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Petroni E, Esnault C, Tetreault D, Dale RK, Storz G, Adams PP. Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi. Nat Commun 2023; 14:3931. [PMID: 37402717 DOI: 10.1038/s41467-023-39576-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/16/2023] [Indexed: 07/06/2023] Open
Abstract
Transcription termination is an essential and dynamic process that can tune gene expression in response to diverse molecular signals. Yet, the genomic positions, molecular mechanisms, and regulatory consequences of termination have only been studied thoroughly in model bacteria. Here, we use several RNA-seq approaches to map RNA ends for the transcriptome of the spirochete Borrelia burgdorferi - the etiological agent of Lyme disease. We identify complex gene arrangements and operons, untranslated regions and small RNAs. We predict intrinsic terminators and experimentally test examples of Rho-dependent transcription termination. Remarkably, 63% of RNA 3' ends map upstream of or internal to open reading frames (ORFs), including genes involved in the unique infectious cycle of B. burgdorferi. We suggest these RNAs result from premature termination, processing and regulatory events such as cis-acting regulation. Furthermore, the polyamine spermidine globally influences the generation of truncated mRNAs. Collectively, our findings provide insights into transcription termination and uncover an abundance of potential RNA regulators in B. burgdorferi.
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Affiliation(s)
- Emily Petroni
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Caroline Esnault
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Daniel Tetreault
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Philip P Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA.
- Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD, 20892, USA.
- Independent Research Scholar Program, Intramural Research Program, National Institutes of Health, Bethesda, MD, 20892, USA.
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Petroni E, Esnault C, Tetreault D, Dale RK, Storz G, Adams PP. Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen B. burgdorferi. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.04.522626. [PMID: 36712141 PMCID: PMC9881889 DOI: 10.1101/2023.01.04.522626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Transcription termination is an essential and dynamic process that can tune gene expression in response to diverse molecular signals. Yet, the genomic positions, molecular mechanisms, and regulatory consequences of termination have only been studied thoroughly in model bacteria. We employed complementary RNA-seq approaches to map RNA ends for the transcriptome of the spirochete Borrelia burgdorferi - the etiological agent of Lyme disease. By systematically mapping B. burgdorferi RNA ends at single nucleotide resolution, we delineated complex gene arrangements and operons and mapped untranslated regions (UTRs) and small RNAs (sRNAs). We experimentally tested modes of B. burgdorferi transcription termination and compared our findings to observations in E. coli , P. aeruginosa , and B. subtilis . We discovered 63% of B. burgdorferi RNA 3' ends map upstream or internal to open reading frames (ORFs), suggesting novel mechanisms of regulation. Northern analysis confirmed the presence of stable 5' derived RNAs from mRNAs encoding gene products involved in the unique infectious cycle of B. burgdorferi . We suggest these RNAs resulted from premature termination and regulatory events, including forms of cis- acting regulation. For example, we documented that the polyamine spermidine globally influences the generation of truncated mRNAs. In one case, we showed that high spermidine concentrations increased levels of RNA fragments derived from an mRNA encoding a spermidine import system, with a concomitant decrease in levels of the full- length mRNA. Collectively, our findings revealed new insight into transcription termination and uncovered an abundance of potential RNA regulators.
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Affiliation(s)
- Emily Petroni
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Caroline Esnault
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Daniel Tetreault
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Ryan K. Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Philip P. Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA.,Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892, USA.,Independent Research Scholar Program, Intramural Research Program, National Institutes of Health, Bethesda, MD 20892, USA.,correspondence:
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3
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Ito Y, Terai G, Ishigami M, Hashiba N, Nakamura Y, Bamba T, Kumokita R, Hasunuma T, Asai K, Ishii J, Kondo A. Exchange of endogenous and heterogeneous yeast terminators in Pichia pastoris to tune mRNA stability and gene expression. Nucleic Acids Res 2021; 48:13000-13012. [PMID: 33257988 PMCID: PMC7736810 DOI: 10.1093/nar/gkaa1066] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/15/2020] [Accepted: 10/22/2020] [Indexed: 12/16/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae, terminator sequences not only terminate transcription but also affect expression levels of the protein-encoded upstream of the terminator. The non-conventional yeast Pichia pastoris (syn. Komagataella phaffii) has frequently been used as a platform for metabolic engineering but knowledge regarding P. pastoris terminators is limited. To explore terminator sequences available to tune protein expression levels in P. pastoris, we created a 'terminator catalog' by testing 72 sequences, including terminators from S. cerevisiae or P. pastoris and synthetic terminators. Altogether, we found that the terminators have a tunable range of 17-fold. We also found that S. cerevisiae terminator sequences maintain function when transferred to P. pastoris. Successful tuning of protein expression levels was shown not only for the reporter gene used to define the catalog but also using betaxanthin production as an example application in pathway flux regulation. Moreover, we found experimental evidence that protein expression levels result from mRNA abundance and in silico evidence that levels reflect the stability of mRNA 3'-UTR secondary structure. In combination with promoter selection, the novel terminator catalog constitutes a basic toolbox for tuning protein expression levels in metabolic engineering and synthetic biology in P. pastoris.
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Affiliation(s)
- Yoichiro Ito
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan.,Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan
| | - Goro Terai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba 277-8561, Japan
| | - Misa Ishigami
- Technology Research Association of Highly Efficient Gene Design, Kobe 650-0047, Japan
| | - Noriko Hashiba
- Technology Research Association of Highly Efficient Gene Design, Kobe 650-0047, Japan
| | - Yasuyuki Nakamura
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan.,Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan
| | - Takahiro Bamba
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan
| | - Ryota Kumokita
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan.,Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan
| | - Kiyoshi Asai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba 277-8561, Japan
| | - Jun Ishii
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan.,Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan.,Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan.,Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Japan
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D'Agostino PM, Al-Sinawi B, Mazmouz R, Muenchhoff J, Neilan BA, Moffitt MC. Identification of promoter elements in the Dolichospermum circinale AWQC131C saxitoxin gene cluster and the experimental analysis of their use for heterologous expression. BMC Microbiol 2020; 20:35. [PMID: 32070286 PMCID: PMC7027233 DOI: 10.1186/s12866-020-1720-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 02/03/2020] [Indexed: 01/06/2023] Open
Abstract
Background Dolichospermum circinale is a filamentous bloom-forming cyanobacterium responsible for biosynthesis of the paralytic shellfish toxins (PST), including saxitoxin. PSTs are neurotoxins and in their purified form are important analytical standards for monitoring the quality of water and seafood and biomedical research tools for studying neuronal sodium channels. More recently, PSTs have been recognised for their utility as local anaesthetics. Characterisation of the transcriptional elements within the saxitoxin (sxt) biosynthetic gene cluster (BGC) is a first step towards accessing these molecules for biotechnology. Results In D. circinale AWQC131C the sxt BGC is transcribed from two bidirectional promoter regions encoding five individual promoters. These promoters were identified experimentally using 5′ RACE and their activity assessed via coupling to a lux reporter system in E. coli and Synechocystis sp. PCC 6803. Transcription of the predicted drug/metabolite transporter (DMT) encoded by sxtPER was found to initiate from two promoters, PsxtPER1 and PsxtPER2. In E. coli, strong expression of lux from PsxtP, PsxtD and PsxtPER1 was observed while expression from Porf24 and PsxtPER2 was remarkably weaker. In contrast, heterologous expression in Synechocystis sp. PCC 6803 showed that expression of lux from PsxtP, PsxtPER1, and Porf24 promoters was statistically higher compared to the non-promoter control, while PsxtD showed poor activity under the described conditions. Conclusions Both of the heterologous hosts investigated in this study exhibited high expression levels from three of the five sxt promoters. These results indicate that the majority of the native sxt promoters appear active in different heterologous hosts, simplifying initial cloning efforts. Therefore, heterologous expression of the sxt BGC in either E. coli or Synechocystis could be a viable first option for producing PSTs for industrial or biomedical purposes.
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Affiliation(s)
- Paul M D'Agostino
- School of Science, Western Sydney University, Sydney, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Biosystems Chemistry, Department of Chemistry, Technische Universität München, Garching, Germany.,Technical Biochemistry, Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, Germany
| | - Bakir Al-Sinawi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Rabia Mazmouz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Julia Muenchhoff
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, Australia
| | - Brett A Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia. .,School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia.
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'Stop' in protein synthesis is modulated with exquisite subtlety by an extended RNA translation signal. Biochem Soc Trans 2018; 46:1615-1625. [PMID: 30420414 DOI: 10.1042/bst20180190] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 09/30/2018] [Accepted: 10/04/2018] [Indexed: 02/08/2023]
Abstract
Translational stop codons, UAA, UAG, and UGA, form an integral part of the universal genetic code. They are of significant interest today for their underlying fundamental role in terminating protein synthesis, but also for their potential utilisation for programmed alternative translation events. In diverse organisms, UAA has wide usage, but it is puzzling that the high fidelity UAG is selected against and yet UGA, vulnerable to suppression, is widely used, particularly in those archaeal and bacterial genomes with a high GC content. In canonical protein synthesis, stop codons are interpreted by protein release factors that structurally and functionally mimic decoding tRNAs and occupy the decoding site on the ribosome. The release factors make close contact with the decoding complex through multiple interactions. Correct interactions cause conformational changes resulting in new and enhanced contacts with the ribosome, particularly between specific bases in the mRNA and rRNA. The base following the stop codon (fourth or +4 base) may strongly influence decoding efficiency, facilitating alternative non-canonical events like frameshifting or selenocysteine incorporation. The fourth base is drawn into the decoding site with a compacted stop codon in the eukaryotic termination complex. Surprisingly, mRNA sequences upstream and downstream of this core tetranucleotide signal have a significant influence on the strength of the signal. Since nine bases downstream of the stop codon are within the mRNA channel, their interactions with rRNA, and r-proteins may affect efficiency. With this understanding, it is now possible to design stop signals of desired strength for specific applied purposes.
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Cridge AG, Crowe-McAuliffe C, Mathew SF, Tate WP. Eukaryotic translational termination efficiency is influenced by the 3' nucleotides within the ribosomal mRNA channel. Nucleic Acids Res 2018; 46:1927-1944. [PMID: 29325104 PMCID: PMC5829715 DOI: 10.1093/nar/gkx1315] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 12/07/2017] [Accepted: 01/05/2018] [Indexed: 01/01/2023] Open
Abstract
When a stop codon is at the 80S ribosomal A site, there are six nucleotides (+4 to +9) downstream that are inferred to be occupying the mRNA channel. We examined the influence of these downstream nucleotides on translation termination success or failure in mammalian cells at the three stop codons. The expected hierarchy in the intrinsic fidelity of the stop codons (UAA>UAG>>UGA) was observed, with highly influential effects on termination readthrough mediated by nucleotides at position +4 and position +8. A more complex influence was observed from the nucleotides at positions +5 and +6. The weakest termination contexts were most affected by increases or decreases in the concentration of the decoding release factor (eRF1), indicating that eRF1 binding to these signals was rate-limiting. When termination efficiency was significantly reduced by cognate suppressor tRNAs, the observed influence of downstream nucleotides was maintained. There was a positive correlation between experimentally measured signal strength and frequency of the signal in eukaryotic genomes, particularly in Saccharomyces cerevisiae and Drosophila melanogaster. We propose that termination efficiency is not only influenced by interrogation of the stop signal directly by the release factor, but also by downstream ribosomal interactions with the mRNA nucleotides in the entry channel.
