41 different
tsRNAs. Two 5’ tsRNAs, tsRNAProAGG and tsRNAValAAC,
differed across time. Two 5’ tsRNAs, tsRNAGlyCCC and
tsRNAGlyGCC, differed between treatment groups across time. Four
days post challenge, 5’ tsRNAGlyCCC and tsRNAGlyGCC were
significantly lower in the challenged group than the control group. Further
studies are needed to identify the importance and function of 5’
tsRNAGlyCCC and tsRNAGlyGCC in serum samples of cattle
challenged with BVDV.
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Affiliation(s)
- Tasia M Taxis
- National Animal Disease Center, USDA, ARS, Ames, IA, USA
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15
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Rogers SO. Integrated evolution of ribosomal RNAs, introns, and intron nurseries. Genetica 2018; 147:103-119. [PMID: 30578455 DOI: 10.1007/s10709-018-0050-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 12/13/2018] [Indexed: 12/21/2022]
Abstract
The initial components of ribosomes first appeared more than 3.8 billion years ago during a time when many types of RNAs were evolving. While modern ribosomes are complex molecular machines consisting of rRNAs and proteins, they were assembled during early evolution by the association and joining of small functional RNA units. Introns may have provided the means to ligate many of these pieces together. All four classes of introns (group I, group II, spliceosomal, and archaeal) are present in many rRNA gene loci over a broad phylogenetic range. A survey of rRNA intron sequences across the three major life domains suggests that some of the classes of introns may have diverged from one another within rRNA gene loci. Analyses of rRNA sequences revealed self-splicing group I and group II introns are present in ancestral regions of the SSU (small subunit) and LSU (large subunit), whereas spliceosomal and archaeal introns appeared in sections of the rRNA that evolved later. Most classes of introns increased in number for approximately 1 billion years. However, their frequencies are low in the most recently evolved regions added to the SSU and LSU rRNAs. Furthermore, many of the introns appear to have been in the same locations for billions of years, suggesting an ancient origin for these sequences. In this Perspectives paper, I reviewed and analyzed rRNA intron sequences, locations, structural characteristics, and splicing mechanisms; and suggest that rRNA gene loci may have served as evolutionary nurseries for intron formation and diversification.
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Affiliation(s)
- Scott O Rogers
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
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16
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Eng MW, Clemons A, Hill C, Engel R, Severson DW, Behura SK. Multifaceted functional implications of an endogenously expressed tRNA fragment in the vector mosquito Aedes aegypti. PLoS Negl Trop Dis 2018; 12:e0006186. [PMID: 29364883 PMCID: PMC5783352 DOI: 10.1371/journal.pntd.0006186] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 12/22/2017] [Indexed: 01/16/2023] Open
Abstract
The mosquito Aedes aegypti is the primary vector of human arboviral diseases caused by dengue, chikungunya and Zika viruses. Many studies have shown the potential roles of small RNA molecules such as microRNA, small interfering RNA and PIWI-interacting RNA in vector mosquitoes. The function of tRNA fragments (tRF), the newly discovered class of small RNAs, in mosquitoes is not known. In this study, we show that specific tRFs are expressed in significantly differential manner between males and females of Ae. aegypti strains. Specific tRFs also show differential response during developmental transition from larvae to adults, as well as after blood feeding of adult females. The expression pattern of tRFs upon blood feeding varied depending upon if the blood contained dengue virus, and also if the females were treated with antibiotic prior to feeding to cleanse of the gut bacteria. Our findings show that a single tRF derived from the precursor sequences of a tRNA-Gly was differentially expressed between males and females, developmental transitions and also upon blood feeding by females of two laboratory strains that vary in midgut susceptibility to dengue virus infection. The multifaceted functional implications of this specific tRF suggest that biogenesis of small regulatory molecules from a tRNA can have wide ranging effects on key aspects of Ae. aegypti vector biology. The mosquito Aedes aegypti is a major vector of arboviral diseases in subtropics and tropics. The confounding effects of immature development and adult microbiome on the ability of Ae. aegypti to transmit diseases (vector competence) have gained renewed attention in the recent years. However, the molecular nature of these links/ effects remains unknown. This is major gap in knowledge regarding how vector competence is regulated at molecular level, and how that regulation may be variable among different strains of this mosquito. In this study, we investigated expression of newly discovered class of small RNAs, called tRNA fragments (tRF) in Ae. aegypti strains. Based on small RNA sequencing and bioinformatics analyses, we show that tRFs are expressed in Ae. aegypti, and they are associated with significant changes in expression between males and females, during development stages, and post blood feeding responses. A single tRF showed association with sex-biased expression, developmental regulation and in response to blood meals between Moyo-S and Moyo-R strains that differ in midgut susceptibility to dengue virus. The findings of this study are expected to guide future research efforts directed toward examining detailed regulatory mechanisms of tRFs in vector competence of Ae. aegypti to disease transmission.
