1
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Lenk R, Kleindienst W, Szabó GT, Baiersdörfer M, Boros G, Keller JM, Mahiny AJ, Vlatkovic I. Understanding the impact of in vitro transcription byproducts and contaminants. Front Mol Biosci 2024; 11:1426129. [PMID: 39050733 PMCID: PMC11266732 DOI: 10.3389/fmolb.2024.1426129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/14/2024] [Indexed: 07/27/2024] Open
Abstract
The success of messenger (m)RNA-based vaccines against SARS-CoV-2 during the COVID-19 pandemic has led to rapid growth and innovation in the field of mRNA-based therapeutics. However, mRNA production, whether in small amounts for research or large-scale GMP-grade for biopharmaceutics, is still based on the In Vitro Transcription (IVT) reaction developed in the early 1980s. The IVT reaction exploits phage RNA polymerase to catalyze the formation of an engineered mRNA that depends on a linearized DNA template, nucleotide building blocks, as well as pH, temperature, and reaction time. But depending on the IVT conditions and subsequent purification steps, diverse byproducts such as dsRNA, abortive RNAs and RNA:DNA hybrids might form. Unwanted byproducts, if not removed, could be formulated together with the full-length mRNA and cause an immune response in cells by activating host pattern recognition receptors. In this review, we summarize the potential types of IVT byproducts, their known biological activity, and how they can impact the efficacy and safety of mRNA therapeutics. In addition, we briefly overview non-nucleotide-based contaminants such as RNases, endotoxin and metal ions that, when present in the IVT reaction, can also influence the activity of mRNA-based drugs. We further discuss current approaches aimed at adjusting the IVT reaction conditions or improving mRNA purification to achieve optimal performance for medical applications.
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2
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Matsuda T, Hori H, Yamagami R. Rational design of oligonucleotides for enhanced in vitro transcription of small RNA. RNA (NEW YORK, N.Y.) 2024; 30:710-727. [PMID: 38423625 PMCID: PMC11098460 DOI: 10.1261/rna.079923.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
All kinds of RNA molecules can be produced by in vitro transcription using T7 RNA polymerase using DNA templates obtained by solid-phase chemical synthesis, primer extension, PCR, or DNA cloning. The oligonucleotide design, however, is a challenge to nonexperts as this relies on a set of rules that have been established empirically over time. Here, we describe a Python program to facilitate the rational design of oligonucleotides, calculated with kinetic parameters for enhanced in vitro transcription (ROCKET). The Python tool uses thermodynamic parameters, performs folding-energy calculations, and selects oligonucleotides suitable for the polymerase extension reaction. These oligonucleotides improve yields of template DNA. With the oligonucleotides selected by the program, the tRNA transcripts can be prepared by a one-pot reaction of the DNA polymerase extension reaction and the transcription reaction. Also, the ROCKET-selected oligonucleotides provide greater transcription yields than that from oligonucleotides selected by Primerize, a leading software for designing oligonucleotides for in vitro transcription, due to the enhancement of template DNA synthesis. Apart from over 50 tRNA genes tested, an in vitro transcribed self-cleaving ribozyme was found to have catalytic activity. In addition, the program can be applied to the synthesis of mRNA, demonstrating the wide applicability of the ROCKET software.
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MESH Headings
- Transcription, Genetic
- Oligonucleotides/chemistry
- Oligonucleotides/genetics
- Oligonucleotides/chemical synthesis
- Software
- DNA-Directed RNA Polymerases/metabolism
- DNA-Directed RNA Polymerases/genetics
- RNA, Catalytic/genetics
- RNA, Catalytic/metabolism
- RNA, Catalytic/chemistry
- Thermodynamics
- RNA, Transfer/genetics
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- Kinetics
- RNA, Messenger/genetics
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- Viral Proteins/genetics
- Viral Proteins/metabolism
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Affiliation(s)
- Teppei Matsuda
- Department of Applied Chemistry, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Hiroyuki Hori
- Department of Applied Chemistry, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Ryota Yamagami
- Department of Applied Chemistry, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
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3
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Akatsu Y, Mutsuro-Aoki H, Tamura K. Development of Allosteric Ribozymes for ATP and l-Histidine Based on the R3C Ligase Ribozyme. Life (Basel) 2024; 14:520. [PMID: 38672790 PMCID: PMC11051094 DOI: 10.3390/life14040520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
During the evolution of the RNA, short RNAs are thought to have joined together to form long RNAs, enhancing their function as ribozymes. Previously, the artificial R3C ligase ribozyme (73 nucleotides) was successfully reduced to 46 nucleotides; however, its activity decreased significantly. Therefore, we aimed to develop allosteric ribozymes, whose activities could be regulated by effector compounds, based on the reduced R3C ligase ribozyme (R3C-A). Among the variants prepared by fusing an ATP-binding aptamer RNA with R3C-A, one mutant showed increased ligation activity in an ATP-dependent manner. Melting temperature measurements of the two RNA mutants suggested that the region around the aptamer site was stabilized by the addition of ATP. This resulted in a suitable conformation for the reaction at the ligation site. Another ribozyme was prepared by fusing R3C-A with a l-histidine-binding aptamer RNA, and the ligase activity increased with increasing l-histidine concentrations. Both ATP and l-histidine play prominent roles in current molecular biology and the interaction of RNAs and these molecules could be a key step in the evolution of the world of RNAs. Our results suggest promise in the development of general allosteric ribozymes that are independent of the type of effector molecule and provide important clues to the evolution of the RNA world.
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Affiliation(s)
- Yuna Akatsu
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; (Y.A.); (H.M.-A.)
| | - Hiromi Mutsuro-Aoki
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; (Y.A.); (H.M.-A.)
| | - Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; (Y.A.); (H.M.-A.)
- Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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4
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Onoguchi M, Otsuka R, Koyama M, Ando T, Mutsuro-Aoki H, Umehara T, Tamura K. Elucidation of productive alanine recognition mechanism by Escherichia coli alanyl-tRNA synthetase. Biosystems 2024; 237:105152. [PMID: 38346553 DOI: 10.1016/j.biosystems.2024.105152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/22/2024]
Abstract
Alanyl-tRNA synthetase (AlaRS) incorrectly recognizes both a slightly smaller glycine and a slightly larger serine in addition to alanine, and the probability of incorrect identification is extremely low at 1/300 and 1/170, respectively. Alanine is the second smallest amino acid after glycine; however, the mechanism by which AlaRS specifically identifies small differences in side chains with high accuracy remains unknown. In this study, using a malachite green assay, we aimed to elucidate the alanine recognition mechanism of a fragment (AlaRS368N) containing only the amino acid activation domain of Escherichia coli AlaRS. This method quantifies monophosphate by decomposing pyrophosphate generated during aminoacyl-AMP production. AlaRS368N produced far more pyrophosphate when glycine or serine was used as a substrate than when alanine was used. Among several mutants tested, an AlaRS mutant in which the widely conserved aspartic acid at the 235th position (D235) near the active center was replaced with glutamic acid (D235E) increased pyrophosphate release for the alanine substrate, compared to that from glycine and serine. These results suggested that D235 is optimal for AlaRS to specifically recognize alanine. Alanylation activities of an RNA minihelix by the mutants of valine at the 214th position (V214) of another fragment (AlaRS442N), which is the smallest AlaRS with alanine charging activity, suggest the existence of the van der Waals-like interaction between the side chain of V214 and the methyl group of the alanine substrate.
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Affiliation(s)
- Mayu Onoguchi
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Riku Otsuka
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Miki Koyama
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Tadashi Ando
- Department of Applied Electronics, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Hiromi Mutsuro-Aoki
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Takuya Umehara
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
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5
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Lucas MC, Pryszcz LP, Medina R, Milenkovic I, Camacho N, Marchand V, Motorin Y, Ribas de Pouplana L, Novoa EM. Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing. Nat Biotechnol 2024; 42:72-86. [PMID: 37024678 DOI: 10.1038/s41587-023-01743-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/08/2023] [Indexed: 04/08/2023]
Abstract
Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult in part because a simple method to simultaneously quantify their abundance and chemical modifications is lacking. Here we introduce Nano-tRNAseq, a nanopore-based approach to sequence native tRNA populations that provides quantitative estimates of both tRNA abundances and modification dynamics in a single experiment. We show that default nanopore sequencing settings discard the vast majority of tRNA reads, leading to poor sequencing yields and biased representations of tRNA abundances based on their transcript length. Re-processing of raw nanopore current intensity signals leads to a 12-fold increase in the number of recovered tRNA reads and enables recapitulation of accurate tRNA abundances. We then apply Nano-tRNAseq to Saccharomyces cerevisiae tRNA populations, revealing crosstalks and interdependencies between different tRNA modification types within the same molecule and changes in tRNA populations in response to oxidative stress.
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Affiliation(s)
- Morghan C Lucas
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Leszek P Pryszcz
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rebeca Medina
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ivan Milenkovic
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Virginie Marchand
- CNRS-Université de Lorraine, UAR2008 IBSLor/UMR7365 IMoPA, Nancy, France
| | - Yuri Motorin
- CNRS-Université de Lorraine, UAR2008 IBSLor/UMR7365 IMoPA, Nancy, France
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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6
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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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7
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Silveira GO, Coelho HS, Pereira ASA, Miyasato PA, Santos DW, Maciel LF, Olberg GGG, Tahira AC, Nakano E, Oliveira MLS, Amaral MS, Verjovski-Almeida S. Long non-coding RNAs are essential for Schistosoma mansoni pairing-dependent adult worm homeostasis and fertility. PLoS Pathog 2023; 19:e1011369. [PMID: 37146077 DOI: 10.1371/journal.ppat.1011369] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/17/2023] [Accepted: 04/18/2023] [Indexed: 05/07/2023] Open
Abstract
The trematode parasite Schistosoma mansoni causes schistosomiasis, which affects over 200 million people worldwide. Schistosomes are dioecious, with egg laying depending on the females' obligatory pairing with males. Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides with low or no protein-coding potential that have been involved in other species with reproduction, stem cell maintenance, and drug resistance. In S. mansoni, we recently showed that the knockdown of one lncRNA affects the pairing status of these parasites. Here, we re-analyzed public RNA-Seq data from paired and unpaired adult male and female worms and their gonads, obtained from mixed-sex or single-sex cercariae infections, and found thousands of differentially expressed pairing-dependent lncRNAs among the 23 biological samples that were compared. The expression levels of selected lncRNAs were validated by RT-qPCR using an in vitro unpairing model. In addition, the in vitro silencing of three selected lncRNAs showed that knockdown of these pairing-dependent lncRNAs reduced cell proliferation in adult worms and their gonads, and are essential for female vitellaria maintenance, reproduction, and/or egg development. Remarkably, in vivo silencing of each of the three selected lncRNAs significantly reduced worm burden in infected mice by 26 to 35%. Whole mount in situ hybridization experiments showed that these pairing-dependent lncRNAs are expressed in reproductive tissues. These results show that lncRNAs are key components intervening in S. mansoni adult worm homeostasis, which affects pairing status and survival in the mammalian host, thus presenting great potential as new therapeutic target candidates.