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Affiliation(s)
- Andrew G Cridge
- Department of Biochemistry, University of Otago, Dunedin, Otago 9054, New Zealand
| | | | - Suneeth F Mathew
- Department of Biochemistry, University of Otago, Dunedin, Otago 9054, New Zealand
| | - Warren P Tate
- Department of Biochemistry, University of Otago, Dunedin, Otago 9054, New Zealand
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7
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Loughran G, Firth AE, Atkins JF, Ivanov IP. Translational autoregulation of BZW1 and BZW2 expression by modulating the stringency of start codon selection. PLoS One 2018; 13:e0192648. [PMID: 29470543 PMCID: PMC5823381 DOI: 10.1371/journal.pone.0192648] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 01/26/2018] [Indexed: 01/20/2023] Open
Abstract
The efficiency of start codon selection during ribosomal scanning in eukaryotic translation initiation is influenced by the context or flanking nucleotides surrounding the AUG codon. The levels of eukaryotic translation initiation factors 1 (eIF1) and 5 (eIF5) play critical roles in controlling the stringency of translation start site selection. The basic leucine zipper and W2 domain-containing proteins 1 and 2 (BZW1 and BZW2), also known as eIF5-mimic proteins, are paralogous human proteins containing C-terminal HEAT domains that resemble the HEAT domain of eIF5. We show that translation of mRNAs encoding BZW1 and BZW2 homologs in fungi, plants and metazoans is initiated by AUG codons in conserved unfavorable initiation contexts. This conservation is reminiscent of the conserved unfavorable initiation context that enables autoregulation of EIF1. We show that overexpression of BZW1 and BZW2 proteins enhances the stringency of start site selection, and that their poor initiation codons confer autoregulation on BZW1 and BZW2 mRNA translation. We also show that overexpression of these two proteins significantly diminishes the effect of overexpressing eIF5 on stringency of start codon selection, suggesting they antagonize this function of eIF5. These results reveal a surprising role for BZW1 and BZW2 in maintaining homeostatic stringency of start codon selection, and taking into account recent biochemical, genetic and structural insights into eukaryotic initiation, suggest a model for BZW1 and BZW2 function.
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Affiliation(s)
- Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Andrew E. Firth
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - John F. Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Ivaylo P. Ivanov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Evfratov SA, Osterman IA, Komarova ES, Pogorelskaya AM, Rubtsova MP, Zatsepin TS, Semashko TA, Kostryukova ES, Mironov AA, Burnaev E, Krymova E, Gelfand MS, Govorun VM, Bogdanov AA, Sergiev PV, Dontsova OA. Application of sorting and next generation sequencing to study 5΄-UTR influence on translation efficiency in Escherichia coli. Nucleic Acids Res 2017; 45:3487-3502. [PMID: 27899632 PMCID: PMC5389652 DOI: 10.1093/nar/gkw1141] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 10/31/2016] [Indexed: 12/24/2022] Open
Abstract
Yield of protein per translated mRNA may vary by four orders of magnitude. Many studies analyzed the influence of mRNA features on the translation yield. However, a detailed understanding of how mRNA sequence determines its propensity to be translated is still missing. Here, we constructed a set of reporter plasmid libraries encoding CER fluorescent protein preceded by randomized 5΄ untranslated regions (5΄-UTR) and Red fluorescent protein (RFP) used as an internal control. Each library was transformed into Escherchia coli cells, separated by efficiency of CER mRNA translation by a cell sorter and subjected to next generation sequencing. We tested efficiency of translation of the CER gene preceded by each of 48 natural 5΄-UTR sequences and introduced random and designed mutations into natural and artificially selected 5΄-UTRs. Several distinct properties could be ascribed to a group of 5΄-UTRs most efficient in translation. In addition to known ones, several previously unrecognized features that contribute to the translation enhancement were found, such as low proportion of cytidine residues, multiple SD sequences and AG repeats. The latter could be identified as translation enhancer, albeit less efficient than SD sequence in several natural 5΄-UTRs.
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Affiliation(s)
- Sergey A Evfratov
- Department of Chemistry, Faculty of Bioinformatics and Bioengeneering, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Ilya A Osterman
- Department of Chemistry, Faculty of Bioinformatics and Bioengeneering, Lomonosov Moscow State University, Moscow, 119992, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143025, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Ekaterina S Komarova
- Department of Chemistry, Faculty of Bioinformatics and Bioengeneering, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Alexandra M Pogorelskaya
- Department of Chemistry, Faculty of Bioinformatics and Bioengeneering, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Maria P Rubtsova
- Department of Chemistry, Faculty of Bioinformatics and Bioengeneering, Lomonosov Moscow State University, Moscow, 119992, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143025, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Timofei S Zatsepin
- Department of Chemistry, Faculty of Bioinformatics and Bioengeneering, Lomonosov Moscow State University, Moscow, 119992, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143025, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Tatiana A Semashko
- Research Institute for Physical-Chemical Medicine, FMBA, Moscow, 119435, Russia
| | - Elena S Kostryukova
- Research Institute for Physical-Chemical Medicine, FMBA, Moscow, 119435, Russia.,Moscow Institute of Physics and Technology, Dolgoprpudny, Moscow, 141700, Russia
| | - Andrey A Mironov
- Department of Chemistry, Faculty of Bioinformatics and Bioengeneering, Lomonosov Moscow State University, Moscow, 119992, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Evgeny Burnaev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143025, Russia.,A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia
| | - Ekaterina Krymova
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia
| | - Mikhail S Gelfand
- Department of Chemistry, Faculty of Bioinformatics and Bioengeneering, Lomonosov Moscow State University, Moscow, 119992, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143025, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia.,National Research University Higher School of Economics, Moscow, 123458, Russia
| | - Vadim M Govorun
- Research Institute for Physical-Chemical Medicine, FMBA, Moscow, 119435, Russia
| | - Alexey A Bogdanov
- Department of Chemistry, Faculty of Bioinformatics and Bioengeneering, Lomonosov Moscow State University, Moscow, 119992, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Petr V Sergiev
- Department of Chemistry, Faculty of Bioinformatics and Bioengeneering, Lomonosov Moscow State University, Moscow, 119992, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143025, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Olga A Dontsova
- Department of Chemistry, Faculty of Bioinformatics and Bioengeneering, Lomonosov Moscow State University, Moscow, 119992, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 143025, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
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Zhang Z, Xu H, Si L, Chen Y, Zhang B, Wang Y, Wu Y, Zhou X, Zhang L, Zhou D. Construction of an inducible stable cell line for efficient incorporation of unnatural amino acids in mammalian cells. Biochem Biophys Res Commun 2017; 489:490-496. [DOI: 10.1016/j.bbrc.2017.05.178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 05/30/2017] [Indexed: 10/19/2022]
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10
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Translation Initiation from Conserved Non-AUG Codons Provides Additional Layers of Regulation and Coding Capacity. mBio 2017; 8:mBio.00844-17. [PMID: 28655822 PMCID: PMC5487733 DOI: 10.1128/mbio.00844-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Neurospora crassa cpc-1 and Saccharomyces cerevisiae GCN4 are homologs specifying transcription activators that drive the transcriptional response to amino acid limitation. The cpc-1 mRNA contains two upstream open reading frames (uORFs) in its >700-nucleotide (nt) 5′ leader, and its expression is controlled at the level of translation in response to amino acid starvation. We used N. crassa cell extracts and obtained data indicating that cpc-1 uORF1 and uORF2 are functionally analogous to GCN4 uORF1 and uORF4, respectively, in controlling translation. We also found that the 5′ region upstream of the main coding sequence of the cpc-1 mRNA extends for more than 700 nucleotides without any in-frame stop codon. For 100 cpc-1 homologs from Pezizomycotina and from selected Basidiomycota, 5′ conserved extensions of the CPC1 reading frame are also observed. Multiple non-AUG near-cognate codons (NCCs) in the CPC1 reading frame upstream of uORF2, some deeply conserved, could potentially initiate translation. At least four NCCs initiated translation in vitro. In vivo data were consistent with initiation at NCCs to produce N-terminally extended N. crassa CPC1 isoforms. The pivotal role played by CPC1, combined with its translational regulation by uORFs and NCC utilization, underscores the emerging significance of noncanonical initiation events in controlling gene expression. There is a deepening and widening appreciation of the diverse roles of translation in controlling gene expression. A central fungal transcription factor, the best-studied example of which is Saccharomyces cerevisiae GCN4, is crucial for the response to amino acid limitation. Two upstream open reading frames (uORFs) in the GCN4 mRNA are critical for controlling GCN4 synthesis. We observed that two uORFs in the corresponding Neurospora crassa cpc-1 mRNA appear functionally analogous to the GCN4 uORFs. We also discovered that, surprisingly, unlike GCN4, the CPC1 coding sequence extends far upstream from the presumed AUG start codon with no other in-frame AUG codons. Similar extensions were seen in homologs from many filamentous fungi. We observed that multiple non-AUG near-cognate codons (NCCs) in this extended reading frame, some conserved, initiated translation to produce longer forms of CPC1, underscoring the significance of noncanonical initiation in controlling gene expression.
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11
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Arnold WK, Savage CR, Brissette CA, Seshu J, Livny J, Stevenson B. RNA-Seq of Borrelia burgdorferi in Multiple Phases of Growth Reveals Insights into the Dynamics of Gene Expression, Transcriptome Architecture, and Noncoding RNAs. PLoS One 2016; 11:e0164165. [PMID: 27706236 PMCID: PMC5051733 DOI: 10.1371/journal.pone.0164165] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/20/2016] [Indexed: 12/25/2022] Open
Abstract
Borrelia burgdorferi, the agent of Lyme disease, differentially expresses numerous genes and proteins as it cycles between mammalian hosts and tick vectors. Insights on regulatory mechanisms have been provided by earlier studies that examined B. burgdorferi gene expression patterns during cultivation. However, prior studies examined bacteria at only a single time point of cultivation, providing only a snapshot of what is likely a dynamic transcriptional program driving B. burgdorferi adaptations to changes during culture growth phases. To address that concern, we performed RNA sequencing (RNA-Seq) analysis of B. burgdorferi cultures at early-exponential, mid-exponential, and early-stationary phases of growth. We found that expression of nearly 18% of annotated B. burgdorferi genes changed significantly during culture maturation. Moreover, genome-wide mapping of the B. burgdorferi transcriptome in different growth phases enabled insight on transcript boundaries, operon structures, and identified numerous putative non-coding RNAs. These RNA-Seq data are discussed and presented as a resource for the community of researchers seeking to better understand B. burgdorferi biology and pathogenesis.
