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Takallou S, Puchacz N, Allard D, Said KB, Nokhbeh MR, Samanfar B, Golshani A. IRES-mediated translation in bacteria. Biochem Biophys Res Commun 2023; 641:110-115. [PMID: 36527744 DOI: 10.1016/j.bbrc.2022.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
Despite the similarity in fundamental goals of translation initiation between different domains of life, it is one of the most phylogenetically diverse steps of the central dogma of molecular biology. In a classical view, the translation signals for prokaryotes and eukaryotes are distinct from each other. This idea was challenged by the finding that the Internal Ribosome Entry Site (IRES) belonging to Plautia stali intestine virus (PSIV) could bypass the domain-specific boundaries and effectively initiate translation in E. coli. This finding led us to investigate whether the ability of PSIV IRES to initiate translation in E. coli is specific to this IRES and also to study features that allow this viral IRES to mediate prokaryotic translation initiation. We observed that certain IRESs may also possess the ability to initiate E. coli translation. Our results also indicated that the structural integrity of the PSIV IRES in translation in prokaryotes does not appear to be as critical as it is in eukaryotes. We also demonstrated that two regions of the PSIV IRES with complementarity to 16S ribosomal RNA are important for the ability of this IRES to initiate translation in E. coli.
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Affiliation(s)
- Sarah Takallou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Nathalie Puchacz
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Danielle Allard
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
| | - Kamaledin B Said
- Department of Pathology and Microbiology, College of Medicine, University of Hail, Saudi Arabia.
| | | | - Bahram Samanfar
- Department of Biology, Carleton University, Ottawa, Ontario, Canada; Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, Ontario, Canada.
| | - Ashkan Golshani
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada.
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2
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Komarova ES, Dontsova OA, Pyshnyi DV, Kabilov MR, Sergiev PV. Flow-Seq Method: Features and Application in Bacterial Translation Studies. Acta Naturae 2022; 14:20-37. [PMID: 36694903 PMCID: PMC9844084 DOI: 10.32607/actanaturae.11820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/11/2022] [Indexed: 01/22/2023] Open
Abstract
The Flow-seq method is based on using reporter construct libraries, where a certain element regulating the gene expression of fluorescent reporter proteins is represented in many thousands of variants. Reporter construct libraries are introduced into cells, sorted according to their fluorescence level, and then subjected to next-generation sequencing. Therefore, it turns out to be possible to identify patterns that determine the expression efficiency, based on tens and hundreds of thousands of reporter constructs in one experiment. This method has become common in evaluating the efficiency of protein synthesis simultaneously by multiple mRNA variants. However, its potential is not confined to this area. In the presented review, a comparative analysis of the Flow-seq method and other alternative approaches used for translation efficiency evaluation of mRNA was carried out; the features of its application and the results obtained by Flow-seq were also considered.
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Affiliation(s)
- E. S. Komarova
- Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, 119234 Russia
| | - O. A. Dontsova
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119234 Russia
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117437 Russia
| | - D. V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - M. R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - P. V. Sergiev
- Institute of Functional Genomics, Lomonosov Moscow State University, Moscow, 119234 Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119234 Russia
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234 Russia
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3
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Wen J, Harp JR, Fozo EM. The 5΄ UTR of the type I toxin ZorO can both inhibit and enhance translation. Nucleic Acids Res 2017; 45:4006-4020. [PMID: 27903909 PMCID: PMC5397157 DOI: 10.1093/nar/gkw1172] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 11/14/2016] [Indexed: 01/30/2023] Open
Abstract
Many bacterial type I toxin mRNAs possess a long 5΄ untranslated region (UTR) that serves as the target site of the corresponding antitoxin sRNA. This is the case for the zorO-orzO type I system where the OrzO antitoxin base pairs to the 174-nucleotide zorO 5΄ UTR. Here, we demonstrate that the full-length 5΄ UTR of the zorO type I toxin hinders its own translation independent of the sRNA whereas a processed 5΄ UTR (zorO Δ28) promotes translation. The full-length zorO 5΄ UTR folds into an extensive secondary structure sequestering the ribosome binding site (RBS). Processing of the 5΄ UTR does not alter the RBS structure, but opens a large region (EAP region) located upstream of the RBS. Truncation of this EAP region impairs zorO translation, but this defect can be rescued upon exposing the RBS. Additionally, the region spanning +35 to +50 of the zorO mRNA is needed for optimal translation of zorO. Importantly, the positive and negative effects on translation imparted by the 5΄ UTR can be transferred onto a reporter gene, indicative that the 5΄ UTR can solely drive regulation. Moreover, we show that the OrzO sRNA can inhibit zorO translation via base pairing to the of the EAP region.
