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Janowski M, Andrzejewska A. The legacy of mRNA engineering: A lineup of pioneers for the Nobel Prize. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 29:272-284. [PMID: 35855896 PMCID: PMC9278038 DOI: 10.1016/j.omtn.2022.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
mRNA is like Hermes, delivering the genetic code to cellular construction sites, so it has long been of interest, but only to a small group of scientists, and only demonstrating its remarkable efficacy in coronavirus disease 2019 (COVID-19) vaccines allowed it to go out into the open. Therefore, now is the right timing to delve into the stepping stones that underpin this success and pay tribute to the underlying scientists. From this perspective, advances in mRNA engineering have proven crucial to the rapidly growing role of this molecule in healthcare. Development of consecutive generations of cap analogs, including anti-reverse cap analogs (ARCAs), has significantly boosted translation efficacy and maintained an enthusiasm for mRNA research. Nucleotide modification to protect mRNA molecules from the host's immune system, followed by finding appropriate purification and packaging methods, were other links in the chain enabling medical breakthroughs. Currently, vaccines are the central area of mRNA research, but it will reach far beyond COVID-19. Supplementation of missing or abnormal proteins is another large field of mRNA research. Ex vivo cell engineering and genome editing have been expanding recently. Thus, it is time to recognize mRNA pioneers while building upon their legacy.
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Affiliation(s)
- Miroslaw Janowski
- Program in Image Guided Neurointerventions, Center for Advanced Imaging Research, Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD 21201, USA,Tumor Immunology and Immunotherapy Program, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD 21201, USA
| | - Anna Andrzejewska
- NeuroRepair Department, Mossakowski Medical Research Institute, PAS, 5 Pawinskiego Street, 02-106 Warsaw, Poland,Corresponding author Anna Andrzejewska, NeuroRepair Department, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawinskiego Street, 02-106 Warsaw, Poland.
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Abstract
Codon usage bias is the preferential or non-random use of synonymous codons, a ubiquitous phenomenon observed in bacteria, plants and animals. Different species have consistent and characteristic codon biases. Codon bias varies not only with species, family or group within kingdom, but also between the genes within an organism. Codon usage bias has evolved through mutation, natural selection, and genetic drift in various organisms. Genome composition, GC content, expression level and length of genes, position and context of codons in the genes, recombination rates, mRNA folding, and tRNA abundance and interactions are some factors influencing codon bias. The factors shaping codon bias may also be involved in evolution of the universal genetic code. Codon-usage bias is critical factor determining gene expression and cellular function by influencing diverse processes such as RNA processing, protein translation and protein folding. Codon usage bias reflects the origin, mutation patterns and evolution of the species or genes. Investigations of codon bias patterns in genomes can reveal phylogenetic relationships between organisms, horizontal gene transfers, molecular evolution of genes and identify selective forces that drive their evolution. Most important application of codon bias analysis is in the design of transgenes, to increase gene expression levels through codon optimization, for development of transgenic crops. The review gives an overview of deviations of genetic code, factors influencing codon usage or bias, codon usage bias of nuclear and organellar genes, computational methods to determine codon usage and the significance as well as applications of codon usage analysis in biological research, with emphasis on plants.
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Affiliation(s)
| | - Varatharajalu Udayasuriyan
- Department of Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - Vijaipal Bhadana
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, 834010, India
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Romanova EV, Bukin YS, Mikhailov KV, Logacheva MD, Aleoshin VV, Sherbakov DY. Hidden cases of tRNA gene duplication and remolding in mitochondrial genomes of amphipods. Mol Phylogenet Evol 2019; 144:106710. [PMID: 31846708 DOI: 10.1016/j.ympev.2019.106710] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 12/13/2019] [Accepted: 12/13/2019] [Indexed: 12/30/2022]
Abstract
The evolution of tRNA genes in mitochondrial (mt) genomes is a complex process that includes duplications, degenerations, and transpositions, as well as a specific process of identity change through mutations in the anticodon (tRNA gene remolding or tRNA gene recruitment). Using amphipod-specific tRNA models for annotation, we show that tRNA duplications are more common in the mt genomes of amphipods than what was revealed by previous annotations. Seventeen cases of tRNA gene duplications were detected in the mt genomes of amphipods, and ten of them were tRNA genes that underwent remolding. The additional tRNA gene findings were verified using phylogenetic analysis and genetic distance analysis. The majority of remolded tRNA genes (seven out of ten cases) were found in the mt genomes of endemic amphipod species from Lake Baikal. All additional mt tRNA genes arose independently in the Baikalian amphipods, indicating the unusual plasticity of tRNA gene evolution in these species assemblages. The possible reasons for the unusual abundance of additional tRNA genes in the mt genomes of Baikalian amphipods are discussed. The amphipod-specific tRNA models developed for MiTFi refine existing predictions of tRNA genes in amphipods and reveal additional cases of duplicated tRNA genes overlooked by using less specific Metazoa-wide models. The application of these models for mt tRNA gene prediction will be useful for the correct annotation of mt genomes of amphipods and probably other crustaceans.