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Affiliation(s)
- William K Arnold
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY, United States of America
| | - Christina R Savage
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY, United States of America
| | - Catherine A Brissette
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, United States of America
| | - Janakiram Seshu
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States of America
| | - Jonathan Livny
- Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Brian Stevenson
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY, United States of America
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12
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Lee BP, Lloyd-Laney HO, Locke JM, McCulloch LJ, Knight B, Yaghootkar H, Cory G, Kos K, Frayling TM, Harries LW. Functional characterisation of ADIPOQ variants using individuals recruited by genotype. Mol Cell Endocrinol 2016; 428:49-57. [PMID: 26996131 DOI: 10.1016/j.mce.2016.03.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 02/18/2016] [Accepted: 03/15/2016] [Indexed: 12/30/2022]
Abstract
Four non-coding GWAS variants in or near the ADIPOQ gene (rs17300539, rs17366653, rs3821799 and rs56354395) together explain 4% of the variation in circulating adiponectin. The functional basis for this is unknown. We tested the effect of these variants on ADIPOQ transcription, splicing and stability respectively in adipose tissue samples from participants recruited by rs17366653 genotype. Transcripts carrying rs17300539 demonstrated a 17% increase in expression (p = 0.001). Variant rs17366653 was associated with disruption of ADIPOQ splicing leading to a 7 fold increase in levels of a non-functional transcript (p = 0.002). Transcripts carrying rs56354395 demonstrated a 59% decrease in expression (p = <0.0001). No effects of rs3821799 genotype on expression was observed. Association between variation in the ADIPOQ gene and serum adiponectin may arise from effects on mRNA transcription, splicing or stability. These studies illustrate the utility of recruit-by-genotype studies in relevant human tissues in functional interpretation of GWAS signals.
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Affiliation(s)
- Benjamin P Lee
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Henry O Lloyd-Laney
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Jonathan M Locke
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Laura J McCulloch
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Bridget Knight
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Hanieh Yaghootkar
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Giles Cory
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Katarina Kos
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Timothy M Frayling
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Lorna W Harries
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK.
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13
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Ryan BC, Werner TS, Howard PL, Chow RL. ImiRP: a computational approach to microRNA target site mutation. BMC Bioinformatics 2016; 17:190. [PMID: 27122020 PMCID: PMC4848830 DOI: 10.1186/s12859-016-1057-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/05/2016] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs that function as post-transcriptional regulators of messenger RNA (mRNA) through base-pairing to 6-8 nucleotide long target sites, usually located within the mRNA 3' untranslated region. A common approach to validate and probe microRNA-mRNA interactions is to mutate predicted target sites within the mRNA and determine whether it affects miRNA-mediated activity. The introduction of miRNA target site mutations, however, is potentially problematic as it may generate new, "illegitimate sites" target sites for other miRNAs, which may affect the experimental outcome. While it is possible to manually generate and check single miRNA target site mutations, this process can be time consuming, and becomes particularly onerous and error prone when multiple sites are to be mutated simultaneously. We have developed a modular Java-based system called ImiRP (Illegitimate miRNA Predictor) to solve this problem and to facilitate miRNA target site mutagenesis. RESULTS The ImiRP interface allows users to input a sequence of interest, specify the locations of multiple predicted target sites to mutate, and set parameters such as species, mutation strategy, and disallowed illegitimate target site types. As mutant sequences are generated, ImiRP utilizes the miRBase high confidence miRNA dataset to identify illegitimate target sites in each mutant sequence by comparing target site predictions between input and mutant sequences. ImiRP then assembles a final mutant sequence in which all specified target sites have been mutated. CONCLUSIONS ImiRP is a mutation generator program that enables selective disruption of specified miRNA target sites while ensuring predicted target sites for other miRNAs are not inadvertently created. ImiRP supports mutagenesis of single and multiple miRNA target sites within a given sequence, including sites that overlap. This software will be particularly useful for studies looking at microRNA cooperativity, where mutagenesis of multiple microRNA target sites may be desired. The software is available at imirp.org and is available open source for download through GitHub ( https://github.com/imirp ).
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Affiliation(s)
- Bridget C Ryan
- Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Torben S Werner
- Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Perry L Howard
- Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3N5, Canada
| | - Robert L Chow
- Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada.
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14
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Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression. Methods Mol Biol 2016; 1358:3-28. [PMID: 26463374 DOI: 10.1007/978-1-4939-3067-8_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Untranslated regions (UTRs) and, to a lesser extent, coding sequences of mRNAs are involved in defining the fate of the mature transcripts through the modulation of three primary control processes, mRNA localization, degradation and translation; the action of trans-factors such as RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) combined with the presence of defined sequence and structural cis-elements ultimately determines translation levels. Identifying functional regions in UTRs and uncovering post-transcriptional regulators acting upon these regions is thus of paramount importance to understand the spectrum of regulatory possibilities for any given mRNA. This tasks can now be approached computationally, to reduce the space of testable hypotheses and to drive experimental validation.This chapter focuses on presenting databases and tools allowing to study the various aspects of post-transcriptional regulation, including motif search (sequence and secondary structure), prediction of regulatory networks (e.g., RBP and ncRNA binding sites), profiling of the mRNAs translational state, and other aspects of this level of gene expression regulation. Two analysis pipelines are also presented as practical examples of how the described tools could be integrated and effectively employed.
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15
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Miyazaki S, Sato Y, Asano T, Nagamura Y, Nonomura KI. Rice MEL2, the RNA recognition motif (RRM) protein, binds in vitro to meiosis-expressed genes containing U-rich RNA consensus sequences in the 3'-UTR. PLANT MOLECULAR BIOLOGY 2015; 89:293-307. [PMID: 26319516 DOI: 10.1007/s11103-015-0369-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 08/22/2015] [Indexed: 06/04/2023]
Abstract
Post-transcriptional gene regulation by RNA recognition motif (RRM) proteins through binding to cis-elements in the 3'-untranslated region (3'-UTR) is widely used in eukaryotes to complete various biological processes. Rice MEIOSIS ARRESTED AT LEPTOTENE2 (MEL2) is the RRM protein that functions in the transition to meiosis in proper timing. The MEL2 RRM preferentially associated with the U-rich RNA consensus, UUAGUU[U/A][U/G][A/U/G]U, dependently on sequences and proportionally to MEL2 protein amounts in vitro. The consensus sequences were located in the putative looped structures of the RNA ligand. A genome-wide survey revealed a tendency of MEL2-binding consensus appearing in 3'-UTR of rice genes. Of 249 genes that conserved the consensus in their 3'-UTR, 13 genes spatiotemporally co-expressed with MEL2 in meiotic flowers, and included several genes whose function was supposed in meiosis; such as Replication protein A and OsMADS3. The proteome analysis revealed that the amounts of small ubiquitin-related modifier-like protein and eukaryotic translation initiation factor3-like protein were dramatically altered in mel2 mutant anthers. Taken together with transcriptome and gene ontology results, we propose that the rice MEL2 is involved in the translational regulation of key meiotic genes on 3'-UTRs to achieve the faithful transition of germ cells to meiosis.
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Affiliation(s)
- Saori Miyazaki
- Experimental Farm, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, 411-8540, Japan.
- Office for the Promotion of Global Education Programs, Shizuoka University, Jyouhoku, Nakaku, Hamamatsu, Shizuoka, 432-8561, Japan.
| | - Yutaka Sato
- Genome Resource Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan.
| | - Tomoya Asano
- Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Takaramachi, Kanazawa, 920-0934, Japan.
- Wakasa Seikatsu Co. Ltd, 22 Naginataboko-cho, Shijo-Karasuma, Shimogyo-ku, Kyoto, 600-8008, Japan.
| | - Yoshiaki Nagamura
- Genome Resource Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan.
| | - Ken-Ichi Nonomura
- Experimental Farm, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, 411-8540, Japan.
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16
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Protacio RU, Storey AJ, Davidson MK, Wahls WP. Nonsense codon suppression in fission yeast due to mutations of tRNA(Ser.11) and translation release factor Sup35 (eRF3). Curr Genet 2015; 61:165-73. [PMID: 25519804 PMCID: PMC4393767 DOI: 10.1007/s00294-014-0465-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/01/2014] [Accepted: 12/03/2014] [Indexed: 02/07/2023]
Abstract
In the fission yeast Schizosaccharomyces pombe, sup9 mutations can suppress the termination of translation at nonsense (stop) codons. We localized sup9 physically to the spctrnaser.11 locus and confirmed that one allele (sup9-UGA) alters the anticodon of a serine tRNA. We also found that another purported allele is not allelic. Instead, strains with that suppressor (renamed sup35-F592S) have a single base pair substitution (T1775C) that introduces an amino acid substitution in the Sup35 protein (Sup35-F592S). Reduced functionality of Sup35 (eRF3), the ubiquitous guanine nucleotide-responsive translation release factor of eukaryotes, increases read-through of stop codons. Tetrad dissection revealed that suppression is tightly linked to (inseparable from) the sup35-F592S mutation and that there are no additional extragenic modifiers. The Mendelian inheritance indicates that the Sup35-F592S protein does not adopt an infectious amyloid state ([PSI (+)] prion) to affect suppression, consistent with recent evidence that fission yeast Sup35 does not form prions. We also report that sup9-UGA and sup35-F592S exhibit different strengths of suppression for opal stop codons of ade6-M26 and ade6-M375. We discuss possible mechanisms for the variation in suppressibility exhibited by the two alleles.
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Affiliation(s)
- Reine U. Protacio
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA
| | - Aaron J. Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA
| | - Mari K. Davidson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA
| | - Wayne P. Wahls
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA
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17
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Murai S, Katagiri Y, Yamashita S. Maturation-associatedDbf4expression is essential for mouse zygotic DNA replication. Dev Growth Differ 2014; 56:625-39. [DOI: 10.1111/dgd.12180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/24/2014] [Accepted: 08/27/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Shin Murai
- Department of Biochemistry; Toho University School of Medicine; 5-21-16 Omorinishi Otaku 143-8540 Tokyo Japan
| | - Yukiko Katagiri
- Department of Obstetrics and Gynecology Reproduction Center; Omori Medical Center; Toho University; 6-11-1, Omori-Nishi Ota-ku 143-8541 Tokyo Japan
| | - Shigeru Yamashita
- Department of Biochemistry; Toho University School of Medicine; 5-21-16 Omorinishi Otaku 143-8540 Tokyo Japan
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18
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Stiebler AC, Freitag J, Schink KO, Stehlik T, Tillmann BAM, Ast J, Bölker M. Ribosomal readthrough at a short UGA stop codon context triggers dual localization of metabolic enzymes in Fungi and animals. PLoS Genet 2014; 10:e1004685. [PMID: 25340584 PMCID: PMC4207609 DOI: 10.1371/journal.pgen.1004685] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 08/18/2014] [Indexed: 11/21/2022] Open
Abstract
Translation of mRNA into a polypeptide chain is a highly accurate process. Many prokaryotic and eukaryotic viruses, however, use leaky termination of translation to optimize their coding capacity. Although growing evidence indicates the occurrence of ribosomal readthrough also in higher organisms, a biological function for the resulting extended proteins has been elucidated only in very few cases. Here, we report that in human cells programmed stop codon readthrough is used to generate peroxisomal isoforms of cytosolic enzymes. We could show for NAD-dependent lactate dehydrogenase B (LDHB) and NAD-dependent malate dehydrogenase 1 (MDH1) that translational readthrough results in C-terminally extended protein variants containing a peroxisomal targeting signal 1 (PTS1). Efficient readthrough occurs at a short sequence motif consisting of a UGA termination codon followed by the dinucleotide CU. Leaky termination at this stop codon context was observed in fungi and mammals. Comparative genome analysis allowed us to identify further readthrough-derived peroxisomal isoforms of metabolic enzymes in diverse model organisms. Overall, our study highlights that a defined stop codon context can trigger efficient ribosomal readthrough to generate dually targeted protein isoforms. We speculate that beyond peroxisomal targeting stop codon readthrough may have also other important biological functions, which remain to be elucidated.