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Affiliation(s)
- Gilbert O Silveira
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Helena S Coelho
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Adriana S A Pereira
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Patrícia A Miyasato
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Daisy W Santos
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Lucas F Maciel
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Giovanna G G Olberg
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Ana C Tahira
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Eliana Nakano
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, São Paulo, Brazil
| | | | - Murilo S Amaral
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Sergio Verjovski-Almeida
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
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8
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Acquisition of Dual Ribozyme-Functions in Nonfunctional Short Hairpin RNAs through Kissing-Loop Interactions. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101561. [PMID: 36294996 PMCID: PMC9604999 DOI: 10.3390/life12101561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/30/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
The acquisition of functions via the elongation of nucleotides is an important factor in the development of the RNA world. In our previous study, we found that the introduction of complementary seven-membered kissing loops into inactive R3C ligase ribozymes revived their ligation activity. In this study, we applied the kissing complex formation-induced rearrangement of RNAs to two nonfunctional RNAs by introducing complementary seven-membered loops into each of them. By combining these two forms of RNAs, the ligase activity (derived from the R3C ligase ribozyme) as well as cleavage activity (derived from the hammerhead ribozyme) was obtained. Thus, effective RNA evolution toward the formation of a life system may require the achievement of “multiple” functions via kissing-loop interactions, as indicated in this study. Our results point toward the versatility of kissing-loop interactions in the evolution of RNA, i.e., two small nonfunctional RNAs can gain dual functions via a kissing-loop interaction.
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9
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Ohira T, Minowa K, Sugiyama K, Yamashita S, Sakaguchi Y, Miyauchi K, Noguchi R, Kaneko A, Orita I, Fukui T, Tomita K, Suzuki T. Reversible RNA phosphorylation stabilizes tRNA for cellular thermotolerance. Nature 2022; 605:372-379. [PMID: 35477761 PMCID: PMC9095486 DOI: 10.1038/s41586-022-04677-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/22/2022] [Indexed: 12/30/2022]
Abstract
Post-transcriptional modifications have critical roles in tRNA stability and function1–4. In thermophiles, tRNAs are heavily modified to maintain their thermal stability under extreme growth temperatures5,6. Here we identified 2′-phosphouridine (Up) at position 47 of tRNAs from thermophilic archaea. Up47 confers thermal stability and nuclease resistance to tRNAs. Atomic structures of native archaeal tRNA showed a unique metastable core structure stabilized by Up47. The 2′-phosphate of Up47 protrudes from the tRNA core and prevents backbone rotation during thermal denaturation. In addition, we identified the arkI gene, which encodes an archaeal RNA kinase responsible for Up47 formation. Structural studies showed that ArkI has a non-canonical kinase motif surrounded by a positively charged patch for tRNA binding. A knockout strain of arkI grew slowly at high temperatures and exhibited a synthetic growth defect when a second tRNA-modifying enzyme was depleted. We also identified an archaeal homologue of KptA as an eraser that efficiently dephosphorylates Up47 in vitro and in vivo. Taken together, our findings show that Up47 is a reversible RNA modification mediated by ArkI and KptA that fine-tunes the structural rigidity of tRNAs under extreme environmental conditions. Reversible internal RNA phosphrylation contributes to thermal stability and nuclease resistance of tRNA, and cellular thermotolerance of hyperthermophiles.
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Affiliation(s)
- Takayuki Ohira
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Keiichi Minowa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kei Sugiyama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Seisuke Yamashita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Ryo Noguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Akira Kaneko
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Izumi Orita
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Toshiaki Fukui
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
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10
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Peptide Bond Formation between Aminoacyl-Minihelices by a Scaffold Derived from the Peptidyl Transferase Center. Life (Basel) 2022; 12:life12040573. [PMID: 35455064 PMCID: PMC9030986 DOI: 10.3390/life12040573] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/01/2022] [Accepted: 04/05/2022] [Indexed: 12/03/2022] Open
Abstract
The peptidyl transferase center (PTC) in the ribosome is composed of two symmetrically arranged tRNA-like units that contribute to peptide bond formation. We prepared units of the PTC components with putative tRNA-like structure and attempted to obtain peptide bond formation between aminoacyl-minihelices (primordial tRNAs, the structures composed of a coaxial stack of the acceptor stem on the T-stem of tRNA). One of the components of the PTC, P1c2UGGU (74-mer), formed a dimer and a peptide bond was formed between two aminoacyl-minihelices tethered by the dimeric P1c2UGGU. Peptide synthesis depended on both the existence of the dimeric P1c2UGGU and the sequence complementarity between the ACCA-3′ sequence of the minihelix. Thus, the tRNA-like structures derived from the PTC could have originated as a scaffold of aminoacyl-minihelices for peptide bond formation through an interaction of the CCA sequence of minihelices. Moreover, with the same origin, some would have evolved to constitute the present PTC of the ribosome, and others to function as present tRNAs.
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11
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Ribosomal protein S18 acetyltransferase RimI is responsible for the acetylation of elongation factor Tu. J Biol Chem 2022; 298:101914. [PMID: 35398352 PMCID: PMC9079301 DOI: 10.1016/j.jbc.2022.101914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 04/02/2022] [Accepted: 04/04/2022] [Indexed: 11/21/2022] Open
Abstract
N-terminal acetylation is widespread in the eukaryotic proteome but in bacteria is restricted to a small number of proteins mainly involved in translation. It was long known that elongation factor Tu (EF-Tu) is N-terminally acetylated, whereas the enzyme responsible for this process was unclear. Here, we report that RimI acetyltransferase, known to modify ribosomal protein S18, is likewise responsible for N-acetylation of the EF-Tu. With the help of inducible tufA expression plasmid, we demonstrated that the acetylation does not alter the stability of EF-Tu. Binding of aminoacyl tRNA to the recombinant EF-Tu in vitro was found to be unaffected by the acetylation. At the same time, with the help of fast kinetics methods, we demonstrate that an acetylated variant of EF-Tu more efficiently accelerates A-site occupation by aminoacyl-tRNA, thus increasing the efficiency of in vitro translation. Finally, we show that a strain devoid of RimI has a reduced growth rate, expanded to an evolutionary timescale, and might potentially promote conservation of the acetylation mechanism of S18 and EF-Tu. This study increased our understanding of the modification of bacterial translation apparatus.
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12
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Biedenbänder T, de Jesus V, Schmidt-Dengler M, Helm M, Corzilius B, Fürtig B. RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics. Nucleic Acids Res 2022; 50:2334-2349. [PMID: 35137185 PMCID: PMC8887418 DOI: 10.1093/nar/gkac040] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/29/2021] [Accepted: 01/14/2022] [Indexed: 11/12/2022] Open
Abstract
A plethora of modified nucleotides extends the chemical and conformational space for natural occurring RNAs. tRNAs constitute the class of RNAs with the highest modification rate. The extensive modification modulates their overall stability, the fidelity and efficiency of translation. However, the impact of nucleotide modifications on the local structural dynamics is not well characterized. Here we show that the incorporation of the modified nucleotides in tRNAfMet from Escherichia coli leads to an increase in the local conformational dynamics, ultimately resulting in the stabilization of the overall tertiary structure. Through analysis of the local dynamics by NMR spectroscopic methods we find that, although the overall thermal stability of the tRNA is higher for the modified molecule, the conformational fluctuations on the local level are increased in comparison to an unmodified tRNA. In consequence, the melting of individual base pairs in the unmodified tRNA is determined by high entropic penalties compared to the modified. Further, we find that the modifications lead to a stabilization of long-range interactions harmonizing the stability of the tRNA's secondary and tertiary structure. Our results demonstrate that the increase in chemical space through introduction of modifications enables the population of otherwise inaccessible conformational substates.
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Affiliation(s)
- Thomas Biedenbänder
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main 60438, Germany.,Institute of Chemistry and Department Life, Light & Matter, University of Rostock, Rostock 18059, Germany
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main 60438, Germany
| | - Martina Schmidt-Dengler
- Institut für pharmazeutische und biomedizinische Wissenschaften (IPBW), Johannes Gutenberg-Universität, Mainz 55128, Germany
| | - Mark Helm
- Institut für pharmazeutische und biomedizinische Wissenschaften (IPBW), Johannes Gutenberg-Universität, Mainz 55128, Germany
| | - Björn Corzilius
- Institute of Chemistry and Department Life, Light & Matter, University of Rostock, Rostock 18059, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität, Frankfurt am Main 60438, Germany
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13
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Horikoshi T, Noguchi H, Umehara T, Mutsuro-Aoki H, Kurihara R, Noguchi R, Hashimoto T, Watanabe Y, Ando T, Kamata K, Park SY, Tamura K. Crystal structure of Nanoarchaeum equitans tyrosyl-tRNA synthetase and its aminoacylation activity toward tRNA Tyr with an extra guanosine residue at the 5'-terminus. Biochem Biophys Res Commun 2021; 575:90-95. [PMID: 34461441 DOI: 10.1016/j.bbrc.2021.08.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/24/2022]
Abstract
tRNATyr of Nanoarchaeum equitans has a remarkable feature with an extra guanosine residue at the 5'-terminus. However, the N. equitans tRNATyr mutant without extra guanosine at the 5'-end was tyrosylated by tyrosyl-tRNA synthase (TyrRS). We solved the crystal structure of N. equitans TyrRS at 2.80 Å resolution. By comparing the present solved structure with the complex structures TyrRS with tRNATyr of Thermus thermophilus and Methanocaldococcus jannaschii, an arginine substitution mutant of N. equitans TyrRS at Ile200 (I200R), which is the putative closest candidate to the 5'-phosphate of C1 of N. equitans tRNATyr, was prepared. The I200R mutant tyrosylated not only wild-type tRNATyr but also the tRNA without the G-1 residue. Further tyrosylation analysis revealed that the second base of the anticodon (U35), discriminator base (A73), and C1:G72 base pair are strong recognition sites.