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Affiliation(s)
- Elena V Romanova
- Laboratory of Molecular Systematics, Limnological Institute, Irkutsk, Russian Federation.
| | - Yurij S Bukin
- Laboratory of Molecular Systematics, Limnological Institute, Irkutsk, Russian Federation; Faculty of Biology and Soil Studies, Irkutsk State University, Irkutsk, Russian Federation
| | - Kirill V Mikhailov
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation; Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Maria D Logacheva
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation; Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir V Aleoshin
- Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation; Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Dmitry Yu Sherbakov
- Laboratory of Molecular Systematics, Limnological Institute, Irkutsk, Russian Federation; Faculty of Biology and Soil Studies, Irkutsk State University, Irkutsk, Russian Federation
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Yakovleva EP, Kolodyaznaya VA, Boikova IV, Belakhov VV. Influence of Aryl-Substituted Xylose Derivatives on Fermentation of Antifungal Antibiotic Imbricin. RUSS J GEN CHEM+ 2019. [DOI: 10.1134/s1070363218130017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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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Hamashima K, Tomita M, Kanai A. Expansion of Noncanonical V-Arm-Containing tRNAs in Eukaryotes. Mol Biol Evol 2015; 33:530-40. [DOI: 10.1093/molbev/msv253] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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Hamashima K, Mori M, Andachi Y, Tomita M, Kohara Y, Kanai A. Analysis of genetic code ambiguity arising from nematode-specific misacylated tRNAs. PLoS One 2015; 10:e0116981. [PMID: 25602944 PMCID: PMC4300185 DOI: 10.1371/journal.pone.0116981] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 12/17/2014] [Indexed: 12/22/2022] Open
Abstract
The faithful translation of the genetic code requires the highly accurate aminoacylation of transfer RNAs (tRNAs). However, it has been shown that nematode-specific V-arm-containing tRNAs (nev-tRNAs) are misacylated with leucine in vitro in a manner that transgresses the genetic code. nev-tRNA(Gly) (CCC) and nev-tRNA(Ile) (UAU), which are the major nev-tRNA isotypes, could theoretically decode the glycine (GGG) codon and isoleucine (AUA) codon as leucine, causing GGG and AUA codon ambiguity in nematode cells. To test this hypothesis, we investigated the functionality of nev-tRNAs and their impact on the proteome of Caenorhabditis elegans. Analysis of the nucleotide sequences in the 3' end regions of the nev-tRNAs showed that they had matured correctly, with the addition of CCA, which is a crucial posttranscriptional modification required for tRNA aminoacylation. The nuclear export of nev-tRNAs was confirmed with an analysis of their subcellular localization. These results show that nev-tRNAs are processed to their mature forms like common tRNAs and are available for translation. However, a whole-cell proteome analysis found no detectable level of nev-tRNA-induced mistranslation in C. elegans cells, suggesting that the genetic code is not ambiguous, at least under normal growth conditions. Our findings indicate that the translational fidelity of the nematode genetic code is strictly maintained, contrary to our expectations, although deviant tRNAs with misacylation properties are highly conserved in the nematode genome.
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Affiliation(s)
- Kiyofumi Hamashima
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Masaru Mori
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Yoshiki Andachi
- Genome Biology Laboratory, National Institute of Genetics, Mishima, Japan
- Department of Genetics, SOKENDAI, Mishima, 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
| | - Yuji Kohara
- Genome Biology Laboratory, National Institute of Genetics, Mishima, Japan
- Department of Genetics, SOKENDAI, Mishima, 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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Fujishima K, Kanai A. tRNA gene diversity in the three domains of life. Front Genet 2014; 5:142. [PMID: 24904642 PMCID: PMC4033280 DOI: 10.3389/fgene.2014.00142] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 04/28/2014] [Indexed: 11/29/2022] Open
Abstract
Transfer RNA (tRNA) is widely known for its key role in decoding mRNA into protein. Despite their necessity and relatively short nucleotide sequences, a large diversity of gene structures and RNA secondary structures of pre-tRNAs and mature tRNAs have recently been discovered in the three domains of life. Growing evidences of disrupted tRNA genes in the genomes of Archaea reveals unique gene structures such as, intron-containing tRNA, split tRNA, and permuted tRNA. Coding sequence for these tRNAs are either separated with introns, fragmented, or permuted at the genome level. Although evolutionary scenario behind the tRNA gene disruption is still unclear, diversity of tRNA structure seems to be co-evolved with their processing enzyme, so-called RNA splicing endonuclease. Metazoan mitochondrial tRNAs (mtRNAs) are known for their unique lack of either one or two arms from the typical tRNA cloverleaf structure, while still maintaining functionality. Recently identified nematode-specific V-arm containing tRNAs (nev-tRNAs) possess long variable arms that are specific to eukaryotic class II tRNASer and tRNALeu but also decode class I tRNA codons. Moreover, many tRNA-like sequences have been found in the genomes of different organisms and viruses. Thus, this review is aimed to cover the latest knowledge on tRNA gene diversity and further recapitulate the evolutionary and biological aspects that caused such uniqueness.
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Affiliation(s)
- Kosuke Fujishima
- NASA Ames Research Center Moffett Field, CA, USA ; Institute for Advanced Biosciences, Keio University Tsuruoka, Japan
| | - Akio Kanai
- Institute for Advanced Biosciences, Keio University Tsuruoka, Japan
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