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Affiliation(s)
- Matthew W. Eng
- Department of Biological Sciences and Eck institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Anthony Clemons
- Department of Biological Sciences and Eck institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Casey Hill
- Department of Biological Sciences and Eck institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Roberta Engel
- Department of Biological Sciences and Eck institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - David W. Severson
- Department of Biological Sciences and Eck institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Susanta K. Behura
- Department of Biological Sciences and Eck institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
- * E-mail:
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17
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Mohanta TK, Syed AS, Ameen F, Bae H. Novel Genomic and Evolutionary Perspective of Cyanobacterial tRNAs. Front Genet 2017; 8:200. [PMID: 29321793 PMCID: PMC5733544 DOI: 10.3389/fgene.2017.00200] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 11/21/2017] [Indexed: 11/30/2022] Open
Abstract
Transfer RNA (tRNA) plays a central role in protein synthesis and acts as an adaptor molecule between an mRNA and an amino acid. A tRNA has an L-shaped clover leaf-like structure and contains an acceptor arm, D-arm, D-loop, anti-codon arm, anti-codon loop, variable loop, Ψ-arm and Ψ-loop. All of these arms and loops are important in protein translation. Here, we aimed to delineate the genomic architecture of these arms and loops in cyanobacterial tRNA. Studies from tRNA sequences from 61 cyanobacterial species showed that, except for few tRNAs (tRNAAsn, tRNALeu, tRNAGln, and tRNAMet), all contained a G nucleotide at the 1st position in the acceptor arm. tRNALeu and tRNAMet did not contain any conserved nucleotides at the 1st position whereas tRNAAsn and tRNAGln contained a conserved U1 nucleotide. In several tRNA families, the variable region also contained conserved nucleotides. Except for tRNAMet and tRNAGlu, all other tRNAs contained a conserved A nucleotide at the 1st position in the D-loop. The Ψ-loop contained a conserved U1-U2-C3-x-A5-x-U7 sequence, except for tRNAGly, tRNAAla, tRNAVal, tRNAPhe, tRNAThr, and tRNAGln in which the U7 nucleotide was not conserved. However, in tRNAAsp, the U7 nucleotide was substituted with a C7 nucleotide. Additionally, tRNAArg, tRNAGly, and tRNALys of cyanobacteria contained a group I intron within the anti-codon loop region. Maximum composite likelihood study on the transition/transversion of cyanobacterial tRNA revealed that the rate of transition was higher than the rate of transversion. An evolutionary tree was constructed to understand the evolution of cyanobacterial tRNA and analyses revealed that cyanobacterial tRNA may have evolved polyphyletically with high rate of gene loss.
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Affiliation(s)
- Tapan K Mohanta
- School of Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Asad S Syed
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Fuad Ameen
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hanhong Bae
- School of Biotechnology, Yeungnam University, Gyeongsan, South Korea
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18
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Szafranski P. Intercompartmental Piecewise Gene Transfer. Genes (Basel) 2017; 8:genes8100260. [PMID: 28984842 PMCID: PMC5664110 DOI: 10.3390/genes8100260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/25/2017] [Accepted: 09/28/2017] [Indexed: 11/16/2022] Open
Abstract
Gene relocation from the residual genomes of organelles to the nuclear genome still continues, although as a scaled down evolutionary phenomenon, limited in occurrence mostly to protists (sensu lato) and land plants. During this process, the structural integrity of transferred genes is usually preserved. However, the relocation of mitochondrial genes that code for respiratory chain and ribosomal proteins is sometimes associated with their fragmentation into two complementary genes. Herein, this review compiles cases of piecewise gene transfer from the mitochondria to the nucleus, and discusses hypothesized mechanistic links between the fission and relocation of those genes.