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Affiliation(s)
- Tatsuya Horikoshi
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Hiroki Noguchi
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Takuya Umehara
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Hiromi Mutsuro-Aoki
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Ryodai Kurihara
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Ryohei Noguchi
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Takahiro Hashimoto
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Yuki Watanabe
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Tadashi Ando
- Department of Applied Electronics, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kenichi Kamata
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Sam-Yong Park
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
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14
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Paleskava A, Maksimova EM, Vinogradova DS, Kasatsky PS, Kirillov SV, Konevega AL. Differential Contribution of Protein Factors and 70S Ribosome to Elongation. Int J Mol Sci 2021; 22:9614. [PMID: 34502523 PMCID: PMC8431766 DOI: 10.3390/ijms22179614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/30/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
The growth of the polypeptide chain occurs due to the fast and coordinated work of the ribosome and protein elongation factors, EF-Tu and EF-G. However, the exact contribution of each of these components in the overall balance of translation kinetics remains not fully understood. We created an in vitro translation system Escherichia coli replacing either elongation factor with heterologous thermophilic protein from Thermus thermophilus. The rates of the A-site binding and decoding reactions decreased an order of magnitude in the presence of thermophilic EF-Tu, indicating that the kinetics of aminoacyl-tRNA delivery depends on the properties of the elongation factor. On the contrary, thermophilic EF-G demonstrated the same translocation kinetics as a mesophilic protein. Effects of translocation inhibitors (spectinomycin, hygromycin B, viomycin and streptomycin) were also similar for both proteins. Thus, the process of translocation largely relies on the interaction of tRNAs and the ribosome and can be efficiently catalysed by thermophilic EF-G even at suboptimal temperatures.
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Affiliation(s)
- Alena Paleskava
- Petersburg Nuclear Physics Institute, NRC “Kurchatov Institute”, 188300 Gatchina, Russia; (A.P.); (E.M.M.); (D.S.V.); (P.S.K.); (S.V.K.)
- Institute of Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Elena M. Maksimova
- Petersburg Nuclear Physics Institute, NRC “Kurchatov Institute”, 188300 Gatchina, Russia; (A.P.); (E.M.M.); (D.S.V.); (P.S.K.); (S.V.K.)
| | - Daria S. Vinogradova
- Petersburg Nuclear Physics Institute, NRC “Kurchatov Institute”, 188300 Gatchina, Russia; (A.P.); (E.M.M.); (D.S.V.); (P.S.K.); (S.V.K.)
| | - Pavel S. Kasatsky
- Petersburg Nuclear Physics Institute, NRC “Kurchatov Institute”, 188300 Gatchina, Russia; (A.P.); (E.M.M.); (D.S.V.); (P.S.K.); (S.V.K.)
| | - Stanislav V. Kirillov
- Petersburg Nuclear Physics Institute, NRC “Kurchatov Institute”, 188300 Gatchina, Russia; (A.P.); (E.M.M.); (D.S.V.); (P.S.K.); (S.V.K.)
| | - Andrey L. Konevega
- Petersburg Nuclear Physics Institute, NRC “Kurchatov Institute”, 188300 Gatchina, Russia; (A.P.); (E.M.M.); (D.S.V.); (P.S.K.); (S.V.K.)
- Institute of Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
- NRC “Kurchatov Institute”, 123182 Moscow, Russia
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15
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Assessment of reference genes at six different developmental stages of Schistosoma mansoni for quantitative RT-PCR. Sci Rep 2021; 11:16816. [PMID: 34413342 PMCID: PMC8376997 DOI: 10.1038/s41598-021-96055-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/31/2021] [Indexed: 12/13/2022] Open
Abstract
Reverse-transcription quantitative real-time polymerase chain reaction (RT-qPCR) is the most used, fast, and reproducible method to confirm large-scale gene expression data. The use of stable reference genes for the normalization of RT-qPCR assays is recognized worldwide. No systematic study for selecting appropriate reference genes for usage in RT-qPCR experiments comparing gene expression levels at different Schistosoma mansoni life-cycle stages has been performed. Most studies rely on genes commonly used in other organisms, such as actin, tubulin, and GAPDH. Therefore, the present study focused on identifying reference genes suitable for RT-qPCR assays across six S. mansoni developmental stages. The expression levels of 25 novel candidates that we selected based on the analysis of public RNA-Seq datasets, along with eight commonly used reference genes, were systematically tested by RT-qPCR across six developmental stages of S. mansoni (eggs, miracidia, cercariae, schistosomula, adult males and adult females). The stability of genes was evaluated with geNorm, NormFinder and RefFinder algorithms. The least stable candidate reference genes tested were actin, tubulin and GAPDH. The two most stable reference genes suitable for RT-qPCR normalization were Smp_101310 (Histone H4 transcription factor) and Smp_196510 (Ubiquitin recognition factor in ER-associated degradation protein 1). Performance of these two genes as normalizers was successfully evaluated with females maintained unpaired or paired to males in culture for 8 days, or with worm pairs exposed for 16 days to double-stranded RNAs to silence a protein-coding gene. This study provides reliable reference genes for RT-qPCR analysis using samples from six different S. mansoni life-cycle stages.
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16
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A single m 6A modification in U6 snRNA diversifies exon sequence at the 5' splice site. Nat Commun 2021; 12:3244. [PMID: 34050143 PMCID: PMC8163875 DOI: 10.1038/s41467-021-23457-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/29/2021] [Indexed: 11/09/2022] Open
Abstract
N6-methyladenosine (m6A) is a modification that plays pivotal roles in RNA metabolism and function, although its functions in spliceosomal U6 snRNA remain unknown. To elucidate its role, we conduct a large-scale transcriptome analysis of a Schizosaccharomyces pombe strain lacking this modification and found a global change of pre-mRNA splicing. The most significantly impacted introns are enriched for adenosine at the fourth position pairing the m6A in U6 snRNA, and exon sequences weakly recognized by U5 snRNA. This suggests cooperative recognition of 5' splice site by U6 and U5 snRNPs, and also a role of m6A facilitating efficient recognition of the splice sites weakly interacting with U5 snRNA, indicating that U6 snRNA m6A relaxes the 5' exon constraint and allows protein sequence diversity along with explosively increasing number of introns over the course of eukaryotic evolution.
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17
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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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18
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Warren JM, Salinas-Giegé T, Hummel G, Coots NL, Svendsen JM, Brown KC, Drouard L, Sloan DB. Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification. RNA Biol 2021; 18:64-78. [PMID: 32715941 PMCID: PMC7834048 DOI: 10.1080/15476286.2020.1792089] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 06/18/2020] [Accepted: 06/30/2020] [Indexed: 12/27/2022] Open
Abstract
Differences in tRNA expression have been implicated in a remarkable number of biological processes. There is growing evidence that tRNA genes can play dramatically different roles depending on both expression and post-transcriptional modification, yet sequencing tRNAs to measure abundance and detect modifications remains challenging. Their secondary structure and extensive post-transcriptional modifications interfere with RNA-seq library preparation methods and have limited the utility of high-throughput sequencing technologies. Here, we combine two modifications to standard RNA-seq methods by treating with the demethylating enzyme AlkB and ligating with tRNA-specific adapters in order to sequence tRNAs from four species of flowering plants, a group that has been shown to have some of the most extensive rates of post-transcriptional tRNA modifications. This protocol has the advantage of detecting full-length tRNAs and sequence variants that can be used to infer many post-transcriptional modifications. We used the resulting data to produce a modification index of almost all unique reference tRNAs in Arabidopsis thaliana, which exhibited many anciently conserved similarities with humans but also positions that appear to be 'hot spots' for modifications in angiosperm tRNAs. We also found evidence based on northern blot analysis and droplet digital PCR that, even after demethylation treatment, tRNA-seq can produce highly biased estimates of absolute expression levels most likely due to biased reverse transcription. Nevertheless, the generation of full-length tRNA sequences with modification data is still promising for assessing differences in relative tRNA expression across treatments, tissues or subcellular fractions and help elucidate the functional roles of tRNA modifications.
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Affiliation(s)
- Jessica M. Warren
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Thalia Salinas-Giegé
- Institut De Biologie Moléculaire Des plantes-CNRS, Université De Strasbourg, Strasbourg, France
| | - Guillaume Hummel
- Institut De Biologie Moléculaire Des plantes-CNRS, Université De Strasbourg, Strasbourg, France
| | - Nicole L. Coots
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Kristen C. Brown
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Laurence Drouard
- Department of Biology, Colorado State University, Fort Collins, CO, USA
- Institut De Biologie Moléculaire Des plantes-CNRS, Université De Strasbourg, Strasbourg, France
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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19
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Kartje ZJ, Janis HI, Mukhopadhyay S, Gagnon KT. Revisiting T7 RNA polymerase transcription in vitro with the Broccoli RNA aptamer as a simplified real-time fluorescent reporter. J Biol Chem 2020; 296:100175. [PMID: 33303627 PMCID: PMC7948468 DOI: 10.1074/jbc.ra120.014553] [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: 05/26/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 11/06/2022] Open
Abstract
Methods for rapid and high-throughput screening of transcription in vitro to examine reaction conditions, enzyme mutants, promoter variants, and small molecule modulators can be extremely valuable tools. However, these techniques may be difficult to establish or inaccessible to many researchers. To develop a straightforward and cost-effective platform for assessing transcription in vitro, we used the "Broccoli" RNA aptamer as a direct, real-time fluorescent transcript readout. To demonstrate the utility of our approach, we screened the effect of common reaction conditions and components on bacteriophage T7 RNA polymerase (RNAP) activity using a common quantitative PCR instrument for fluorescence detection. Several essential conditions for in vitro transcription by T7 RNAP were confirmed with this assay, including the importance of enzyme and substrate concentrations, covariation of magnesium and nucleoside triphosphates, and the effects of several typical additives. When we used this method to assess all possible point mutants of a canonical T7 RNAP promoter, our results coincided well with previous reports. This approach should translate well to a broad variety of bacteriophage in vitro transcription systems and provides a platform for developing fluorescence-based readouts of more complex transcription systems in vitro.
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Affiliation(s)
- Zachary J Kartje
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Helen I Janis
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Shaoni Mukhopadhyay
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois, USA
| | - Keith T Gagnon
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA; Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois, USA.