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Affiliation(s)
- Alina C. Stiebler
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Johannes Freitag
- Department of Biology, Philipps-University Marburg, Marburg, Germany
- LOEWE Excellence Cluster for Integrative Fungal Research (IPF), Senckenberg Society, Frankfurt am Main, Germany
| | - Kay O. Schink
- Faculty of Medicine, Centre for Cancer Biomedicine, University of Oslo, Montebello, Oslo, Norway
- Department of Biochemistry, Institute for Cancer Research, Oslo University Hospital, Montebello, Oslo, Norway
| | - Thorsten Stehlik
- Department of Biology, Philipps-University Marburg, Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | | | - Julia Ast
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Michael Bölker
- Department of Biology, Philipps-University Marburg, Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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19
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Jodoin R, Bauer L, Garant JM, Mahdi Laaref A, Phaneuf F, Perreault JP. The folding of 5'-UTR human G-quadruplexes possessing a long central loop. RNA (NEW YORK, N.Y.) 2014; 20:1129-1141. [PMID: 24865610 PMCID: PMC4114690 DOI: 10.1261/rna.044578.114] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/21/2014] [Indexed: 05/31/2023]
Abstract
G-quadruplexes are widespread four-stranded structures that are adopted by G-rich regions of both DNA and RNA and are involved in essential biological processes such as mRNA translation. They are formed by the stacking of two or more G-quartets that are linked together by three loops. Although the maximal loop length is usually fixed to 7 nt in most G-quadruplex-predicting software, it has already been demonstrated that artificial DNA G-quadruplexes containing two distal loops that are limited to 1 nt each and a central loop up to 30 nt long are likely to form in vitro. This report demonstrates that such structures possessing a long central loop are actually found in the 5'-UTRs of human mRNAs. Firstly, 1453 potential G-quadruplex-forming sequences (PG4s) were identified through a bioinformatic survey that searched for sequences respecting the requirement for two 1-nt long distal loops and a long central loop of 2-90 nt in length. Secondly, in vitro in-line probing experiments confirmed and characterized the folding of eight candidates possessing central loops of 10-70 nt long. Finally, the biological effect of several G-quadruplexes with a long central loop on mRNA expression was studied in cellulo using a luciferase gene reporter assay. Clearly, the actual definition of G-quadruplex-forming sequences is too conservative and must be expanded to include the long central loop. This greatly expands the number of expected PG4s in the transcriptome. Consideration of these new candidates might aid in elucidating the potentially important biological implications of the G-quadruplex structure.
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Affiliation(s)
- Rachel Jodoin
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Québec, Canada J1E 4K8
| | - Lubos Bauer
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Québec, Canada J1E 4K8
| | - Jean-Michel Garant
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Québec, Canada J1E 4K8
| | - Abdelhamid Mahdi Laaref
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Québec, Canada J1E 4K8
| | - Francis Phaneuf
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Québec, Canada J1E 4K8
| | - Jean-Pierre Perreault
- Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Québec, Canada J1E 4K8
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20
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Biswas A, Brown CM. Scan for Motifs: a webserver for the analysis of post-transcriptional regulatory elements in the 3' untranslated regions (3' UTRs) of mRNAs. BMC Bioinformatics 2014; 15:174. [PMID: 24909639 PMCID: PMC4067372 DOI: 10.1186/1471-2105-15-174] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/16/2014] [Indexed: 11/21/2022] Open
Abstract
Background Gene expression in vertebrate cells may be controlled post-transcriptionally through regulatory elements in mRNAs. These are usually located in the untranslated regions (UTRs) of mRNA sequences, particularly the 3′UTRs. Results Scan for Motifs (SFM) simplifies the process of identifying a wide range of regulatory elements on alignments of vertebrate 3′UTRs. SFM includes identification of both RNA Binding Protein (RBP) sites and targets of miRNAs. In addition to searching pre-computed alignments, the tool provides users the flexibility to search their own sequences or alignments. The regulatory elements may be filtered by expected value cutoffs and are cross-referenced back to their respective sources and literature. The output is an interactive graphical representation, highlighting potential regulatory elements and overlaps between them. The output also provides simple statistics and links to related resources for complementary analyses. The overall process is intuitive and fast. As SFM is a free web-application, the user does not need to install any software or databases. Conclusions Visualisation of the binding sites of different classes of effectors that bind to 3′UTRs will facilitate the study of regulatory elements in 3′ UTRs.
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Affiliation(s)
| | - Chris M Brown
- Department of Biochemistry, Genetics Otago, University of Otago, Dunedin, New Zealand.
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21
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Stockwell PA, Chatterjee A, Rodger EJ, Morison IM. DMAP: differential methylation analysis package for RRBS and WGBS data. ACTA ACUST UNITED AC 2014; 30:1814-22. [PMID: 24608764 DOI: 10.1093/bioinformatics/btu126] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
MOTIVATION The rapid development of high-throughput sequencing technologies has enabled epigeneticists to quantify DNA methylation on a massive scale. Progressive increase in sequencing capacity present challenges in terms of processing analysis and the interpretation of the large amount of data; investigating differential methylation between genome-scale data from multiple samples highlights this challenge. RESULTS We have developed a differential methylation analysis package (DMAP) to generate coverage-filtered reference methylomes and to identify differentially methylated regions across multiple samples from reduced representation bisulphite sequencing and whole genome bisulphite sequencing experiments. We introduce a novel fragment-based approach for investigating DNA methylation patterns for reduced representation bisulphite sequencing data. Further, DMAP provides the identity of gene and CpG features and distances to the differentially methylated regions in a format that is easily analyzed with limited bioinformatics knowledge. AVAILABILITY AND IMPLEMENTATION The software has been implemented in C and has been written to ensure portability between different platforms. The source code and documentation is freely available (DMAP: as compressed TAR archive folder) from http://biochem.otago.ac.nz/research/databases-software/. Two test datasets are also available for download from the Web site. Test dataset 1 contains reads from chromosome 1 of a patient and a control, which is used for comparative analysis in the current article. Test dataset 2 contains reads from a part of chromosome 21 of three disease and three control samples for testing the operation of DMAP, especially for the analysis of variance. Example commands for the analyses are included.
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Affiliation(s)
- Peter A Stockwell
- Department of Biochemistry, University of Otago, 710 Cumberland Street, Dunedin 9054, New Zealand, Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand and Gravida: National Centre for Growth and Development, 2-6 Park Ave, Grafton, Auckland 1142, New Zealand
| | - Aniruddha Chatterjee
- Department of Biochemistry, University of Otago, 710 Cumberland Street, Dunedin 9054, New Zealand, Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand and Gravida: National Centre for Growth and Development, 2-6 Park Ave, Grafton, Auckland 1142, New ZealandDepartment of Biochemistry, University of Otago, 710 Cumberland Street, Dunedin 9054, New Zealand, Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand and Gravida: National Centre for Growth and Development, 2-6 Park Ave, Grafton, Auckland 1142, New Zealand
| | - Euan J Rodger
- Department of Biochemistry, University of Otago, 710 Cumberland Street, Dunedin 9054, New Zealand, Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand and Gravida: National Centre for Growth and Development, 2-6 Park Ave, Grafton, Auckland 1142, New Zealand
| | - Ian M Morison
- Department of Biochemistry, University of Otago, 710 Cumberland Street, Dunedin 9054, New Zealand, Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand and Gravida: National Centre for Growth and Development, 2-6 Park Ave, Grafton, Auckland 1142, New Zealand
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Törner K, Nakanishi T, Matsuura T, Kato Y, Watanabe H. Optimization of mRNA design for protein expression in the crustacean Daphnia magna. Mol Genet Genomics 2014; 289:707-15. [PMID: 24585253 DOI: 10.1007/s00438-014-0830-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 02/13/2014] [Indexed: 12/01/2022]
Abstract
The water flea Daphnia is a new model organism for ecological, evolutionary, and toxicological genomics. Detailed functional analysis of genes newly discovered through genomic approaches often requires overexpression of the identified protein. In the present study, we report the microinjection of in vitro-synthesized RNAs into the eggs as a method for overexpressing ubiquitous proteins in Daphnia magna. We injected a 1.3-kb mRNA that coded for the red fluorescent protein (DsRed2) flanked by UTRs from the ubiquitously expressed elongation factor 1α-1 (EF1α-1) into D. magna embryos. DsRed2 fluorescence in the embryos was measured 24 h after microinjection. Unexpectedly, the reporter RNA containing the 522-bp full-length EF1α-1 3' UTR failed to induce fluorescence. To assess reporter expression, the length of the 3' UTR that potentially contained negative regulatory elements of protein expression, including AU-rich regions and Musashi binding elements, was serially reduced from the 3' end. Assessing all injected RNA alternatives, mRNA containing the first 60 bp of the 3' UTR gave rise to the highest fluorescence, 14 times the Daphnia auto-fluorescence. In contrast, mRNA lacking the entire 3' UTR hardly induced any change in fluorescence intensity. This is the first evaluation of UTRs of mRNAs delivered into Daphnia embryos by microinjection for overexpressing proteins. The mRNA with truncated 3' UTRs of Daphnia EF1α-1 will be useful not only for gain-of-function analyses but also for labeling proteins and organelles with fluorescent proteins in Daphnia.
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Affiliation(s)
- Kerstin Törner
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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Kaushik M, Kukreti S. Differential structural status of the RNA counterpart of an undecamer quasi-palindromic DNA sequence present in LCR of human β-globin gene cluster. J Biomol Struct Dyn 2014; 33:244-52. [DOI: 10.1080/07391102.2013.877402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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24
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Arrigo P. MicroRNA and noncoding RNA-related data sources. Methods Mol Biol 2014; 1107:73-89. [PMID: 24272432 DOI: 10.1007/978-1-62703-748-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Noncoding RNAs (ncRNAs) are ribonucleic acids capable of controlling different genetic and metabolic functions. These molecules have been recently organized into different classes, and among them microRNAs (miRNAs) are extensively studied. MicroRNAs are short oligomers mainly involved in posttranscriptional gene silencing. The specific research field, focused on structural and functional characterization of microRNAs, is commonly called mirnomics. The exploitation of the interest in microRNAs has stimulated the organization of several databases that are often integrated with analytical tools in order to predict microRNA targets, or to find those miRNAs capable to inhibit the expression of a specific protein. This work attempts to provide an overview of accessible information about microRNAs and other noncoding RNAs that has been gathered in curated databases.