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Affiliation(s)
- Jia Wen
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - John R Harp
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Elizabeth M Fozo
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
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4
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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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5
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Locati MD, Pagano JFB, Girard G, Ensink WA, van Olst M, van Leeuwen S, Nehrdich U, Spaink HP, Rauwerda H, Jonker MJ, Dekker RJ, Breit TM. Expression of distinct maternal and somatic 5.8S, 18S, and 28S rRNA types during zebrafish development. RNA (NEW YORK, N.Y.) 2017; 23:1188-1199. [PMID: 28500251 PMCID: PMC5513064 DOI: 10.1261/rna.061515.117] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/09/2017] [Indexed: 05/27/2023]
Abstract
There is mounting evidence that the ribosome is not a static translation machinery, but a cell-specific, adaptive system. Ribosomal variations have mostly been studied at the protein level, even though the essential transcriptional functions are primarily performed by rRNAs. At the RNA level, oocyte-specific 5S rRNAs are long known for Xenopus. Recently, we described for zebrafish a similar system in which the sole maternal-type 5S rRNA present in eggs is replaced completely during embryonic development by a somatic-type. Here, we report the discovery of an analogous system for the 45S rDNA elements: 5.8S, 18S, and 28S. The maternal-type 5.8S, 18S, and 28S rRNA sequences differ substantially from those of the somatic-type, plus the maternal-type rRNAs are also replaced by the somatic-type rRNAs during embryogenesis. We discuss the structural and functional implications of the observed sequence differences with respect to the translational functions of the 5.8S, 18S, and 28S rRNA elements. Finally, in silico evidence suggests that expansion segments (ES) in 18S rRNA, previously implicated in ribosome-mRNA interaction, may have a preference for interacting with specific mRNA genes. Taken together, our findings indicate that two distinct types of ribosomes exist in zebrafish during development, each likely conducting the translation machinery in a unique way.
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MESH Headings
- Animals
- Base Pairing
- Base Sequence
- DNA, Ribosomal/genetics
- Embryo, Nonmammalian/cytology
- Embryo, Nonmammalian/metabolism
- Nucleic Acid Conformation
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- RNA, Ribosomal, 28S/genetics
- RNA, Ribosomal, 28S/metabolism
- RNA, Ribosomal, 5.8S/genetics
- RNA, Ribosomal, 5.8S/metabolism
- Ribosomes/metabolism
- Sequence Alignment
- Zebrafish/genetics
- Zebrafish/growth & development
- Zebrafish/metabolism
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Affiliation(s)
- Mauro D Locati
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Johanna F B Pagano
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Geneviève Girard
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Wim A Ensink
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Marina van Olst
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Selina van Leeuwen
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Ulrike Nehrdich
- Department of Molecular Cell Biology, Institute of Biology, Leiden University, Gorlaeus Laboratories-Cell Observatorium, Leiden 2333 CE, the Netherlands
| | - Herman P Spaink
- Department of Molecular Cell Biology, Institute of Biology, Leiden University, Gorlaeus Laboratories-Cell Observatorium, Leiden 2333 CE, the Netherlands
| | - Han Rauwerda
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Martijs J Jonker
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Rob J Dekker
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Timo M Breit
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
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6
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Schrader JM, Zhou B, Li GW, Lasker K, Childers WS, Williams B, Long T, Crosson S, McAdams HH, Weissman JS, Shapiro L. The coding and noncoding architecture of the Caulobacter crescentus genome. PLoS Genet 2014; 10:e1004463. [PMID: 25078267 PMCID: PMC4117421 DOI: 10.1371/journal.pgen.1004463] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 05/13/2014] [Indexed: 11/24/2022] Open
Abstract