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20
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Avcilar-Kucukgoze I, Gamper H, Hou YM, Kashina A. Purification and Use of tRNA for Enzymatic Post-translational Addition of Amino Acids to Proteins. STAR Protoc 2020; 1:100207. [PMID: 33377101 PMCID: PMC7757669 DOI: 10.1016/j.xpro.2020.100207] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Post-translational addition of amino acids to proteins by enzymes using aminoacyl-tRNA is an emerging regulatory mechanism. Examples include Arg transfer in eukaryotes, Leu/Phe transfer in bacteria, and tRNA-synthetase-mediated addition of amino acids to Lys side chains. Here, we present a method of purification and use of tRNA for such reactions, focusing on tRNAArg and its use for arginylation. This method can also be used for other tRNA-mediated reactions. For complete details on the use and execution of this protocol, please refer to Avcilar-Kucukgoze et al. (2020) Preparing specific tRNAs by in vitro transcription and enriched bacterial expression tRNA aminoacylation and preparation of charged aa-tRNA for enzymatic reactions Preparation of aa-tRNA-derived fragments (aa-tRF) using in vitro cleavage with RNase T2 Using Arg-tRNA and Arg-tRF for in vitro arginylation
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Affiliation(s)
- Irem Avcilar-Kucukgoze
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19144, USA
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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21
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Advanced approaches for elucidating structures of large RNAs using NMR spectroscopy and complementary methods. Methods 2020; 183:93-107. [DOI: 10.1016/j.ymeth.2020.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/11/2019] [Accepted: 01/16/2020] [Indexed: 11/23/2022] Open
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Mutsuro-Aoki H, Hamachi K, Kurihara R, Tamura K. Aminoacylation of short hairpin RNAs through kissing-loop interactions indicates evolutionary trend of RNA molecules. Biosystems 2020; 197:104206. [PMID: 32640271 DOI: 10.1016/j.biosystems.2020.104206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/30/2020] [Accepted: 06/30/2020] [Indexed: 12/24/2022]
Abstract
The unique G3:U70 base pair in the acceptor stem of tRNAAla has been shown to be a critical recognition site by alanyl-tRNA synthetase (AlaRS). The base pair resides on one of the arms of the L-shaped structure of tRNA (minihelix) and the genetic code has likely evolved from a primordial tRNA-aaRS (aminoacyl-tRNA synthetase) system. In terms of the evolution of tRNA, incorporation of a G:U base pair in the structure would be important. Here, we found that two independent short hairpin RNAs change their conformation through kissing-loop interactions, finally forming a minihelix-like structure, in which the G3:U70 base pair is incorporated. The RNA system can be properly aminoacylated by the minimal Escherichia coli AlaRS variant with alanylation activity (AlaRS442N). Thus, characteristic structural features produced via kissing-loop interactions may provide important clues into the evolution of RNA.
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Affiliation(s)
- Hiromi Mutsuro-Aoki
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Kokoro Hamachi
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Ryodai Kurihara
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
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23
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Arutaki M, Kurihara R, Matsuoka T, Inami A, Tokunaga K, Ohno T, Takahashi H, Takano H, Ando T, Mutsuro-Aoki H, Umehara T, Tamura K. G:U-Independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl-tRNA Synthetase: An Insight into the Evolution of Aminoacyl-tRNA Synthetases. J Mol Evol 2020; 88:501-509. [DOI: 10.1007/s00239-020-09945-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 04/28/2020] [Indexed: 11/25/2022]
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Abstract
The modern version of the RNA World Hypothesis begins with activated ribonucleotides condensing (nonenzymatically) to make RNA molecules, some of which possess (perhaps slight) catalytic activity. We propose that noncanonical ribonucleotides, which would have been inevitable under prebiotic conditions, might decrease the RNA length required to have useful catalytic function by allowing short RNAs to possess a more versatile collection of folded motifs. We argue that modified versions of the standard bases, some with features that resemble cofactors, could have facilitated that first moment in which early RNA molecules with catalytic capability began their evolutionary path toward self-replication.
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25
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Kelly P, Hadi-Nezhad F, Liu DY, Lawrence TJ, Linington RG, Ibba M, Ardell DH. Targeting tRNA-synthetase interactions towards novel therapeutic discovery against eukaryotic pathogens. PLoS Negl Trop Dis 2020; 14:e0007983. [PMID: 32106219 PMCID: PMC7046186 DOI: 10.1371/journal.pntd.0007983] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/10/2019] [Indexed: 12/22/2022] Open
Abstract
The development of chemotherapies against eukaryotic pathogens is especially challenging because of both the evolutionary conservation of drug targets between host and parasite, and the evolution of strain-dependent drug resistance. There is a strong need for new nontoxic drugs with broad-spectrum activity against trypanosome parasites such as Leishmania and Trypanosoma. A relatively untested approach is to target macromolecular interactions in parasites rather than small molecular interactions, under the hypothesis that the features specifying macromolecular interactions diverge more rapidly through coevolution. We computed tRNA Class-Informative Features in humans and independently in eight distinct clades of trypanosomes, identifying parasite-specific informative features, including base pairs and base mis-pairs, that are broadly conserved over approximately 250 million years of trypanosome evolution. Validating these observations, we demonstrated biochemically that tRNA:aminoacyl-tRNA synthetase (aaRS) interactions are a promising target for anti-trypanosomal drug discovery. From a marine natural products extract library, we identified several fractions with inhibitory activity toward Leishmania major alanyl-tRNA synthetase (AlaRS) but no activity against the human homolog. These marine natural products extracts showed cross-reactivity towards Trypanosoma cruzi AlaRS indicating the broad-spectrum potential of our network predictions. We also identified Leishmania major threonyl-tRNA synthetase (ThrRS) inhibitors from the same library. We discuss why chemotherapies targeting multiple aaRSs should be less prone to the evolution of resistance than monotherapeutic or synergistic combination chemotherapies targeting only one aaRS. Trypanosome parasites pose a significant health risk worldwide. Conventional drug development strategies have proven challenging given the high conservation between humans and pathogens, with off-target toxicity being a common problem. Protein synthesis inhibitors have historically been an attractive target for antimicrobial discovery against bacteria, and more recently for eukaryotic pathogens. Here we propose that exploiting pathogen-specific tRNA-synthetase interactions offers the potential for highly targeted drug discovery. To this end, we improved tRNA gene annotations in trypanosome genomes, identified functionally informative trypanosome-specific tRNA features, and showed that these features are highly conserved over approximately 250 million years of trypanosome evolution. Highlighting the species-specific and broad-spectrum potential of our approach, we identified natural product inhibitors against the parasite translational machinery that have no effect on the homologous human enzyme.
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Affiliation(s)
- Paul Kelly
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Fatemeh Hadi-Nezhad
- Quantitative and Systems Biology Program, University of California, Merced, California, United States of America
| | - Dennis Y. Liu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Travis J. Lawrence
- Quantitative and Systems Biology Program, University of California, Merced, California, United States of America
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, Tennessee, United States of America
| | - Roger G. Linington
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Michael Ibba
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (MI); (DHA)
| | - David H. Ardell
- Quantitative and Systems Biology Program, University of California, Merced, California, United States of America
- Department of Molecular & Cell Biology, University of California, Merced, California, United States of America
- * E-mail: (MI); (DHA)
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26
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RNA Aptamers for a tRNA-Binding Protein from Aeropyrum pernix with Homologous Counterparts Distributed Throughout Evolution. Life (Basel) 2020; 10:life10020011. [PMID: 32024042 PMCID: PMC7175363 DOI: 10.3390/life10020011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 01/15/2020] [Accepted: 01/28/2020] [Indexed: 12/02/2022] Open
Abstract
In the present in vitro selection study, we isolated and characterized RNA aptamers for a tRNA-binding protein (Trbp) from an extremophile archaeon Aeropyrum pernix. Trbp-like structures are frequently found not only in aminoacyl-tRNA synthetases but also in diverse types of proteins from different organisms. They likely arose early in evolution and have played important roles in evolution through interactions with key RNA structures. RNA aptamers specific for A. pernix Trbp were successfully selected from a pool of RNAs composed of 60 nucleotides, including a random 30-nucleotide region. From the secondary structures, we obtained a shortened sequence composed of 21 nucleotides, of which the 3′-terminal single stranded CA nucleotides are essential for binding. This may be related to the initial evolutionary role of the universal CCA-3′ terminus of tRNA in the interaction with Trbp-like structures.
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27
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Shinoda S, Kitagawa S, Nakagawa S, Wei FY, Tomizawa K, Araki K, Araki M, Suzuki T, Suzuki T. Mammalian NSUN2 introduces 5-methylcytidines into mitochondrial tRNAs. Nucleic Acids Res 2019; 47:8734-8745. [PMID: 31287866 PMCID: PMC6895283 DOI: 10.1093/nar/gkz575] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/15/2019] [Accepted: 06/20/2019] [Indexed: 12/11/2022] Open
Abstract
Post-transcriptional modifications in mitochondrial tRNAs (mt-tRNAs) play critical roles in mitochondrial protein synthesis, which produces respiratory chain complexes. In this study, we took advantage of mass spectrometric analysis to map 5-methylcytidine (m5C) at positions 48–50 in eight mouse and six human mt-tRNAs. We also confirmed the absence of m5C in mt-tRNAs isolated from Nsun2 knockout (KO) mice, as well as from NSUN2 KO human culture cells. In addition, we successfully reconstituted m5C at positions 48–50 of mt-tRNA in vitro with NSUN2 protein in the presence of S-adenosylmethionine. Although NSUN2 is predominantly localized to the nucleus and introduces m5C into cytoplasmic tRNAs and mRNAs, structured illumination microscopy clearly revealed NSUN2 foci inside mitochondria. These observations provide novel insights into the role of NSUN2 in the physiology and pathology of mitochondrial functions.