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Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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19
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Self-Referential Encoding on Modules of Anticodon Pairs-Roots of the Biological Flow System. Life (Basel) 2017; 7:life7020016. [PMID: 28383509 PMCID: PMC5492138 DOI: 10.3390/life7020016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/24/2017] [Accepted: 03/26/2017] [Indexed: 12/22/2022] Open
Abstract
The proposal that the genetic code was formed on the basis of (proto)tRNA Dimer-Directed Protein Synthesis is reviewed and updated. The tRNAs paired through the anticodon loops are an indication on the process. Dimers are considered mimics of the ribosomes-structures that hold tRNAs together and facilitate the transferase reaction, and of the translation process-anticodons are at the same time codons for each other. The primitive protein synthesis system gets stabilized when the product peptides are stable and apt to bind the producers therewith establishing a self-stimulating production cycle. The chronology of amino acid encoding starts with Glycine and Serine, indicating the metabolic support of the Glycine-Serine C1-assimilation pathway, which is also consistent with evidence on origins of bioenergetics mechanisms. Since it is not possible to reach for substrates simpler than C1 and compounds in the identified pathway are apt for generating the other central metabolic routes, it is considered that protein synthesis is the beginning and center of a succession of sink-effective mechanisms that drive the formation and evolution of the metabolic flow system. Plasticity and diversification of proteins construct the cellular system following the orientation given by the flow and implementing it. Nucleic acid monomers participate in bioenergetics and the polymers are conservative memory systems for the synthesis of proteins. Protoplasmic fission is the final sink-effective mechanism, part of cell reproduction, guaranteeing that proteins don't accumulate to saturation, which would trigger inhibition.
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20
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Macé K, Gillet R. Origins of tmRNA: the missing link in the birth of protein synthesis? Nucleic Acids Res 2016; 44:8041-51. [PMID: 27484476 PMCID: PMC5041485 DOI: 10.1093/nar/gkw693] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/22/2016] [Accepted: 07/26/2016] [Indexed: 12/20/2022] Open
Abstract
The RNA world hypothesis refers to the early period on earth in which RNA was central in assuring both genetic continuity and catalysis. The end of this era coincided with the development of the genetic code and protein synthesis, symbolized by the apparition of the first non-random messenger RNA (mRNA). Modern transfer-messenger RNA (tmRNA) is a unique hybrid molecule which has the properties of both mRNA and transfer RNA (tRNA). It acts as a key molecule during trans-translation, a major quality control pathway of modern bacterial protein synthesis. tmRNA shares many common characteristics with ancestral RNA. Here, we present a model in which proto-tmRNAs were the first molecules on earth to support non-random protein synthesis, explaining the emergence of early genetic code. In this way, proto-tmRNA could be the missing link between the first mRNA and tRNA molecules and modern ribosome-mediated protein synthesis.