Caulobacter crescentus undergoes an asymmetric cell division controlled by a genetic circuit that cycles in space and time. We provide a universal strategy for defining the coding potential of bacterial genomes by applying ribosome profiling, RNA-seq, global 5′-RACE, and liquid chromatography coupled with tandem mass spectrometry (LC-MS) data to the 4-megabase C. crescentus genome. We mapped transcript units at single base-pair resolution using RNA-seq together with global 5′-RACE. Additionally, using ribosome profiling and LC-MS, we mapped translation start sites and coding regions with near complete coverage. We found most start codons lacked corresponding Shine-Dalgarno sites although ribosomes were observed to pause at internal Shine-Dalgarno sites within the coding DNA sequence (CDS). These data suggest a more prevalent use of the Shine-Dalgarno sequence for ribosome pausing rather than translation initiation in C. crescentus. Overall 19% of the transcribed and translated genomic elements were newly identified or significantly improved by this approach, providing a valuable genomic resource to elucidate the complete C. crescentus genetic circuitry that controls asymmetric cell division. Caulobacter crescentus is a model system for studying asymmetric cell division, a fundamental process that, through differential gene expression in the two daughter cells, enables the generation of cells with different fates. To explore how the genome directs and maintains asymmetry upon cell division, we performed a coordinated analysis of multiple genomic and proteomic datasets to identify the RNA and protein coding features in the C. crescentus genome. Our integrated analysis identifies many new genetic regulatory elements, adding significant regulatory complexity to the C. crescentus genome. Surprisingly, 75.4% of protein coding genes lack a canonical translation initiation sequence motif (the Shine-Dalgarno site) which hybridizes to the 3′ end of the ribosomal RNA allowing translation initiation. We find Shine-Dalgarno sites primarily inside of genes where they cause translating ribosomes to pause, possibly allowing nascent proteins to correctly fold. With our detailed map of genomic transcription and translation elements, a systems view of the genetic network that controls asymmetric cell division is within reach.
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Affiliation(s)
- Jared M. Schrader
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Bo Zhou
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Gene-Wei Li
- Department of Cellular and Molecular Pharmacology, California Institute of Quantitative Biology, Center for RNA Systems Biology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Keren Lasker
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - W. Seth Childers
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Brandon Williams
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Tao Long
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Sean Crosson
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Harley H. McAdams
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Jonathan S. Weissman
- Department of Cellular and Molecular Pharmacology, California Institute of Quantitative Biology, Center for RNA Systems Biology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
- * E-mail:
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7
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An RNA-seq method for defining endoribonuclease cleavage specificity identifies dual rRNA substrates for toxin MazF-mt3. Nat Commun 2014; 5:3538. [PMID: 24709835 PMCID: PMC4090939 DOI: 10.1038/ncomms4538] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 03/03/2014] [Indexed: 11/10/2022] Open
Abstract
Toxin-antitoxin (TA) systems are widespread in prokaryotes. Among these, the mazEF TA system encodes an endoribonucleolytic toxin, MazF, that inhibits growth by sequence-specific cleavage of single-stranded RNA. Defining the physiological targets of a MazF toxin first requires the identification of its cleavage specificity, yet the current toolkit is antiquated and limited. We describe a rapid genome-scale approach, MORE (Mapping by Overexpression of an RNase in Escherichia coli) RNA-seq, for defining the cleavage specificity of endoribonucleolytic toxins. Application of MORE RNA-seq to MazF-mt3 from Mycobacterium tuberculosis reveals two critical ribosomal targets — the essential, evolutionarily conserved helix/loop 70 of 23S rRNA and the anti-Shine-Dalgarno (aSD) sequence of 16S rRNA. Our findings support an emerging model where both rRNA and mRNA are principal targets of MazF toxins and suggest that, as in E. coli, removal of the aSD sequence by a MazF toxin modifies ribosomes to selectively translate leaderless mRNAs in M. tuberculosis.