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25
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Ulrich LE, Zhulin IB. SeqDepot: streamlined database of biological sequences and precomputed features. Bioinformatics 2013; 30:295-7. [PMID: 24234005 DOI: 10.1093/bioinformatics/btt658] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED Assembling and/or producing integrated knowledge of sequence features continues to be an onerous and redundant task despite a large number of existing resources. We have developed SeqDepot-a novel database that focuses solely on two primary goals: (i) assimilating known primary sequences with predicted feature data and (ii) providing the most simple and straightforward means to procure and readily use this information. Access to >28.5 million sequences and 300 million features is provided through a well-documented and flexible RESTful interface that supports fetching specific data subsets, bulk queries, visualization and searching by MD5 digests or external database identifiers. We have also developed an HTML5/JavaScript web application exemplifying how to interact with SeqDepot and Perl/Python scripts for use with local processing pipelines. AVAILABILITY Freely available on the web at http://seqdepot.net/. RESTaccess via http://seqdepot.net/api/v1. Database files and scripts maybe downloaded from http://seqdepot.net/download.
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Affiliation(s)
- Luke E Ulrich
- Agile Genomics, LLC, Mount Pleasant, SC 29466, USA, Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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26
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Kramps T, Probst J. Messenger RNA-based vaccines: progress, challenges, applications. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:737-49. [PMID: 23893949 DOI: 10.1002/wrna.1189] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 06/27/2013] [Accepted: 06/27/2013] [Indexed: 12/21/2022]
Abstract
Twenty years after the demonstration that messenger RNA (mRNA) was expressed and immunogenic upon direct injection in mice, the first successful proof-of-concept of specific protection against viral infection in small and large animals was reported. These data indicate wider applicability to infectious disease and should encourage continued translation of mRNA-based prophylactic vaccines into human clinical trials. At the conceptual level, mRNA-based vaccines-more than other genetic vectors-combine the simplicity, safety, and focused immunogenicity of subunit vaccines with favorable immunological properties of live viral vaccines: (1) mRNA vaccines are molecularly defined and carry no excess information. In the environment and upon physical contact, RNA is rapidly degraded by ubiquitous RNases and cannot persist. These characteristics also guarantee tight control over their immunogenic profile (including avoidance of vector-specific immune responses that could interfere with repeated administration), pharmacokinetics, and dosing. (2) mRNA vaccines are synthetically produced by an enzymatic process, just requiring information about the nucleic acid sequence of the desired antigen. This greatly reduces general complications associated with biological vaccine production, such as handling of infectious agents, genetic variability, environmental risks, or restrictions to vaccine distribution. (3) RNA can be tailored to provide potent adjuvant stimuli to the innate immune system by direct activation of RNA-specific receptors; this may reduce the need for additional adjuvants. The formation of native antigen in situ affords great versatility, including intracellular localization, membrane association, posttranslational modification, supra-molecular assembly, or targeted structural optimization of delivered antigen. Messenger RNA vaccines induce balanced immune responses including B cells, helper T cells, and cytotoxic T lymphocytes, rendering them an extremely adaptable platform. This article surveys the design, mode of action, and capabilities of state-of-the-art mRNA vaccines, focusing on the paradigm of influenza prophylaxis.
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27
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Lytic infection of Lactococcus lactis by bacteriophages Tuc2009 and c2 triggers alternative transcriptional host responses. Appl Environ Microbiol 2013; 79:4786-98. [PMID: 23728817 DOI: 10.1128/aem.01197-13] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Here we present an entire temporal transcriptional profile of Lactococcus lactis subsp. cremoris UC509.9 undergoing lytic infection with two distinct bacteriophages, Tuc2009 and c2. Furthermore, corresponding high-resolution whole-phage genome tiling arrays of both bacteriophages were performed throughout lytic infection. Whole-genome microarrays performed at various time points postinfection demonstrated a rather modest impact on host transcription. The majority of changes in the host transcriptome occur during late infection stages; few changes in host gene transcription occur during the immediate and early infection stages. Alterations in the L. lactis UC509.9 transcriptome during lytic infection appear to be phage specific, with relatively few differentially transcribed genes shared between cells infected with Tuc2009 and those infected with c2. Despite the apparent lack of a coordinated general phage response, three themes common to both infections were noted: alternative transcription of genes involved in catabolic flux and energy production, differential transcription of genes involved in cell wall modification, and differential transcription of genes involved in the conversion of ribonucleotides to deoxyribonucleotides. The transcriptional profiles of both bacteriophages during lytic infection generally correlated with the findings of previous studies and allowed the confirmation of previously predicted promoter sequences. In addition, the host transcriptional response to lysogenization with Tuc2009 was monitored along with tiling array analysis of Tuc2009 in the lysogenic state. Analysis identified 44 host genes with altered transcription during lysogeny, 36 of which displayed levels of transcription significantly reduced from those for uninfected cells.
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28
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Barendt PA, Shah NA, Barendt GA, Kothari PA, Sarkar CA. Evidence for context-dependent complementarity of non-Shine-Dalgarno ribosome binding sites to Escherichia coli rRNA. ACS Chem Biol 2013; 8:958-66. [PMID: 23427812 DOI: 10.1021/cb3005726] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
While the ribosome has evolved to function in complex intracellular environments, these contexts do not easily allow for the study of its inherent capabilities. We have used a synthetic, well-defined Escherichia coli (E. coli)-based translation system in conjunction with ribosome display, a powerful in vitro selection method, to identify ribosome binding sites (RBSs) that can promote the efficient translation of messenger RNAs (mRNAs) with a leader length representative of natural E. coli mRNAs. In previous work, we used a longer leader sequence and unexpectedly recovered highly efficient cytosine-rich sequences with complementarity to the 16S ribosomal RNA (rRNA) and similarity to eukaryotic RBSs. In the current study, Shine-Dalgarno (SD) sequences were prevalent, but non-SD sequences were also heavily enriched and were dominated by novel guanine- and uracil-rich motifs that showed statistically significant complementarity to the 16S rRNA. Additionally, only SD motifs exhibited position-dependent decreases in sequence entropy, indicating that non-SD motifs likely operate by increasing the local concentration of ribosomes in the vicinity of the start codon, rather than by a position-dependent mechanism. These results further support the putative generality of mRNA-rRNA complementarity in facilitating mRNA translation but also suggest that context (e.g., leader length and composition) dictates the specific subset of possible RBSs that are used for efficient translation of a given transcript.
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Affiliation(s)
- Pamela A. Barendt
- Department of Bioengineering, ‡Genomics and Computational Biology Graduate Group, §Penn Medicine Academic Computing Services, and ∥Department of Chemical & Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Najaf A. Shah
- Department of Bioengineering, ‡Genomics and Computational Biology Graduate Group, §Penn Medicine Academic Computing Services, and ∥Department of Chemical & Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Gregory A. Barendt
- Department of Bioengineering, ‡Genomics and Computational Biology Graduate Group, §Penn Medicine Academic Computing Services, and ∥Department of Chemical & Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Parth A. Kothari
- Department of Bioengineering, ‡Genomics and Computational Biology Graduate Group, §Penn Medicine Academic Computing Services, and ∥Department of Chemical & Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Casim A. Sarkar
- Department of Bioengineering, ‡Genomics and Computational Biology Graduate Group, §Penn Medicine Academic Computing Services, and ∥Department of Chemical & Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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29
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Dassi E, Zuccotti P, Leo S, Provenzani A, Assfalg M, D’Onofrio M, Riva P, Quattrone A. Hyper conserved elements in vertebrate mRNA 3'-UTRs reveal a translational network of RNA-binding proteins controlled by HuR. Nucleic Acids Res 2013; 41:3201-16. [PMID: 23376935 PMCID: PMC3597683 DOI: 10.1093/nar/gkt017] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 12/20/2012] [Accepted: 12/26/2012] [Indexed: 02/06/2023] Open
Abstract
Little is known regarding the post-transcriptional networks that control gene expression in eukaryotes. Additionally, we still need to understand how these networks evolve, and the relative role played in them by their sequence-dependent regulatory factors, non-coding RNAs (ncRNAs) and RNA-binding proteins (RBPs). Here, we used an approach that relied on both phylogenetic sequence sharing and conservation in the whole mapped 3'-untranslated regions (3'-UTRs) of vertebrate species to gain knowledge on core post-transcriptional networks. The identified human hyper conserved elements (HCEs) were predicted to be preferred binding sites for RBPs and not for ncRNAs, namely microRNAs and long ncRNAs. We found that the HCE map identified a well-known network that post-transcriptionally regulates histone mRNAs. We were then able to discover and experimentally confirm a translational network composed of RNA Recognition Motif (RRM)-type RBP mRNAs that are positively controlled by HuR, another RRM-type RBP. HuR shows a preference for these RBP mRNAs bound in stem-loop motifs, confirming its role as a 'regulator of regulators'. Analysis of the transcriptome-wide HCE distribution revealed a profile of prevalently small clusters separated by unconserved intercluster RNA stretches, which predicts the formation of discrete small ribonucleoprotein complexes in the 3'-UTRs.
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Affiliation(s)
- Erik Dassi
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, via delle Regole, 101 38123 Mattarello (TN) Italy, Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, via Viotti, 3/5 20133 Milano, Italy, Laboratory of Genomic Screening, Centre for Integrative Biology, University of Trento, Trento, via delle Regole, 101 38123 Mattarello (TN) Italy and Department of Biotechnology, University of Verona, Province of Verona, Ca' Vignal 1, Strada Le Grazie 15 37134 Verona, Italy
| | - Paola Zuccotti
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, via delle Regole, 101 38123 Mattarello (TN) Italy, Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, via Viotti, 3/5 20133 Milano, Italy, Laboratory of Genomic Screening, Centre for Integrative Biology, University of Trento, Trento, via delle Regole, 101 38123 Mattarello (TN) Italy and Department of Biotechnology, University of Verona, Province of Verona, Ca' Vignal 1, Strada Le Grazie 15 37134 Verona, Italy
| | - Sara Leo
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, via delle Regole, 101 38123 Mattarello (TN) Italy, Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, via Viotti, 3/5 20133 Milano, Italy, Laboratory of Genomic Screening, Centre for Integrative Biology, University of Trento, Trento, via delle Regole, 101 38123 Mattarello (TN) Italy and Department of Biotechnology, University of Verona, Province of Verona, Ca' Vignal 1, Strada Le Grazie 15 37134 Verona, Italy
| | - Alessandro Provenzani
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, via delle Regole, 101 38123 Mattarello (TN) Italy, Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, via Viotti, 3/5 20133 Milano, Italy, Laboratory of Genomic Screening, Centre for Integrative Biology, University of Trento, Trento, via delle Regole, 101 38123 Mattarello (TN) Italy and Department of Biotechnology, University of Verona, Province of Verona, Ca' Vignal 1, Strada Le Grazie 15 37134 Verona, Italy
| | - Michael Assfalg
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, via delle Regole, 101 38123 Mattarello (TN) Italy, Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, via Viotti, 3/5 20133 Milano, Italy, Laboratory of Genomic Screening, Centre for Integrative Biology, University of Trento, Trento, via delle Regole, 101 38123 Mattarello (TN) Italy and Department of Biotechnology, University of Verona, Province of Verona, Ca' Vignal 1, Strada Le Grazie 15 37134 Verona, Italy
| | - Mariapina D’Onofrio
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, via delle Regole, 101 38123 Mattarello (TN) Italy, Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, via Viotti, 3/5 20133 Milano, Italy, Laboratory of Genomic Screening, Centre for Integrative Biology, University of Trento, Trento, via delle Regole, 101 38123 Mattarello (TN) Italy and Department of Biotechnology, University of Verona, Province of Verona, Ca' Vignal 1, Strada Le Grazie 15 37134 Verona, Italy
| | - Paola Riva
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, via delle Regole, 101 38123 Mattarello (TN) Italy, Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, via Viotti, 3/5 20133 Milano, Italy, Laboratory of Genomic Screening, Centre for Integrative Biology, University of Trento, Trento, via delle Regole, 101 38123 Mattarello (TN) Italy and Department of Biotechnology, University of Verona, Province of Verona, Ca' Vignal 1, Strada Le Grazie 15 37134 Verona, Italy
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, via delle Regole, 101 38123 Mattarello (TN) Italy, Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, via Viotti, 3/5 20133 Milano, Italy, Laboratory of Genomic Screening, Centre for Integrative Biology, University of Trento, Trento, via delle Regole, 101 38123 Mattarello (TN) Italy and Department of Biotechnology, University of Verona, Province of Verona, Ca' Vignal 1, Strada Le Grazie 15 37134 Verona, Italy
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Stevens SG, Brown CM. In silico estimation of translation efficiency in human cell lines: potential evidence for widespread translational control. PLoS One 2013; 8:e57625. [PMID: 23460887 PMCID: PMC3584024 DOI: 10.1371/journal.pone.0057625] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/27/2013] [Indexed: 11/19/2022] Open
Abstract
Recently large scale transcriptome and proteome datasets for human cells have become available. A striking finding from these studies is that the level of an mRNA typically predicts no more than 40% of the abundance of protein. This correlation represents the overall figure for all genes. We present here a bioinformatic analysis of translation efficiency – the rate at which mRNA is translated into protein. We have analysed those human datasets that include genome wide mRNA and protein levels determined in the same study. The analysis comprises five distinct human cell lines that together provide comparable data for 8,170 genes. For each gene we have used levels of mRNA and protein combined with protein stability data from the HeLa cell line to estimate translation efficiency. This was possible for 3,990 genes in one or more cell lines and 1,807 genes in all five cell lines. Interestingly, our analysis and modelling shows that for many genes this estimated translation efficiency has considerable consistency between cell lines. Some deviations from this consistency likely result from the regulation of protein degradation. Others are likely due to known translational control mechanisms. These findings suggest it will be possible to build improved models for the interpretation of mRNA expression data. The results we present here provide a view of translation efficiency for many genes. We provide an online resource allowing the exploration of translation efficiency in genes of interest within different cell lines (http://bioanalysis.otago.ac.nz/TranslationEfficiency).