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Affiliation(s)
- Saori Shinoda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Sho Kitagawa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shinichi Nakagawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Hokkaido 060-0812, Japan
| | - Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012 Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Kimi Araki
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto 860-0811, Japan
| | - Masatake Araki
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto 860-0811, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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28
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Li S, Su Z, Lehmann J, Stamatopoulou V, Giarimoglou N, Henderson FE, Fan L, Pintilie GD, Zhang K, Chen M, Ludtke SJ, Wang YX, Stathopoulos C, Chiu W, Zhang J. Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions. Nat Struct Mol Biol 2019; 26:1094-1105. [PMID: 31740854 PMCID: PMC6899168 DOI: 10.1038/s41594-019-0326-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/07/2019] [Indexed: 12/11/2022]
Abstract
Amino acid availability in Gram-positive bacteria is monitored by T-box riboswitches. T-boxes directly bind tRNAs, assess their aminoacylation state, and regulate the transcription or translation of downstream genes to maintain nutritional homeostasis. Here, we report cocrystal and cryo-EM structures of Geobacillus kaustophilus and Bacillus subtilis T-box-tRNA complexes, detailing their multivalent, exquisitely selective interactions. The T-box forms a U-shaped molecular vise that clamps the tRNA, captures its 3' end using an elaborate 'discriminator' structure, and interrogates its aminoacylation state using a steric filter fashioned from a wobble base pair. In the absence of aminoacylation, T-boxes clutch tRNAs and form a continuously stacked central spine, permitting transcriptional readthrough or translation initiation. A modeled aminoacyl disrupts tRNA-T-box stacking, severing the central spine and blocking gene expression. Our data establish a universal mechanism of amino acid sensing on tRNAs and gene regulation by T-box riboswitches and exemplify how higher-order RNA-RNA interactions achieve multivalency and specificity.
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Affiliation(s)
- Shuang Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Zhaoming Su
- Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Jean Lehmann
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Campus Paris-Saclay, Gif-sur-Yvette, France
| | | | - Nikoleta Giarimoglou
- Department of Biochemistry, School of Medicine, University of Patras, Patras, Greece
| | - Frances E Henderson
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Lixin Fan
- Small-Angle X-ray Scattering Core Facility, Center for Cancer Research of the National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA
| | - Grigore D Pintilie
- Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Kaiming Zhang
- Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Muyuan Chen
- Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Steven J Ludtke
- Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Yun-Xing Wang
- Small-Angle X-ray Scattering Core Facility, Center for Cancer Research of the National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA.,Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | | | - Wah Chiu
- Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, USA. .,Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, Stanford University, Stanford, CA, USA.
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
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29
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Bottino-Rojas V, Pereira LOR, Silva G, Talyuli OAC, Dunkov BC, Oliveira PL, Paiva-Silva GO. Non-canonical transcriptional regulation of heme oxygenase in Aedes aegypti. Sci Rep 2019; 9:13726. [PMID: 31551499 PMCID: PMC6760526 DOI: 10.1038/s41598-019-49396-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/22/2019] [Indexed: 12/19/2022] Open
Abstract
Heme oxygenase (HO) is a ubiquitous enzyme responsible for heme breakdown, which yields carbon monoxide (CO), biliverdin (BV) and ferrous ion. Here we show that the Aedes aegypti heme oxygenase gene (AeHO - AAEL008136) is expressed in different developmental stages and tissues. AeHO expression increases after a blood meal in the midgut, and its maximal transcription levels overlaps with the maximal rate of the further modified A. aegypti biglutaminyl-biliverdin (AeBV) pigment production. HO is a classical component of stress response in eukaryotic cells, being activated under oxidative stress or increased heme levels. Indeed, the final product of HO activity in the mosquito midgut, AeBV, exerts a protective antioxidant activity. AeHO, however, does not seem to be under a classical redox-sensitive transcriptional regulation, being unresponsive to heme itself, and even down regulated when insects face a pro-oxidant insult. In contrast, AeHO gene expression responds to nutrient sensing mechanisms, through the target of rapamycin (TOR) pathway. This unusual transcriptional control of AeHO, together with the antioxidant properties of AeBV, suggests that heme degradation by HO, in addition to its important role in protection of Aedes aegypti against heme exposure, also acts as a digestive feature, being an essential adaptation to blood feeding.
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Affiliation(s)
- Vanessa Bottino-Rojas
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Luiza O R Pereira
- Laboratório de Pesquisas em Leishmaniose, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, 21040-360, Brazil
| | - Gabriela Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Octavio A C Talyuli
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Boris C Dunkov
- Center for Insect Science, The University of Arizona, Tucson, AZ, 85721-0106, USA
| | - Pedro L Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Gabriela O Paiva-Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil.
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30
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Jühling T, Duchardt-Ferner E, Bonin S, Wöhnert J, Pütz J, Florentz C, Betat H, Sauter C, Mörl M. Small but large enough: structural properties of armless mitochondrial tRNAs from the nematode Romanomermis culicivorax. Nucleic Acids Res 2019; 46:9170-9180. [PMID: 29986062 PMCID: PMC6158502 DOI: 10.1093/nar/gky593] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 06/20/2018] [Indexed: 12/19/2022] Open
Abstract
As adapter molecules to convert the nucleic acid information into the amino acid sequence, tRNAs play a central role in protein synthesis. To fulfill this function in a reliable way, tRNAs exhibit highly conserved structural features common in all organisms and in all cellular compartments active in translation. However, in mitochondria of metazoans, certain dramatic deviations from the consensus tRNA structure are described, where some tRNAs lack the D- or T-arm without losing their function. In Enoplea, this miniaturization comes to an extreme, and functional mitochondrial tRNAs can lack both arms, leading to a considerable size reduction. Here, we investigate the secondary and tertiary structure of two such armless tRNAs from Romanomermis culicivorax. Despite their high AU content, the transcripts fold into a single and surprisingly stable hairpin structure, deviating from standard tRNAs. The three-dimensional form is boomerang-like and diverges from the standard L-shape. These results indicate that such unconventional miniaturized tRNAs can still fold into a tRNA-like shape, although their length and secondary structure are very unusual. They highlight the remarkable flexibility of the protein synthesis apparatus and suggest that the translational machinery of Enoplea mitochondria may show compensatory adaptations to accommodate these armless tRNAs for efficient translation.
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Affiliation(s)
- Tina Jühling
- Institute for Biochemistry, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany.,Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences, Goethe-University and Center of Biomolecular Magnetic Resonance (BMRZ), Frankfurt/M., Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Sonja Bonin
- Institute for Biochemistry, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences, Goethe-University and Center of Biomolecular Magnetic Resonance (BMRZ), Frankfurt/M., Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Joern Pütz
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Catherine Florentz
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Heike Betat
- Institute for Biochemistry, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany
| | - Claude Sauter
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstrasse 34, 04103 Leipzig, Germany
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31
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Asano K, Suzuki T, Saito A, Wei FY, Ikeuchi Y, Numata T, Tanaka R, Yamane Y, Yamamoto T, Goto T, Kishita Y, Murayama K, Ohtake A, Okazaki Y, Tomizawa K, Sakaguchi Y, Suzuki T. Metabolic and chemical regulation of tRNA modification associated with taurine deficiency and human disease. Nucleic Acids Res 2019; 46:1565-1583. [PMID: 29390138 PMCID: PMC5829720 DOI: 10.1093/nar/gky068] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/23/2018] [Indexed: 12/21/2022] Open
Abstract
Modified uridine containing taurine, 5-taurinomethyluridine (τm5U), is found at the anticodon first position of mitochondrial (mt-)transfer RNAs (tRNAs). Previously, we reported that τm5U is absent in mt-tRNAs with pathogenic mutations associated with mitochondrial diseases. However, biogenesis and physiological role of τm5U remained elusive. Here, we elucidated τm5U biogenesis by confirming that 5,10-methylene-tetrahydrofolate and taurine are metabolic substrates for τm5U formation catalyzed by MTO1 and GTPBP3. GTPBP3-knockout cells exhibited respiratory defects and reduced mitochondrial translation. Very little τm5U34 was detected in patient's cells with the GTPBP3 mutation, demonstrating that lack of τm5U results in pathological consequences. Taurine starvation resulted in downregulation of τm5U frequency in cultured cells and animal tissues (cat liver and flatfish). Strikingly, 5-carboxymethylaminomethyluridine (cmnm5U), in which the taurine moiety of τm5U is replaced with glycine, was detected in mt-tRNAs from taurine-depleted cells. These results indicate that tRNA modifications are dynamically regulated via sensing of intracellular metabolites under physiological condition.
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Affiliation(s)
- Kana Asano
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ayaka Saito
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, University of Tokyo, Meguro-ku, Tokyo 153-8505, Japan
| | - Tomoyuki Numata
- Biological Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Ryou Tanaka
- Department of Veterinary Surgery, Tokyo University of Agriculture and Technology, Animal Medical Center, Fuchu, Tokyo 183-8509, Japan
| | - Yoshihisa Yamane
- Department of Veterinary Surgery, Tokyo University of Agriculture and Technology, Animal Medical Center, Fuchu, Tokyo 183-8509, Japan
| | - Takeshi Yamamoto
- Tamaki Laboratory, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Tamaki, Mie 519-0423, Japan
| | - Takanobu Goto
- Department of Chemistry & Biochemistry, National Institute of Technology, Numazu College, Numazu, Shizuoka 410-8501, Japan
| | - Yoshihito Kishita
- Division of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1240, Japan
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Midori-ku, Chiba 266-0007, Japan
| | - Akira Ohtake
- Department of Pediatrics, Saitama Medical University, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan
| | - Yasushi Okazaki
- Division of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1240, Japan.,Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama 350-1240, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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32
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Keller P, Freund I, Marchand V, Bec G, Huang R, Motorin Y, Eigenbrod T, Dalpke A, Helm M. Double methylation of tRNA-U54 to 2'-O-methylthymidine (Tm) synergistically decreases immune response by Toll-like receptor 7. Nucleic Acids Res 2019; 46:9764-9775. [PMID: 30102387 PMCID: PMC6182150 DOI: 10.1093/nar/gky644] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/02/2018] [Indexed: 12/25/2022] Open
Abstract
Sensing of nucleic acids for molecular discrimination between self and non-self is a challenging task for the innate immune system. RNA acts as a potent stimulus for pattern recognition receptors including in particular human Toll-like receptor 7 (TLR7). Certain RNA modifications limit potentially harmful self-recognition of endogenous RNA. Previous studies had identified the 2′-O-methylation of guanosine 18 (Gm18) within tRNAs as an antagonist of TLR7 leading to an impaired immune response. However, human tRNALys3 was non-stimulatory despite lacking Gm18. To identify the underlying molecular principle, interferon responses of human peripheral blood mononuclear cells to differentially modified tRNALys3 were determined. The investigation of synthetic modivariants allowed attributing a significant part of the immunosilencing effect to the 2′-O-methylthymidine (m5Um) modification at position 54. The effect was contingent upon the synergistic presence of both methyl groups at positions C5 and 2’O, as shown by the fact that neither Um54 nor m5U54 produced any effect alone. Testing permutations of the nucleobase at ribose-methylated position 54 suggested that the extent of silencing and antagonism of the TLR7 response was governed by hydrogen patterns and lipophilic interactions of the nucleobase. The results identify a new immune-modulatory endogenous RNA modification that limits TLR7 activation by RNA.