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Affiliation(s)
- Kevin Macé
- Université de Rennes 1, CNRS UMR 6290 IGDR, Translation and Folding Team, 35042 Rennes cedex, France
| | - Reynald Gillet
- Université de Rennes 1, CNRS UMR 6290 IGDR, Translation and Folding Team, 35042 Rennes cedex, France Institut Universitaire de France
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21
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Duechler M, Leszczyńska G, Sochacka E, Nawrot B. Nucleoside modifications in the regulation of gene expression: focus on tRNA. Cell Mol Life Sci 2016; 73:3075-95. [PMID: 27094388 PMCID: PMC4951516 DOI: 10.1007/s00018-016-2217-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 03/25/2016] [Accepted: 04/04/2016] [Indexed: 01/10/2023]
Abstract
Both, DNA and RNA nucleoside modifications contribute to the complex multi-level regulation of gene expression. Modified bases in tRNAs modulate protein translation rates in a highly dynamic manner. Synonymous codons, which differ by the third nucleoside in the triplet but code for the same amino acid, may be utilized at different rates according to codon-anticodon affinity. Nucleoside modifications in the tRNA anticodon loop can favor the interaction with selected codons by stabilizing specific base pairs. Similarly, weakening of base pairing can discriminate against binding to near-cognate codons. mRNAs enriched in favored codons are translated in higher rates constituting a fine-tuning mechanism for protein synthesis. This so-called codon bias establishes a basic protein level, but sometimes it is necessary to further adjust the production rate of a particular protein to actual requirements, brought by, e.g., stages in circadian rhythms, cell cycle progression or exposure to stress. Such an adjustment is realized by the dynamic change of tRNA modifications resulting in the preferential translation of mRNAs coding for example for stress proteins to facilitate cell survival. Furthermore, tRNAs contribute in an entirely different way to another, less specific stress response consisting in modification-dependent tRNA cleavage that contributes to the general down-regulation of protein synthesis. In this review, we summarize control functions of nucleoside modifications in gene regulation with a focus on recent findings on protein synthesis control by tRNA base modifications.
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Affiliation(s)
- Markus Duechler
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland.
| | - Grażyna Leszczyńska
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
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22
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Abstract
In the last few decades, small regulatory RNA (sRNA) molecules emerged as key regulators in every kingdom of life. Resolving the full targetome of sRNAs has however remained a challenge. To address this, we used an in vivo tagging MS2-affinity purification protocol coupled with RNA sequencing technology, namely MAPS, to assemble full bacterial small RNAs targetomes. The impressive potential of MAPS has been supported by a number of reports. Here, we concisely overview RNA-tagging history that preceded the development of the MAPS assay and expose the range of possible uses of this technology.
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Affiliation(s)
- Marie-Claude Carrier
- a Department of Biochemistry , RNA Group, Université de Sherbrooke , Sherbrooke, Québec , Canada
| | - David Lalaouna
- a Department of Biochemistry , RNA Group, Université de Sherbrooke , Sherbrooke, Québec , Canada
| | - Eric Massé
- a Department of Biochemistry , RNA Group, Université de Sherbrooke , Sherbrooke, Québec , Canada
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23
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Transfer RNA: From pioneering crystallographic studies to contemporary tRNA biology. Arch Biochem Biophys 2016; 602:95-105. [PMID: 26968773 DOI: 10.1016/j.abb.2016.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/29/2016] [Accepted: 03/03/2016] [Indexed: 12/17/2022]
Abstract
Transfer RNAs (tRNAs) play a key role in protein synthesis as adaptor molecules between messenger RNA and protein sequences on the ribosome. Their discovery in the early sixties provoked a worldwide infatuation with the study of their architecture and their function in the decoding of genetic information. tRNAs are also emblematic molecules in crystallography: the determination of the first tRNA crystal structures represented a milestone in structural biology and tRNAs were for a long period the sole source of information on RNA folding, architecture, and post-transcriptional modifications. Crystallographic data on tRNAs in complex with aminoacyl-tRNA synthetases (aaRSs) also provided the first insight into protein:RNA interactions. Beyond the translation process and the history of structural investigations on tRNA, this review also illustrates the renewal of tRNA biology with the discovery of a growing number of tRNA partners in the cell, the involvement of tRNAs in a variety of regulatory and metabolic pathways, and emerging applications in biotechnology and synthetic biology.