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Affiliation(s)
- Stewart G. Stevens
- Biochemistry and Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Chris M Brown
- Biochemistry and Genetics Otago, University of Otago, Dunedin, New Zealand
- * E-mail:
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31
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Wei J, Zhang Y, Ivanov IP, Sachs MS. The stringency of start codon selection in the filamentous fungus Neurospora crassa. J Biol Chem 2013; 288:9549-62. [PMID: 23396971 DOI: 10.1074/jbc.m112.447177] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In eukaryotic cells initiation may occur from near-cognate codons that differ from AUG by a single nucleotide. The stringency of start codon selection impacts the efficiency of initiation at near-cognate codons and the efficiency of initiation at AUG codons in different contexts. We used a codon-optimized firefly luciferase reporter initiated with AUG or each of the nine near-cognate codons in preferred context to examine the stringency of start codon selection in the model filamentous fungus Neurospora crassa. In vivo results indicated that the hierarchy of initiation at start codons in N. crassa (AUG ≫ CUG > GUG > ACG > AUA ≈ UUG > AUU > AUC) is similar to that in human cells. Similar results were obtained by translating mRNAs in a homologous N. crassa in vitro translation system or in rabbit reticulocyte lysate. We next examined the efficiency of initiation at AUG, CUG, and UUG codons in different contexts in vitro. The preferred context was more important for efficient initiation from near-cognate codons than from AUG. These studies demonstrated that near-cognate codons are used for initiation in N. crassa. Such events could provide additional coding capacity or have regulatory functions. Analyses of the 5'-leader regions in the N. crassa transcriptome revealed examples of highly conserved near-cognate codons in preferred contexts that could extend the N termini of the predicted polypeptides.
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Affiliation(s)
- Jiajie Wei
- Department of Biology, Texas A&M University, College Station, TX 77843-3258, USA
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32
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Chen XS, Brown CM. Computational identification of new structured cis-regulatory elements in the 3'-untranslated region of human protein coding genes. Nucleic Acids Res 2012; 40:8862-73. [PMID: 22821558 PMCID: PMC3467077 DOI: 10.1093/nar/gks684] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/15/2012] [Accepted: 06/20/2012] [Indexed: 01/14/2023] Open
Abstract
Messenger ribonucleic acids (RNAs) contain a large number of cis-regulatory RNA elements that function in many types of post-transcriptional regulation. These cis-regulatory elements are often characterized by conserved structures and/or sequences. Although some classes are well known, given the wide range of RNA-interacting proteins in eukaryotes, it is likely that many new classes of cis-regulatory elements are yet to be discovered. An approach to this is to use computational methods that have the advantage of analysing genomic data, particularly comparative data on a large scale. In this study, a set of structural discovery algorithms was applied followed by support vector machine (SVM) classification. We trained a new classification model (CisRNA-SVM) on a set of known structured cis-regulatory elements from 3'-untranslated regions (UTRs) and successfully distinguished these and groups of cis-regulatory elements not been strained on from control genomic and shuffled sequences. The new method outperformed previous methods in classification of cis-regulatory RNA elements. This model was then used to predict new elements from cross-species conserved regions of human 3'-UTRs. Clustering of these elements identified new classes of potential cis-regulatory elements. The model, training and testing sets and novel human predictions are available at: http://mRNA.otago.ac.nz/CisRNA-SVM.
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Affiliation(s)
- Xiaowei Sylvia Chen
- Department of Biochemistry and Genetics Otago, University of Otago, Dunedin 9054, New Zealand.
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Dassi E, Quattrone A. Tuning the engine: an introduction to resources on post-transcriptional regulation of gene expression. RNA Biol 2012; 9:1224-32. [PMID: 22995832 DOI: 10.4161/rna.22035] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In the last years post-transcriptional regulation (PTR) of gene expression has been increasingly recognized to be a powerful and general determinant of the quantitative changes in proteomes, and therefore a driving force for cell phenotypes. By means of networks of trans-factors on one hand, and cis-elements found primarily in untranslated regions (UTRs) of mRNA on the other hand, mRNA availability to translation and translation rates are tightly controlled and can be rapidly tuned according to the changing state of the cell. A number of dedicated resources and tools, including databases and predictive algorithms, have been proposed as bioinformatics aids for the study of this fundamental layer of gene expression regulation. Their use, however, is rendered difficult by heterogeneity and fragmentation. This review aims to locate these resources in their proper space, classifying them according to their goals, limitations and integration capabilities and, in the end, to provide the user with an initial toolbox for the bioinformatic analysis of post-transcriptional regulation of gene expression. The accompanying website, available at www.ptrguide.org, lists all resources, provides summary and features for each one and will be regularly updated in the future.
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Affiliation(s)
- Erik Dassi
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, Italy
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34
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Millot GA, Carvalho MA, Caputo SM, Vreeswijk MPG, Brown MA, Webb M, Rouleau E, Neuhausen SL, Hansen TVO, Galli A, Brandão RD, Blok MJ, Velkova A, Couch FJ, Monteiro ANA. A guide for functional analysis of BRCA1 variants of uncertain significance. Hum Mutat 2012; 33:1526-37. [PMID: 22753008 DOI: 10.1002/humu.22150] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 05/29/2012] [Indexed: 12/12/2022]
Abstract
Germline mutations in the tumor suppressor gene BRCA1 confer an estimated lifetime risk of 56-80% for breast cancer and 15-60% for ovarian cancer. Since the mid 1990s when BRCA1 was identified, genetic testing has revealed over 1,500 unique germline variants. However, for a significant number of these variants, the effect on protein function is unknown making it difficult to infer the consequences on risks of breast and ovarian cancers. Thus, many individuals undergoing genetic testing for BRCA1 mutations receive test results reporting a variant of uncertain clinical significance (VUS), leading to issues in risk assessment, counseling, and preventive care. Here, we describe functional assays for BRCA1 to directly or indirectly assess the impact of a variant on protein conformation or function and how these results can be used to complement genetic data to classify a VUS as to its clinical significance. Importantly, these methods may provide a framework for genome-wide pathogenicity assignment.
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Affiliation(s)
- Gaël A Millot
- Institut Curie, CNRS, UMR 3244 Université Pierre et Marie Curie, Paris, France
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35
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Broad-specificity mRNA-rRNA complementarity in efficient protein translation. PLoS Genet 2012; 8:e1002598. [PMID: 22457640 PMCID: PMC3310771 DOI: 10.1371/journal.pgen.1002598] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Accepted: 02/03/2012] [Indexed: 12/30/2022] Open
Abstract
Studies of synthetic, well-defined biomolecular systems can elucidate inherent capabilities that may be difficult to uncover in a native biological context. Here, we used a minimal, reconstituted translation system from Escherichia coli to identify efficient ribosome binding sites (RBSs) in an unbiased, high-throughput manner. We applied ribosome display, a powerful in vitro selection method, to enrich only those mRNA sequences which could direct rapid protein translation. In addition to canonical Shine-Dalgarno (SD) motifs, we unexpectedly recovered highly efficient cytosine-rich (C-rich) sequences that exhibit unmistakable complementarity to the 16S rRNA of the small subunit of the ribosome, indicating that broad-specificity base-pairing may be an inherent, general mechanism for efficient translation. Furthermore, given the conservation of ribosomal structure and function across species, the broader relevance of C-rich RBS sequences identified through our in vitro evolution approach is supported by multiple, diverse examples in nature, including C-rich RBSs in several bacteriophage and plants, a poly-C consensus before the start codon in a lower eukaryote, and Kozak-like sequences in vertebrates. In order to maintain an appropriate balance of proteins in the cell, the protein factories (ribosomes) translate different messages (mRNAs) into protein at different rates. Many human diseases, including cancer and certain hereditary diseases, are caused by making too much or too little protein. Additionally, infections caused by bacteria and viruses are enabled by the ability of these organisms to produce protein very quickly while situated in their host. For these reasons, it is important to understand the ways in which ribosomes may recognize mRNAs and initiate translation into protein. We developed an experimental system that allowed us to uncover the inherent mRNA–binding ability of the ribosomes in a common bacterium, Escherichia coli. We found evidence that, when removed from the native cellular environment, these ribosomes are able to make protein very efficiently using previously unidentified ribosome binding sites on the mRNA that closely resemble known ribosome binding sites in diverse organisms, including plants and humans. Our results suggest a general, ubiquitous mechanism of mRNA–ribosome association during translation initiation.