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Affiliation(s)
- Patrick Keller
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University of Mainz, Staudingerweg 5, D-55128 Mainz, Germany
| | - Isabel Freund
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Virginie Marchand
- Next Generation Sequencing Platform, UMS2008 Ingénierie Biologie Santé en Lorraine (IBSLor), BioPôle de l'Université de Lorraine Campus Biologie-Santé, 9, avenue de la Forêt de Haye, CS 50184, 54505 Vandoeuvre-les-Nancy, France
| | - Guillaume Bec
- Biophysics and Structural Biology Team, Unité Architecture et réactivité de l'ARN (UPR9002), Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15, rue René Descartes, F67084, Strasbourg cedex, France
| | - Raven Huang
- Department of Biochemistry, Center for Biophysics & Computational Biology, University of Illinois at Urbana-Champaign, 411 Roger Adams Lab., 600 S. Mathews Ave. Urbana, IL 61801, USA
| | - Yuri Motorin
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA) UMR7365 CNRS-UL, BioPôle de l'Université de Lorraine Campus Biologie-Santé, 9, avenue de la Forêt de Haye, CS 50184, 54505 Vandoeuvre-les-Nancy, France
| | - Tatjana Eigenbrod
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Alexander Dalpke
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University of Mainz, Staudingerweg 5, D-55128 Mainz, Germany
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33
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Baumann T, Hauf M, Richter F, Albers S, Möglich A, Ignatova Z, Budisa N. Computational Aminoacyl-tRNA Synthetase Library Design for Photocaged Tyrosine. Int J Mol Sci 2019; 20:ijms20092343. [PMID: 31083552 PMCID: PMC6539999 DOI: 10.3390/ijms20092343] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/07/2019] [Accepted: 05/09/2019] [Indexed: 01/20/2023] Open
Abstract
Engineering aminoacyl-tRNA synthetases (aaRSs) provides access to the ribosomal incorporation of noncanonical amino acids via genetic code expansion. Conventional targeted mutagenesis libraries with 5–7 positions randomized cover only marginal fractions of the vast sequence space formed by up to 30 active site residues. This frequently results in selection of weakly active enzymes. To overcome this limitation, we use computational enzyme design to generate a focused library of aaRS variants. For aaRS enzyme redesign, photocaged ortho-nitrobenzyl tyrosine (ONBY) was chosen as substrate due to commercial availability and its diverse applications. Diversifying 17 first- and second-shell sites and performing conventional aaRS positive and negative selection resulted in a high-activity aaRS. This MjTyrRS variant carries ten mutations and outperforms previously reported ONBY-specific aaRS variants isolated from traditional libraries. In response to a single in-frame amber stop codon, it mediates the in vivo incorporation of ONBY with an efficiency matching that of the wild type MjTyrRS enzyme acylating cognate tyrosine. These results exemplify an improved general strategy for aaRS library design and engineering.
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Affiliation(s)
- Tobias Baumann
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany.
| | - Matthias Hauf
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany.
| | - Florian Richter
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
| | - Suki Albers
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.
| | - Andreas Möglich
- Biophysikalische Chemie, Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
- Lehrstuhl für Biochemie, Universität Bayreuth, 95447 Bayreuth, Germany.
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.
| | - Nediljko Budisa
- Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623 Berlin, Germany.
- Department of Chemistry, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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34
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Glycyl-tRNA synthetase from Nanoarchaeum equitans: The first crystal structure of archaeal GlyRS and analysis of its tRNA glycylation. Biochem Biophys Res Commun 2019; 511:228-233. [PMID: 30771900 DOI: 10.1016/j.bbrc.2019.01.142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 01/31/2019] [Indexed: 11/23/2022]
Abstract
This study reports the X-ray crystallographic structure of the glycyl-tRNA synthetase (GlyRS) of Nanoarchaeum equitans - a hyperthermophilic archaeal species. This is the first archaeal GlyRS crystal structure elucidated. The GlyRS comprises an N-terminal catalytic domain and a C-terminal anticodon-binding domain with a long β-sheet inserted between these domains. An unmodified transcript of the wild-type N. equitans tRNAGly was successfully glycylated using GlyRS. Substitution of the discriminator base A73 of tRNAGly with any other nucleotide caused a significant decrease in glycylation activity. Mutational analysis of the second base-pair C2G71 of the acceptor stem of tRNAGly elucidated the importance of the base-pair, especially G71, as an identity element for recognition by GlyRS. Glycylation assays using tRNAGly G71 substitution mutants and a GlyRS mutant where Arg223 is mutated to alanine strengthen the possibility that the carbonyl oxygen at position 6 of G71 would hydrogen-bond with the guanidine nitrogen of Arg223 in N. equitans GlyRS.
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35
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Akichika S, Hirano S, Shichino Y, Suzuki T, Nishimasu H, Ishitani R, Sugita A, Hirose Y, Iwasaki S, Nureki O, Suzuki T. Cap-specific terminal N 6-methylation of RNA by an RNA polymerase II-associated methyltransferase. Science 2018; 363:science.aav0080. [PMID: 30467178 DOI: 10.1126/science.aav0080] [Citation(s) in RCA: 234] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 11/14/2018] [Indexed: 12/14/2022]
Abstract
N 6-methyladenosine (m6A), a major modification of messenger RNAs (mRNAs), plays critical roles in RNA metabolism and function. In addition to the internal m6A, N 6, 2'-O-dimethyladenosine (m6Am) is present at the transcription start nucleotide of capped mRNAs in vertebrates. However, its biogenesis and functional role remain elusive. Using a reverse genetics approach, we identified PCIF1, a factor that interacts with the serine-5-phosphorylated carboxyl-terminal domain of RNA polymerase II, as a cap-specific adenosine methyltransferase (CAPAM) responsible for N 6-methylation of m6Am. The crystal structure of CAPAM in complex with substrates revealed the molecular basis of cap-specific m6A formation. A transcriptome-wide analysis revealed that N 6-methylation of m6Am promotes the translation of capped mRNAs. Thus, a cap-specific m6A writer promotes translation of mRNAs starting from m6Am.
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Affiliation(s)
- Shinichiro Akichika
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Seiichi Hirano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuichi Shichino
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroshi Nishimasu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ai Sugita
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yutaka Hirose
- Laboratory of Gene Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Shintaro Iwasaki
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo 277-8562, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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36
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Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis. Nat Chem Biol 2018; 14:1010-1020. [PMID: 30150682 DOI: 10.1038/s41589-018-0119-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 07/09/2018] [Indexed: 11/08/2022]
Abstract
Modification of tRNA anticodons plays a critical role in ensuring accurate translation. N4-acetylcytidine (ac4C) is present at the anticodon first position (position 34) of bacterial elongator tRNAMet. Herein, we identified Bacillus subtilis ylbM (renamed tmcAL) as a novel gene responsible for ac4C34 formation. Unlike general acetyltransferases that use acetyl-CoA, TmcAL activates an acetate ion to form acetyladenylate and then catalyzes ac4C34 formation through a mechanism similar to tRNA aminoacylation. The crystal structure of TmcAL with an ATP analog reveals the molecular basis of ac4C34 formation. The ΔtmcAL strain displayed a cold-sensitive phenotype and a strong genetic interaction with tilS that encodes the enzyme responsible for synthesizing lysidine (L) at position 34 of tRNAIle to facilitate AUA decoding. Mistranslation of the AUA codon as Met in the ΔtmcAL strain upon tilS repression suggests that ac4C34 modification of tRNAMet and L34 modification of tRNAIle act cooperatively to prevent misdecoding of the AUA codon.
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37
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Lin H, Miyauchi K, Harada T, Okita R, Takeshita E, Komaki H, Fujioka K, Yagasaki H, Goto YI, Yanaka K, Nakagawa S, Sakaguchi Y, Suzuki T. CO 2-sensitive tRNA modification associated with human mitochondrial disease. Nat Commun 2018; 9:1875. [PMID: 29760464 PMCID: PMC5951830 DOI: 10.1038/s41467-018-04250-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 04/16/2018] [Indexed: 12/21/2022] Open
Abstract
It has been generally thought that tRNA modifications are stable and static, and their frequencies are rarely regulated. N6-threonylcarbamoyladenosine (t6A) occurs at position 37 of five mitochondrial (mt-)tRNA species. We show that YRDC and OSGEPL1 are responsible for t6A37 formation, utilizing L-threonine, ATP, and CO2/bicarbonate as substrates. OSGEPL1-knockout cells exhibit respiratory defects and reduced mitochondrial translation. We find low level of t6A37 in mutant mt-tRNA isolated from the MERRF-like patient’s cells, indicating that lack of t6A37 results in pathological consequences. Kinetic measurements of t6A37 formation reveal that the Km value of CO2/bicarbonate is extremely high (31 mM), suggesting that CO2/bicarbonate is a rate-limiting factor for t6A37 formation. Consistent with this, we observe a low frequency of t6A37 in mt-tRNAs isolated from human cells cultured without bicarbonate. These findings indicate that t6A37 is regulated by sensing intracellular CO2/bicarbonate concentration, implying that mitochondrial translation is modulated in a codon-specific manner under physiological conditions. Transfer RNA modifications play critical roles in protein synthesis. Here the authors reveal the t6A37 tRNA modification is dynamically regulated by sensing intracellular CO2 concentration in mitochondria, implying metabolic regulation of protein synthesis.