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8
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Lentini R, Forlin M, Martini L, Del Bianco C, Spencer AC, Torino D, Mansy SS. Fluorescent proteins and in vitro genetic organization for cell-free synthetic biology. ACS Synth Biol 2013; 2:482-9. [PMID: 23654270 DOI: 10.1021/sb400003y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To facilitate the construction of cell-free genetic devices, we evaluated the ability of 17 different fluorescent proteins to give easily detectable fluorescence signals in real-time from in vitro transcription-translation reactions with a minimal system consisting of T7 RNA polymerase and E. coli translation machinery, i.e., the PUREsystem. The data were used to construct a ratiometric fluorescence assay to quantify the effect of genetic organization on in vitro expression levels. Synthetic operons with varied spacing and sequence composition between two genes that coded for fluorescent proteins were then assembled. The resulting data indicated which restriction sites and where the restriction sites should be placed in order to build genetic devices in a manner that does not interfere with protein expression. Other simple design rules were identified, such as the spacing and sequence composition influences of regions upstream and downstream of ribosome binding sites and the ability of non-AUG start codons to function in vitro.
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Affiliation(s)
- Roberta Lentini
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN),
Italy
| | - Michele Forlin
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN),
Italy
| | - Laura Martini
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN),
Italy
| | - Cristina Del Bianco
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN),
Italy
| | - Amy C. Spencer
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN),
Italy
| | - Domenica Torino
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN),
Italy
| | - Sheref S. Mansy
- CIBIO, University of Trento, via delle Regole 101, 38123 Mattarello (TN),
Italy
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9
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Murray CJ, Baliga R. Cell-free translation of peptides and proteins:from high throughput screening to clinical production. Curr Opin Chem Biol 2013; 17:420-6. [DOI: 10.1016/j.cbpa.2013.02.014] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 02/14/2013] [Indexed: 12/01/2022]
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10
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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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11
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Shabalina SA, Spiridonov NA, Kashina A. Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. Nucleic Acids Res 2013; 41:2073-94. [PMID: 23293005 PMCID: PMC3575835 DOI: 10.1093/nar/gks1205] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Messenger RNA is a key component of an intricate regulatory network of its own. It accommodates numerous nucleotide signals that overlap protein coding sequences and are responsible for multiple levels of regulation and generation of biological complexity. A wealth of structural and regulatory information, which mRNA carries in addition to the encoded amino acid sequence, raises the question of how these signals and overlapping codes are delineated along non-synonymous and synonymous positions in protein coding regions, especially in eukaryotes. Silent or synonymous codon positions, which do not determine amino acid sequences of the encoded proteins, define mRNA secondary structure and stability and affect the rate of translation, folding and post-translational modifications of nascent polypeptides. The RNA level selection is acting on synonymous sites in both prokaryotes and eukaryotes and is more common than previously thought. Selection pressure on the coding gene regions follows three-nucleotide periodic pattern of nucleotide base-pairing in mRNA, which is imposed by the genetic code. Synonymous positions of the coding regions have a higher level of hybridization potential relative to non-synonymous positions, and are multifunctional in their regulatory and structural roles. Recent experimental evidence and analysis of mRNA structure and interspecies conservation suggest that there is an evolutionary tradeoff between selective pressure acting at the RNA and protein levels. Here we provide a comprehensive overview of the studies that define the role of silent positions in regulating RNA structure and processing that exert downstream effects on proteins and their functions.
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Affiliation(s)
- Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20984, USA.
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