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36
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Downregulation of HuR as a new mechanism of doxorubicin resistance in breast cancer cells. Mol Cancer 2012; 11:13. [PMID: 22436134 PMCID: PMC3325864 DOI: 10.1186/1476-4598-11-13] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 03/21/2012] [Indexed: 11/10/2022] Open
Abstract
Background HuR, an RNA binding protein involved in the post-transcriptional regulation of a wide spectrum of mRNAs, has been demonstrated to be a determinant of carcinogenesis and tumor aggressiveness in several cancer types. In this study, we investigated the role of HuR in the apoptosis and in the chemoresistance induced by the widely used anticancer drug doxorubicin in human breast cancer cells (MCF-7). Results We showed that HuR acts in the early phase of cell response to doxorubicin, being induced to translocate into the cytoplasm upon phosphorylation. Reducing HuR levels diminished the apoptotic response to doxorubicin. Doxorubicin-induced apoptosis was also correlated with the presence of HuR in the cytoplasm. Rottlerin, which was able to block HuR nuclear export, had correspondingly antagonistic effects with doxorubicin on cell toxicity. The proapoptotic activity of HuR was not due to cleavage to an active form, as was previously reported. In in vitro selected doxorubicin resistant MCF-7 cells (MCF-7/doxoR) overexpressing the multidrug resistance (MDR) related ABCG2 transporter, we observed a significant HuR downregulation that was paralleled by a corresponding downregulation of HuR targets and by loss of rottlerin toxicity. Restoration of HuR expression in these cells resensitized MCF-7/doxoR cells to doxorubicin, reactivating the apoptotic response. Conclusions The present study shows that HuR is necessary to elicit the apoptotic cell response to doxorubicin and that restoration of HuR expression in resistant cells resensitizes them to the action of this drug, thereby identifying HuR as a key protein in doxorubicin pharmacology.
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Lange SJ, Maticzka D, Möhl M, Gagnon JN, Brown CM, Backofen R. Global or local? Predicting secondary structure and accessibility in mRNAs. Nucleic Acids Res 2012; 40:5215-26. [PMID: 22373926 PMCID: PMC3384308 DOI: 10.1093/nar/gks181] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Determining the structural properties of mRNA is key to understanding vital post-transcriptional processes. As experimental data on mRNA structure are scarce, accurate structure prediction is required to characterize RNA regulatory mechanisms. Although various structure prediction approaches are available, it is often unclear which to choose and how to set their parameters. Furthermore, no standard measure to compare predictions of local structure exists. We assessed the performance of different methods using two types of data: transcriptome-wide enzymatic probing information and a large, curated set of cis-regulatory elements. To compare the approaches, we introduced structure accuracy, a measure that is applicable to both global and local methods. Our results showed that local folding was more accurate than the classic global approach. We investigated how the locality parameters, maximum base pair span and window size, influenced the prediction performance. A span of 150 provided a reasonable balance between maximizing the number of accurately predicted base pairs, while minimizing effects of incorrect long-range predictions. We characterized the error at artificial sequence ends, which we reduced by setting the window size sufficiently greater than the maximum span. Our method, LocalFold, diminished all border effects and produced the most robust performance.
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Affiliation(s)
- Sita J Lange
- Department of Computer Science and Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-Universität Freiburg, Germany
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38
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Christie-Oleza JA, Miotello G, Armengaud J. High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade. BMC Genomics 2012; 13:73. [PMID: 22336032 PMCID: PMC3305630 DOI: 10.1186/1471-2164-13-73] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 02/15/2012] [Indexed: 11/10/2022] Open
Abstract
Background The structural and functional annotation of genomes is now heavily based on data obtained using automated pipeline systems. The key for an accurate structural annotation consists of blending similarities between closely related genomes with biochemical evidence of the genome interpretation. In this work we applied high-throughput proteogenomics to Ruegeria pomeroyi, a member of the Roseobacter clade, an abundant group of marine bacteria, as a seed for the annotation of the whole clade. Results A large dataset of peptides from R. pomeroyi was obtained after searching over 1.1 million MS/MS spectra against a six-frame translated genome database. We identified 2006 polypeptides, of which thirty-four were encoded by open reading frames (ORFs) that had not previously been annotated. From the pool of 'one-hit-wonders', i.e. those ORFs specified by only one peptide detected by tandem mass spectrometry, we could confirm the probable existence of five additional new genes after proving that the corresponding RNAs were transcribed. We also identified the most-N-terminal peptide of 486 polypeptides, of which sixty-four had originally been wrongly annotated. Conclusions By extending these re-annotations to the other thirty-six Roseobacter isolates sequenced to date (twenty different genera), we propose the correction of the assigned start codons of 1082 homologous genes in the clade. In addition, we also report the presence of novel genes within operons encoding determinants of the important tricarboxylic acid cycle, a feature that seems to be characteristic of some Roseobacter genomes. The detection of their corresponding products in large amounts raises the question of their function. Their discoveries point to a possible theory for protein evolution that will rely on high expression of orphans in bacteria: their putative poor efficiency could be counterbalanced by a higher level of expression. Our proteogenomic analysis will increase the reliability of the future annotation of marine bacterial genomes.
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Mortlock DP, Pregizer S. Identifying Functional Annotation for Noncoding Genomic Sequences. ACTA ACUST UNITED AC 2012; Chapter 1:Unit1.10. [DOI: 10.1002/0471142905.hg0110s72] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Douglas P. Mortlock
- Department of Molecular Physiology & Biophysics, Vanderbilt University Medical Center Nashville Tennessee
- Center for Human Genetics Research, Vanderbilt University Medical Center Nashville Tennessee
| | - Steven Pregizer
- Department of Molecular Physiology & Biophysics, Vanderbilt University Medical Center Nashville Tennessee
- Center for Human Genetics Research, Vanderbilt University Medical Center Nashville Tennessee
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40
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Complete genome sequence of the giant virus OBP and comparative genome analysis of the diverse ΦKZ-related phages. J Virol 2011; 86:1844-52. [PMID: 22130535 DOI: 10.1128/jvi.06330-11] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 283,757-bp double-stranded DNA genome of Pseudomonas fluorescens phage OBP shares a general genomic organization with Pseudomonas aeruginosa phage EL. Comparison of this genomic organization, assembled in syntenic genomic blocks interspersed with hyperplastic regions of the ΦKZ-related phages, supports the proposed division in the "EL-like viruses," and the "phiKZ-like viruses" within a larger subfamily. Identification of putative early transcription promoters scattered throughout the hyperplastic regions explains several features of the ΦKZ-related genome organization (existence of genomic islands) and evolution (multi-inversion in hyperplastic regions). When hidden Markov modeling was used, typical conserved core genes could be identified, including the portal protein, the injection needle, and two polypeptides with respective similarity to the 3'-5' exonuclease domain and the polymerase domain of the T4 DNA polymerase. While the N-terminal domains of the tail fiber module and peptidoglycan-degrading proteins are conserved, the observation of C-terminal catalytic domains typical for the different genera supports the further subdivision of the ΦKZ-related phages.
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Dassi E, Malossini A, Re A, Mazza T, Tebaldi T, Caputi L, Quattrone A. AURA: Atlas of UTR Regulatory Activity. ACTA ACUST UNITED AC 2011; 28:142-4. [PMID: 22057158 DOI: 10.1093/bioinformatics/btr608] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
SUMMARY The Atlas of UTR Regulatory Activity (AURA) is a manually curated and comprehensive catalog of human mRNA untranslated regions (UTRs) and UTR regulatory annotations. Through its intuitive web interface, it provides full access to a wealth of information on UTRs that integrates phylogenetic conservation, RNA sequence and structure data, single nucleotide variation, gene expression and gene functional descriptions from literature and specialized databases. AVAILABILITY http://aura.science.unitn.it CONTACT aura@science.unitn.it; dassi@science.unitn SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- E Dassi
- Laboratory of Translational Genomics - Centre for Integrative Biology, University of Trento, Via delle Regole, 101, 38123 Mattarello (TN), Italy
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42
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Hamby SE, Thomas NST, Cooper DN, Chuzhanova N. A meta-analysis of single base-pair substitutions in translational termination codons ('nonstop' mutations) that cause human inherited disease. Hum Genomics 2011; 5:241-64. [PMID: 21712188 PMCID: PMC3525242 DOI: 10.1186/1479-7364-5-4-241] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
'Nonstop' mutations are single base-pair substitutions that occur within translational termination (stop) codons and which can lead to the continued and inappropriate translation of the mRNA into the 3'-untranslated region. We have performed a meta-analysis of the 119 nonstop mutations (in 87 different genes) known to cause human inherited disease, examining the sequence context of the mutated stop codons and the average distance to the next alternative in-frame stop codon downstream, in comparison with their counterparts from control (non-mutated) gene sequences. A paucity of alternative in-frame stop codons was noted in the immediate vicinity (0-49 nucleotides downstream) of the mutated stop codons as compared with their control counterparts (p = 7.81 × 10-4). This implies that at least some nonstop mutations with alternative stop codons in close proximity will not have come to clinical attention, possibly because they will have given rise to stable mRNAs (not subject to nonstop mRNA decay) that are translatable into proteins of near-normal length and biological function. A significant excess of downstream in-frame stop codons was, however, noted in the range 150-199 nucleotides from the mutated stop codon (p = 8.55 × 10-4). We speculate that recruitment of an alternative stop codon at greater distance from the mutated stop codon may trigger nonstop mRNA decay, thereby decreasing the amount of protein product and yielding a readily discernible clinical phenotype. Confirmation or otherwise of this postulate must await the emergence of a clearer understanding of the mechanism of nonstop mRNA decay in mammalian cells.
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Affiliation(s)
- Stephen E Hamby
- School of Science and Technology, Nottingham Trent University, UK
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43
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Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker R, Pedersen JS. New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. Genome Res 2011; 21:1929-43. [PMID: 21994249 DOI: 10.1101/gr.112516.110] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Regulatory RNA structures are often members of families with multiple paralogous instances across the genome. Family members share functional and structural properties, which allow them to be studied as a whole, facilitating both bioinformatic and experimental characterization. We have developed a comparative method, EvoFam, for genome-wide identification of families of regulatory RNA structures, based on primary sequence and secondary structure similarity. We apply EvoFam to a 41-way genomic vertebrate alignment. Genome-wide, we identify 220 human, high-confidence families outside protein-coding regions comprising 725 individual structures, including 48 families with known structural RNA elements. Known families identified include both noncoding RNAs, e.g., miRNAs and the recently identified MALAT1/MEN β lincRNA family; and cis-regulatory structures, e.g., iron-responsive elements. We also identify tens of new families supported by strong evolutionary evidence and other statistical evidence, such as GO term enrichments. For some of these, detailed analysis has led to the formulation of specific functional hypotheses. Examples include two hypothesized auto-regulatory feedback mechanisms: one involving six long hairpins in the 3'-UTR of MAT2A, a key metabolic gene that produces the primary human methyl donor S-adenosylmethionine; the other involving a tRNA-like structure in the intron of the tRNA maturation gene POP1. We experimentally validate the predicted MAT2A structures. Finally, we identify potential new regulatory networks, including large families of short hairpins enriched in immunity-related genes, e.g., TNF, FOS, and CTLA4, which include known transcript destabilizing elements. Our findings exemplify the diversity of post-transcriptional regulation and provide a resource for further characterization of new regulatory mechanisms and families of noncoding RNAs.