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Affiliation(s)
- Huan Lin
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tai Harada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Ryo Okita
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Eri Takeshita
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan.,Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan
| | - Hirofumi Komaki
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan.,Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan
| | - Kaoru Fujioka
- Department of Pediatrics, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, Yamanashi, 409-3898, Japan
| | - Hideki Yagasaki
- Department of Pediatrics, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, Yamanashi, 409-3898, Japan
| | - Yu-Ichi Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan.,Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan.,Medical Genome Center, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, Tokyo, 187-8502, Japan
| | - Kaori Yanaka
- RNA Biology Laboratory, RIKEN Advanced Research Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo, 060-0812, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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38
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Bottino-Rojas V, Talyuli OAC, Carrara L, Martins AJ, James AA, Oliveira PL, Paiva-Silva GO. The redox-sensing gene Nrf2 affects intestinal homeostasis, insecticide resistance, and Zika virus susceptibility in the mosquito Aedes aegypti. J Biol Chem 2018; 293:9053-9063. [PMID: 29685890 DOI: 10.1074/jbc.ra117.001589] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 04/19/2018] [Indexed: 12/17/2022] Open
Abstract
Production and degradation of reactive oxygen species (ROS) are extensively regulated to ensure proper cellular responses to various environmental stimuli and stresses. Moreover, physiologically generated ROS function as secondary messengers that can influence tissue homeostasis. The cap'n'collar transcription factor known as nuclear factor erythroid-derived factor 2 (Nrf2) coordinates an evolutionarily conserved transcriptional activation pathway that mediates antioxidant and detoxification responses in many animal species, including insects and mammals. Here, we show that Nrf2-mediated signaling affects embryo survival, midgut homeostasis, and redox biology in Aedes aegypti, a mosquito species vector of dengue, Zika, and other disease-causing viruses. We observed that AeNrf2 silencing increases ROS levels and stimulates intestinal stem cell proliferation. Because ROS production is a major aspect of innate immunity in mosquito gut, we found that a decrease in Nrf2 signaling results in reduced microbiota growth and Zika virus infection. Moreover, we provide evidence that AeNrf2 signaling also controls transcriptional adaptation of A. aegypti to insecticide challenge. Therefore, we conclude that Nrf2-mediated response regulates assorted gene clusters in A. aegypti that determine cellular and midgut redox balance, affecting overall xenobiotic resistance and vectorial adaptation of the mosquito.
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Affiliation(s)
- Vanessa Bottino-Rojas
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902 Brazil
| | - Octavio A C Talyuli
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902 Brazil
| | - Luana Carrara
- Laficave, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
| | - Ademir J Martins
- Laficave, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil.,the Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, RJ, Brazil, and
| | - Anthony A James
- the Departments of Microbiology and Molecular Genetics and of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900
| | - Pedro L Oliveira
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902 Brazil.,the Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, RJ, Brazil, and
| | - Gabriela O Paiva-Silva
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902 Brazil, .,the Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, RJ, Brazil, and
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39
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Carlsson L, Clarke JC, Yen C, Gregoire F, Albery T, Billger M, Egnell AC, Gan LM, Jennbacken K, Johansson E, Linhardt G, Martinsson S, Sadiq MW, Witman N, Wang QD, Chen CH, Wang YP, Lin S, Ticho B, Hsieh PCH, Chien KR, Fritsche-Danielson R. Biocompatible, Purified VEGF-A mRNA Improves Cardiac Function after Intracardiac Injection 1 Week Post-myocardial Infarction in Swine. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2018; 9:330-346. [PMID: 30038937 PMCID: PMC6054703 DOI: 10.1016/j.omtm.2018.04.003] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 04/04/2018] [Indexed: 12/02/2022]
Abstract
mRNA can direct dose-dependent protein expression in cardiac muscle without genome integration, but to date has not been shown to improve cardiac function in a safe, clinically applicable way. Herein, we report that a purified and optimized mRNA in a biocompatible citrate-saline formulation is tissue specific, long acting, and does not stimulate an immune response. In small- and large-animal, permanent occlusion myocardial infarction models, VEGF-A 165 mRNA improves systolic ventricular function and limits myocardial damage. Following a single administration a week post-infarction in mini pigs, left ventricular ejection fraction, inotropy, and ventricular compliance improved, border zone arteriolar and capillary density increased, and myocardial fibrosis decreased at 2 months post-treatment. Purified VEGF-A mRNA establishes the feasibility of improving cardiac function in the sub-acute therapeutic window and may represent a new class of therapies for ischemic injury.
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Affiliation(s)
- Leif Carlsson
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
| | - Jonathan C Clarke
- Integrated Cardiometabolic Center, Karolinska Institute, Huddinge 141 52, Sweden.,Department of Cell and Molecular Biology and Medicine, Karolinska Institute, Stockholm 171 77, Sweden
| | - Christopher Yen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | | | - Tamsin Albery
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
| | - Martin Billger
- Drug Safety and Metabolism, Regulatory Safety, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Ann-Charlotte Egnell
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
| | - Li-Ming Gan
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
| | - Karin Jennbacken
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
| | - Edvin Johansson
- Personalised Healthcare and Biomarkers, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Gunilla Linhardt
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
| | - Sofia Martinsson
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
| | - Muhammad Waqas Sadiq
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
| | - Nevin Witman
- Department of Cell and Molecular Biology and Medicine, Karolinska Institute, Stockholm 171 77, Sweden
| | - Qing-Dong Wang
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
| | - Chien-Hsi Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Ping Wang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Susan Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | | | - Patrick C H Hsieh
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.,Institute of Medical Genomics and Proteomics, Institute of Clinical Medicine and Cardiovascular Surgery Division, National Taiwan University and Hospital, Taipei 100, Taiwan
| | - Kenneth R Chien
- Integrated Cardiometabolic Center, Karolinska Institute, Huddinge 141 52, Sweden.,Department of Cell and Molecular Biology and Medicine, Karolinska Institute, Stockholm 171 77, Sweden
| | - Regina Fritsche-Danielson
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
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40
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Han L, Guy MP, Kon Y, Phizicky EM. Lack of 2'-O-methylation in the tRNA anticodon loop of two phylogenetically distant yeast species activates the general amino acid control pathway. PLoS Genet 2018; 14:e1007288. [PMID: 29596413 PMCID: PMC5892943 DOI: 10.1371/journal.pgen.1007288] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 04/10/2018] [Accepted: 03/05/2018] [Indexed: 01/03/2023] Open
Abstract
Modification defects in the tRNA anticodon loop often impair yeast growth and cause human disease. In the budding yeast Saccharomyces cerevisiae and the phylogenetically distant fission yeast Schizosaccharomyces pombe, trm7Δ mutants grow poorly due to lack of 2'-O-methylation of C32 and G34 in the tRNAPhe anticodon loop, and lesions in the human TRM7 homolog FTSJ1 cause non-syndromic X-linked intellectual disability (NSXLID). However, it is unclear why trm7Δ mutants grow poorly. We show here that despite the fact that S. cerevisiae trm7Δ mutants had no detectable tRNAPhe charging defect in rich media, the cells constitutively activated a robust general amino acid control (GAAC) response, acting through Gcn2, which senses uncharged tRNA. Consistent with reduced available charged tRNAPhe, the trm7Δ growth defect was suppressed by spontaneous mutations in phenylalanyl-tRNA synthetase (PheRS) or in the pol III negative regulator MAF1, and by overexpression of tRNAPhe, PheRS, or EF-1A; all of these also reduced GAAC activation. Genetic analysis also demonstrated that the trm7Δ growth defect was due to the constitutive robust GAAC activation as well as to the reduced available charged tRNAPhe. Robust GAAC activation was not observed with several other anticodon loop modification mutants. Analysis of S. pombe trm7 mutants led to similar observations. S. pombe Trm7 depletion also resulted in no observable tRNAPhe charging defect and a robust GAAC response, and suppressors mapped to PheRS and reduced GAAC activation. We speculate that GAAC activation is widely conserved in trm7 mutants in eukaryotes, including metazoans, and might play a role in FTSJ1-mediated NSXLID. The ubiquitous tRNA anticodon loop modifications have important but poorly understood functions in decoding mRNAs in the ribosome to ensure accurate and efficient protein synthesis, and their lack often impairs yeast growth and causes human disease. Here we investigate why ribose methylation of residues 32 and 34 in the anticodon loop is important. Mutations in the corresponding methyltransferase Trm7/FTSJ1 cause poor growth in the budding yeast Saccharomyces cerevisiae and near lethality in the evolutionarily distant fission yeast Schizosaccharomyces pombe, each due to reduced functional tRNAPhe. We previously showed that tRNAPhe anticodon loop modification in yeast and humans required two evolutionarily conserved Trm7 interacting proteins for Cm32 and Gm34 modification, which then stimulated G37 modification. We show here that both S. cerevisiae and S. pombe trm7Δ mutants have apparently normal tRNAPhe charging, but constitutively activate a robust general amino acid control (GAAC) response, acting through Gcn2, which senses uncharged tRNA. We also show that S. cerevisiae trm7Δ mutants grow poorly due in part to constitutive GAAC activation as well as to the uncharged tRNAPhe. We propose that TRM7 is important to prevent constitutive GAAC activation throughout eukaryotes, including metazoans, which may explain non-syndromic X-linked intellectual disability associated with human FTSJ1 mutations.
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Affiliation(s)
- Lu Han
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY, United States of America
| | - Michael P. Guy
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY, United States of America
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, KY, United States of America
| | - Yoshiko Kon
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY, United States of America
| | - Eric M. Phizicky
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY, United States of America
- * E-mail:
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41
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Holman KM, Puppala AK, Lee JW, Lee H, Simonović M. Insights into substrate promiscuity of human seryl-tRNA synthetase. RNA (NEW YORK, N.Y.) 2017; 23:1685-1699. [PMID: 28808125 PMCID: PMC5648036 DOI: 10.1261/rna.061069.117] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 08/08/2017] [Indexed: 06/07/2023]
Abstract
Seryl-tRNA synthetase (SerRS) attaches L-serine to the cognate serine tRNA (tRNASer) and the noncognate selenocysteine tRNA (tRNASec). The latter activity initiates the anabolic cycle of selenocysteine (Sec), proper decoding of an in-frame Sec UGA codon, and synthesis of selenoproteins across all domains of life. While the accuracy of SerRS is important for overall proteome integrity, it is its substrate promiscuity that is vital for the integrity of the selenoproteome. This raises a question as to what elements in the two tRNA species, harboring different anticodon sequences and adopting distinct folds, facilitate aminoacylation by a common aminoacyl-tRNA synthetase. We sought to answer this question by analyzing the ability of human cytosolic SerRS to bind and act on tRNASer, tRNASec, and 10 mutant and chimeric constructs in which elements of tRNASer were transposed onto tRNASec We show that human SerRS only subtly prefers tRNASer to tRNASec, and that discrimination occurs at the level of the serylation reaction. Surprisingly, the tRNA mutants predicted to adopt either the 7/5 or 8/5 fold are poor SerRS substrates. In contrast, shortening of the acceptor arm of tRNASec by a single base pair yields an improved SerRS substrate that adopts an 8/4 fold. We suggest that an optimal tertiary arrangement of structural elements within tRNASec and tRNASer dictate their utility for serylation. We also speculate that the extended acceptor-TΨC arm of tRNASec evolved as a compromise for productive binding to SerRS while remaining the major recognition element for other enzymes involved in Sec and selenoprotein synthesis.