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24
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The RNA World: 4,000,000,050 years old. Life (Basel) 2015; 5:1583-6. [PMID: 26791312 PMCID: PMC4695837 DOI: 10.3390/life5041583] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 10/13/2015] [Indexed: 12/26/2022] Open
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25
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Caetano-Anollés G, Caetano-Anollés D. Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology. Comput Struct Biotechnol J 2015; 13:427-47. [PMID: 27096056 PMCID: PMC4823900 DOI: 10.1016/j.csbj.2015.07.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/16/2015] [Accepted: 07/19/2015] [Indexed: 12/11/2022] Open
Abstract
Accretion occurs pervasively in nature at widely different timeframes. The process also manifests in the evolution of macromolecules. Here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. Computational studies uncover explicit timelines of accretion of structural parts in molecular repertoires and molecules. Phylogenetic trees of protein structural domains and proteomes and their molecular functions were built from a genomic census of millions of encoded proteins and associated terminal Gene Ontology terms. Trees reveal a ‘metabolic-first’ origin of proteins, the late development of translation, and a patchwork distribution of proteins in biological networks mediated by molecular recruitment. Similarly, the natural history of ancient RNA molecules inferred from trees of molecular substructures built from a census of molecular features shows patchwork-like accretion patterns. Ideographic analyses of ribosomal history uncover the early appearance of structures supporting mRNA decoding and tRNA translocation, the coevolution of ribosomal proteins and RNA, and a first evolutionary transition that brings ribosomal subunits together into a processive protein biosynthetic complex. Nomothetic structural biology studies of tertiary interactions and ancient insertions in rRNA complement these findings, once concentric layering assumptions are removed. Patterns of coaxial helical stacking reveal a frustrated dynamics of outward and inward ribosomal growth possibly mediated by structural grafting. The early rise of the ribosomal ‘turnstile’ suggests an evolutionary transition in natural biological computation. Results make explicit the need to understand processes of molecular growth and information transfer of macromolecules.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101W. Peabody Drive, Urbana, IL 61801, USA; C.R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Derek Caetano-Anollés
- C.R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
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26
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Hirose Y, Ikeda KT, Noro E, Hiraoka K, Tomita M, Kanai A. Precise mapping and dynamics of tRNA-derived fragments (tRFs) in the development of Triops cancriformis (tadpole shrimp). BMC Genet 2015; 16:83. [PMID: 26168920 PMCID: PMC4501094 DOI: 10.1186/s12863-015-0245-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 06/30/2015] [Indexed: 12/03/2022] Open
Abstract
Background In a deep sequencing analysis of small RNAs prepared from a living fossil, the tadpole shrimp Triops cancriformis, a 32-nt small RNA was specifically detected in the adult stage. A nucleotide sequence comparison between the 32-nt small RNA and predicted tRNA sequences in the draft nuclear genomic DNA showed that the small RNA was derived from tRNAGly(GCC). To determine the overall features of the tRNA-derived fragments (tRFs) of T. cancriformis, the small RNA sequences in each of the six developmental stages (egg, 1st − 4th instar larvae, and adult) were compared with the mitochondrial and nuclear tRNA sequences. Results We found that the tRFs were derived from mitochondrial and nuclear tRNAs corresponding to 16 and 39 anticodons, respectively. The total read number of nuclear tRFs was approximately 400 times larger than the number of mitochondrial tRFs. Interestingly, the main regions in each parental tRNA from which these tRFs were derived differed, depending on the parental anticodon. Mitochondrial tRFSer(GCU)s were abundantly produced from the 5’ half regions of the parental tRNA, whereas mitochondrial tRFVal(UAC)s were mainly produced from the 3’ end regions. Highly abundant nuclear tRFs, tRFGly(GCC)s, tRFGly(CCC)s, tRFGlu(CUC)s, and tRFLys(CUU)s were derived from the 5’ half regions of the parental tRNAs. Further analysis of the tRF read counts in the individual developmental stages suggested that the expression of mitochondrial and nuclear tRFs differed during the six stages. Based on these data, we precisely summarized the positions of the tRFs in their parental tRNAs and their expression changes during development. Conclusions Our results reveal the entire dynamics of the tRFs from both the nuclear and mitochondrial genomes of T. cancriformis and indicate that the majority of tRFs in the cell are derived from nuclear tRNAs. This study provides the first examples of developmentally expressed mitochondrial tRFs. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0245-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuka Hirose
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan. .,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-8520, Japan.
| | - Kahori T Ikeda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan. .,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-8520, Japan.
| | - Emiko Noro
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan.
| | - Kiriko Hiraoka
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan.
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan. .,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-8520, Japan. .,Faculty of Environment and Information Studies, Keio University, Fujisawa, 252-0882, Japan.
| | - Akio Kanai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan. .,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-8520, Japan. .,Faculty of Environment and Information Studies, Keio University, Fujisawa, 252-0882, Japan.
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