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Affiliation(s)
- Brian J Parker
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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44
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Ivanov IP, Firth AE, Michel AM, Atkins JF, Baranov PV. Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences. Nucleic Acids Res 2011; 39:4220-34. [PMID: 21266472 PMCID: PMC3105428 DOI: 10.1093/nar/gkr007] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In eukaryotes, it is generally assumed that translation initiation occurs at the AUG codon closest to the messenger RNA 5' cap. However, in certain cases, initiation can occur at codons differing from AUG by a single nucleotide, especially the codons CUG, UUG, GUG, ACG, AUA and AUU. While non-AUG initiation has been experimentally verified for a handful of human genes, the full extent to which this phenomenon is utilized--both for increased coding capacity and potentially also for novel regulatory mechanisms--remains unclear. To address this issue, and hence to improve the quality of existing coding sequence annotations, we developed a methodology based on phylogenetic analysis of predicted 5' untranslated regions from orthologous genes. We use evolutionary signatures of protein-coding sequences as an indicator of translation initiation upstream of annotated coding sequences. Our search identified novel conserved potential non-AUG-initiated N-terminal extensions in 42 human genes including VANGL2, FGFR1, KCNN4, TRPV6, HDGF, CITED2, EIF4G3 and NTF3, and also affirmed the conservation of known non-AUG-initiated extensions in 17 other genes. In several instances, we have been able to obtain independent experimental evidence of the expression of non-AUG-initiated products from the previously published literature and ribosome profiling data.
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Affiliation(s)
- Ivaylo P Ivanov
- BioSciences Institute, University College Cork, Cork, Ireland.
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Abstract
Despite their name, synonymous mutations have significant consequences for cellular processes in all taxa. As a result, an understanding of codon bias is central to fields as diverse as molecular evolution and biotechnology. Although recent advances in sequencing and synthetic biology have helped to resolve longstanding questions about codon bias, they have also uncovered striking patterns that suggest new hypotheses about protein synthesis. Ongoing work to quantify the dynamics of initiation and elongation is as important for understanding natural synonymous variation as it is for designing transgenes in applied contexts.
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Affiliation(s)
- Joshua B Plotkin
- Department of Biology and Program in Applied Mathematics and Computational Science, University of Pennsylvania, 433 South University Avenue, Philadelphia, Pennsylvania 19104, USA.
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Esparza M, Cárdenas JP, Bowien B, Jedlicki E, Holmes DS. Genes and pathways for CO2 fixation in the obligate, chemolithoautotrophic acidophile, Acidithiobacillus ferrooxidans, carbon fixation in A. ferrooxidans. BMC Microbiol 2010; 10:229. [PMID: 20799944 PMCID: PMC2942843 DOI: 10.1186/1471-2180-10-229] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Accepted: 08/27/2010] [Indexed: 11/10/2022] Open
Abstract
Background Acidithiobacillus ferrooxidans is chemolithoautotrophic γ-proteobacterium that thrives at extremely low pH (pH 1-2). Although a substantial amount of information is available regarding CO2 uptake and fixation in a variety of facultative autotrophs, less is known about the processes in obligate autotrophs, especially those living in extremely acidic conditions, prompting the present study. Results Four gene clusters (termed cbb1-4) in the A. ferrooxidans genome are predicted to encode enzymes and structural proteins involved in carbon assimilation via the Calvin-Benson-Bassham (CBB) cycle including form I of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO, EC 4.1.1.39) and the CO2-concentrating carboxysomes. RT-PCR experiments demonstrated that each gene cluster is a single transcriptional unit and thus is an operon. Operon cbb1 is divergently transcribed from a gene, cbbR, encoding the LysR-type transcriptional regulator CbbR that has been shown in many organisms to regulate the expression of RubisCO genes. Sigma70-like -10 and -35 promoter boxes and potential CbbR-binding sites (T-N11-A/TNA-N7TNA) were predicted in the upstream regions of the four operons. Electrophoretic mobility shift assays (EMSAs) confirmed that purified CbbR is able to bind to the upstream regions of the cbb1, cbb2 and cbb3 operons, demonstrating that the predicted CbbR-binding sites are functional in vitro. However, CbbR failed to bind the upstream region of the cbb4 operon that contains cbbP, encoding phosphoribulokinase (EC 2.7.1.19). Thus, other factors not present in the assay may be required for binding or the region lacks a functional CbbR-binding site. The cbb3 operon contains genes predicted to encode anthranilate synthase components I and II, catalyzing the formation of anthranilate and pyruvate from chorismate. This suggests a novel regulatory connection between CO2 fixation and tryptophan biosynthesis. The presence of a form II RubisCO could promote the ability of A. ferrooxidans to fix CO2 at different concentrations of CO2. Conclusions A. ferrooxidans has features of cbb gene organization for CO2-assimilating functions that are characteristic of obligate chemolithoautotrophs and distinguish this group from facultative autotrophs. The most conspicuous difference is a separate operon for the cbbP gene. It is hypothesized that this organization may provide greater flexibility in the regulation of expression of genes involved in inorganic carbon assimilation.
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Affiliation(s)
- Mario Esparza
- Center for Bioinformatics and Genome Biology, MIFAB, Fundación Ciencia para la Vida and Depto. de Ciencias Biologicas, Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
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47
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Mantsyzov AB, Ivanova EV, Birdsall B, Alkalaeva EZ, Kryuchkova PN, Kelly G, Frolova LY, Polshakov VI. NMR solution structure and function of the C-terminal domain of eukaryotic class 1 polypeptide chain release factor. FEBS J 2010. [PMID: 20553496 PMCID: PMC2909394 DOI: 10.1111/j.1742-4658.2010.07672.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Termination of translation in eukaryotes is triggered by two polypeptide chain release factors, eukaryotic class 1 polypeptide chain release factor (eRF1) and eukaryotic class 2 polypeptide chain release factor 3. eRF1 is a three-domain protein that interacts with eukaryotic class 2 polypeptide chain release factor 3 via its C-terminal domain (C-domain). The high-resolution NMR structure of the human C-domain (residues 277–437) has been determined in solution. The overall fold and the structure of the β-strand core of the protein in solution are similar to those found in the crystal structure. The structure of the minidomain (residues 329–372), which was ill-defined in the crystal structure, has been determined in solution. The protein backbone dynamics, studied using 15N-relaxation experiments, showed that the C-terminal tail 414–437 and the minidomain are the most flexible parts of the human C-domain. The minidomain exists in solution in two conformational states, slowly interconverting on the NMR timescale. Superposition of this NMR solution structure of the human C-domain onto the available crystal structure of full-length human eRF1 shows that the minidomain is close to the stop codon-recognizing N-terminal domain. Mutations in the tip of the minidomain were found to affect the stop codon specificity of the factor. The results provide new insights into the possible role of the C-domain in the process of translation termination.
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Affiliation(s)
- Alexey B Mantsyzov
- Center for Magnetic Tomography and Spectroscopy, M. V. Lomonosov Moscow State University, Russia
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48
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Beaudoin JD, Perreault JP. 5'-UTR G-quadruplex structures acting as translational repressors. Nucleic Acids Res 2010; 38:7022-36. [PMID: 20571090 PMCID: PMC2978341 DOI: 10.1093/nar/gkq557] [Citation(s) in RCA: 175] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Given that greater than 90% of the human genome is expressed, it is logical to assume that post-transcriptional regulatory mechanisms must be the primary means of controlling the flow of information from mRNA to protein. This report describes a robust approach that includes in silico, in vitro and in cellulo experiments permitting an in-depth evaluation of the impact of G-quadruplexes as translational repressors. Sequences including potential G-quadruplexes were selected within nine distinct genes encoding proteins involved in various biological processes. Their abilities to fold into G-quadruplex structures in vitro were evaluated using circular dichroism, thermal denaturation and the novel use of in-line probing. Six sequences were observed to fold into G-quadruplex structures in vitro, all of which exhibited translational inhibition in cellulo when linked to a reporter gene. Sequence analysis, direct mutagenesis and subsequent experiments were performed in order to define the rules governing the folding of G-quadruplexes. In addition, the impact of single-nucleotide polymorphism was shown to be important in the formation of G-quadruplexes located within the 5'-untranslated region of an mRNA. In light of these results, clearly the 5'-UTR G-quadruplexes represent a class of translational repressors that is broadly distributed in the cell.
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Affiliation(s)
- Jean-Denis Beaudoin
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, QC, J1H 5N4, Canada
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49
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Mantsyzov AB, Ivanova EV, Birdsall B, Alkalaeva EZ, Kryuchkova PN, Kelly G, Frolova LY, Polshakov VI. NMR solution structure and function of the C-terminal domain of eukaryotic class 1 polypeptide chain release factor. FEBS J 2010; 277:2611-27. [PMID: 20553496 PMCID: PMC2909394 DOI: 10.1111/j.1742-464x.2010.07672.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 04/01/2010] [Accepted: 04/08/2010] [Indexed: 11/27/2022]
Abstract
Termination of translation in eukaryotes is triggered by two polypeptide chain release factors, eukaryotic class 1 polypeptide chain release factor (eRF1) and eukaryotic class 2 polypeptide chain release factor 3. eRF1 is a three-domain protein that interacts with eukaryotic class 2 polypeptide chain release factor 3 via its C-terminal domain (C-domain). The high-resolution NMR structure of the human C-domain (residues 277-437) has been determined in solution. The overall fold and the structure of the beta-strand core of the protein in solution are similar to those found in the crystal structure. The structure of the minidomain (residues 329-372), which was ill-defined in the crystal structure, has been determined in solution. The protein backbone dynamics, studied using (15)N-relaxation experiments, showed that the C-terminal tail 414-437 and the minidomain are the most flexible parts of the human C-domain. The minidomain exists in solution in two conformational states, slowly interconverting on the NMR timescale. Superposition of this NMR solution structure of the human C-domain onto the available crystal structure of full-length human eRF1 shows that the minidomain is close to the stop codon-recognizing N-terminal domain. Mutations in the tip of the minidomain were found to affect the stop codon specificity of the factor. The results provide new insights into the possible role of the C-domain in the process of translation termination.
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Affiliation(s)
- Alexey B Mantsyzov
- Center for Magnetic Tomography and Spectroscopy, M. V. Lomonosov Moscow State University, Russia
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50
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Crowther-Swanepoel D, Broderick P, Ma Y, Robertson L, Pittman AM, Price A, Twiss P, Vijayakrishnan J, Qureshi M, Dyer MJS, Matutes E, Dearden C, Catovsky D, Houlston RS. Fine-scale mapping of the 6p25.3 chronic lymphocytic leukaemia susceptibility locus. Hum Mol Genet 2010; 19:1840-5. [PMID: 20123861 DOI: 10.1093/hmg/ddq044] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A recent genome-wide association study of chronic lymphocytic leukaemia (CLL) has identified a susceptibility locus on 6p25.3 associated with a modest but highly significant increase in CLL risk. Using a set of single nucleotide polymorphism (SNP) markers, we generated a fine-scale map and narrowed the association signal to a 18 kb DNA segment within the 3'-untranslated region (UTR) of the IRF4 (interferon regulatory factor 4) gene. Resequencing this segment in European subjects identified 55 common polymorphisms, including 13 highly correlated candidate causal variants. In a large case-control study, it was shown that all but four variants could be excluded with 95% confidence. These four SNPs map to a 3 kb region of the 3'-UTR of IRF4, consistent with the causal basis of the association being mediated through differential IRF4 expression.
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