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MESH Headings
- Base Sequence
- Binding Sites
- Cytosol/enzymology
- Humans
- Kinetics
- Models, Molecular
- Mutagenesis
- Nucleic Acid Conformation
- RNA Folding
- RNA, Transfer, Amino Acid-Specific/chemistry
- RNA, Transfer, Amino Acid-Specific/genetics
- RNA, Transfer, Amino Acid-Specific/metabolism
- RNA, Transfer, Ser/chemistry
- RNA, Transfer, Ser/genetics
- RNA, Transfer, Ser/metabolism
- Serine-tRNA Ligase/metabolism
- Substrate Specificity
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Affiliation(s)
- Kaitlyn M Holman
- Department of Biochemistry and Molecular Genetics, College of Medicine, The University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Anupama K Puppala
- Department of Biochemistry and Molecular Genetics, College of Medicine, The University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Jonathan W Lee
- College of Liberal Arts and Sciences, The University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Hyun Lee
- Center for Biomolecular Sciences, Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Miljan Simonović
- Department of Biochemistry and Molecular Genetics, College of Medicine, The University of Illinois at Chicago, Chicago, Illinois 60607, USA
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42
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Nagao A, Ohara M, Miyauchi K, Yokobori SI, Yamagishi A, Watanabe K, Suzuki T. Hydroxylation of a conserved tRNA modification establishes non-universal genetic code in echinoderm mitochondria. Nat Struct Mol Biol 2017; 24:778-782. [PMID: 28783151 DOI: 10.1038/nsmb.3449] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/11/2017] [Indexed: 12/13/2022]
Abstract
The genetic code is not frozen but still evolving, which can result in the acquisition of 'dialectal' codons that deviate from the universal genetic code. RNA modifications in the anticodon region of tRNAs play a critical role in establishing such non-universal genetic codes. In echinoderm mitochondria, the AAA codon specifies asparagine instead of lysine. By analyzing mitochondrial (mt-) tRNALys isolated from the sea urchin (Mesocentrotus nudus), we discovered a novel modified nucleoside, hydroxy-N6-threonylcarbamoyladenosine (ht6A), 3' adjacent to the anticodon (position 37). Biochemical analysis revealed that ht6A37 has the ability to prevent mt-tRNALys from misreading AAA as lysine, thereby indicating that hydroxylation of N6-threonylcarbamoyladenosine (t6A) contributes to the establishment of the non-universal genetic code in echinoderm mitochondria.
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Affiliation(s)
- Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Mitsuhiro Ohara
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Shin-Ichi Yokobori
- Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Akihiko Yamagishi
- Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Kimitsuna Watanabe
- Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
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43
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Suzuki H, Kaneko A, Yamamoto T, Nambo M, Hirasawa I, Umehara T, Yoshida H, Park SY, Tamura K. Binding Properties of Split tRNA to the C-terminal Domain of Methionyl-tRNA Synthetase of Nanoarchaeum equitans. J Mol Evol 2017; 84:267-278. [PMID: 28589220 DOI: 10.1007/s00239-017-9796-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 05/30/2017] [Indexed: 11/28/2022]
Abstract
The C-terminal domain of methionyl-tRNA synthetase (MetRS-C) from Nanoarchaeum equitans is homologous to a tRNA-binding protein consisting of 111 amino acids (Trbp111) from Aquifex aeolicus. The crystal structure of MetRS-C showed that it existed as a homodimer, and that each monomer possessed an oligonucleotide/oligosaccharide-binding fold (OB-fold). Analysis using a quartz crystal microbalance indicated that MetRS-C freshly isolated from N. equitans was bound to tRNA. However, binding of the split 3'-half tRNA species was stronger than that of the 5'-half species. The T-loop and the 3'-end regions of the split 3'-half tRNA were found to be responsible for the binding. The minimum structure for binding to MetRS-C might be a minihelix-like stem-loop with single-stranded 3'-terminus. After successive duplications of such a small hairpin structure with the assistance of a Trbp-like structure, the interaction of the T-loop region of the 3'-half with a Trbp-like structure could have been evolutionarily replaced by RNA-RNA interactions, along with many combinational tertiary interactions, to form the modern tRNA structure.
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Affiliation(s)
- Hidemichi Suzuki
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Akihiro Kaneko
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Taro Yamamoto
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Mahoko Nambo
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Ito Hirasawa
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Takuya Umehara
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Hisashi Yoshida
- Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Sam-Yong Park
- Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan. .,Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
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44
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Characterization of tRNALeu binding interactions with Cu2+ and Pb2+ and their biological implications. J Inorg Biochem 2017; 171:90-99. [DOI: 10.1016/j.jinorgbio.2017.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/12/2017] [Accepted: 03/19/2017] [Indexed: 11/17/2022]
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Lorenz C, Lünse CE, Mörl M. tRNA Modifications: Impact on Structure and Thermal Adaptation. Biomolecules 2017; 7:E35. [PMID: 28375166 PMCID: PMC5485724 DOI: 10.3390/biom7020035] [Citation(s) in RCA: 216] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 03/27/2017] [Accepted: 03/28/2017] [Indexed: 12/27/2022] Open
Abstract
Transfer RNAs (tRNAs) are central players in translation, functioning as adapter molecules between the informational level of nucleic acids and the functional level of proteins. They show a highly conserved secondary and tertiary structure and the highest density of post-transcriptional modifications among all RNAs. These modifications concentrate in two hotspots-the anticodon loop and the tRNA core region, where the D- and T-loop interact with each other, stabilizing the overall structure of the molecule. These modifications can cause large rearrangements as well as local fine-tuning in the 3D structure of a tRNA. The highly conserved tRNA shape is crucial for the interaction with a variety of proteins and other RNA molecules, but also needs a certain flexibility for a correct interplay. In this context, it was shown that tRNA modifications are important for temperature adaptation in thermophilic as well as psychrophilic organisms, as they modulate rigidity and flexibility of the transcripts, respectively. Here, we give an overview on the impact of modifications on tRNA structure and their importance in thermal adaptation.
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Affiliation(s)
- Christian Lorenz
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
| | - Christina E Lünse
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
| | - Mario Mörl
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
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Li Y, Fin A, McCoy L, Tor Y. Polymerase-Mediated Site-Specific Incorporation of a Synthetic Fluorescent Isomorphic G Surrogate into RNA. Angew Chem Int Ed Engl 2017; 56:1303-1307. [PMID: 28000329 PMCID: PMC5241218 DOI: 10.1002/anie.201609327] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/10/2016] [Indexed: 12/22/2022]
Abstract
An enzyme-mediated approach for the assembly of singly modified RNA constructs in which specific G residues are replaced with th G, an emissive isomorphic G surrogate, is reported. Transcription in the presence of th G and native nucleoside triphosphates enforces initiation with the unnatural analogue, yielding 5'-end modified transcripts that can be mono-phosphorylated and ligated to provide longer site-specifically modified RNA constructs. The scope of this unprecedented enzymatic approach to non-canonical purine-containing RNAs is explored via the assembly of several altered hammerhead (HH) ribozymes and a singly modified HH substrate. By strategically modifying key positions, a mechanistic insight into the ribozyme-mediated cleavage is gained. Additionally, the emissive features of the modified nucleoside and its responsiveness to environmental changes can be used to monitor cleavage in real time by steady state fluorescence spectroscopy.
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Affiliation(s)
- Yao Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Andrea Fin
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Lisa McCoy
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
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47
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Li Y, Fin A, McCoy L, Tor Y. Polymerase‐Mediated Site‐Specific Incorporation of a Synthetic Fluorescent Isomorphic G Surrogate into RNA. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609327] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yao Li
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Andrea Fin
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Lisa McCoy
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
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Abstract
Over the past 2 decades, different types of circular RNAs have been discovered in all kingdoms of life, and apparently, those circular species are more abundant than previously thought. Apart from circRNAs in viroids and viruses, circular transcripts have been discovered in rodents more than 20 y ago and recently have been reported to be abundant in many organisms including humans. Their exact function remains still unknown, although one may expect extensive functional studies to follow the currently dominant research into identification and discovery of circRNA by sophisticated sequencing techniques and bioinformatics. Functional studies require models and as such methods for preparation of circRNA in vitro. Here, we will review current protocols for RNA circularization and discuss future prospects in the field.
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Affiliation(s)
- Sabine Müller
- a Universität Greifswald, Institut für Biochemie , Greifswald , Germany
| | - Bettina Appel
- a Universität Greifswald, Institut für Biochemie , Greifswald , Germany
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Lanier KA, Athavale SS, Petrov AS, Wartell R, Williams LD. Imprint of Ancient Evolution on rRNA Folding. Biochemistry 2016; 55:4603-13. [DOI: 10.1021/acs.biochem.6b00168] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Kathryn A. Lanier
- School of Chemistry and Biochemistry and ‡School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Shreyas S. Athavale
- School of Chemistry and Biochemistry and ‡School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Anton S. Petrov
- School of Chemistry and Biochemistry and ‡School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Roger Wartell
- School of Chemistry and Biochemistry and ‡School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Loren Dean Williams
- School of Chemistry and Biochemistry and ‡School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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NSUN3 methylase initiates 5-formylcytidine biogenesis in human mitochondrial tRNA(Met). Nat Chem Biol 2016; 12:546-51. [PMID: 27214402 DOI: 10.1038/nchembio.2099] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/15/2016] [Indexed: 12/18/2022]
Abstract
In human mitochondria, the AUA codon encodes methionine via a mitochondrial transfer RNA for methionine (mt-tRNA(Met)) that contains 5-formylcytidine (f(5)C) at the first position of the anticodon (position 34). f(5)C34 is required for deciphering the AUA codon during protein synthesis. Until now, the biogenesis and physiological role of f(5)C34 were unknown. We demonstrate that biogenesis of f(5)C34 is initiated by S-adenosylmethionine (AdoMet)-dependent methylation catalyzed by NSUN3, a putative methyltransferase in mitochondria. NSUN3-knockout cells showed strong reduction in mitochondrial protein synthesis and reduced oxygen consumption, leading to deficient mitochondrial activity. We reconstituted formation of 5-methylcytidine (m(5)C) at position 34 (m(5)C34) on mt-tRNA(Met) with recombinant NSUN3 in the presence of AdoMet, demonstrating that NSUN3-mediated m(5)C34 formation initiates f(5)C34 biogenesis. We also found two disease-associated point mutations in mt-tRNA(Met) that impaired m(5)C34 formation by NSUN3, indicating that a lack of f(5)C34 has pathological consequences.
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