151
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Osterrieder N, Kunec D. Attenuation of Viruses by Large-Scale Recoding of their Genomes: the Selection Is Always Biased. CURRENT CLINICAL MICROBIOLOGY REPORTS 2018; 5:66-72. [PMID: 32226716 PMCID: PMC7100164 DOI: 10.1007/s40588-018-0080-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
PURPOSE OF REVIEW This review summarizes the current understanding of virus attenuation by large-scale recoding of viral genomes and discusses what would ultimately be necessary for construction of better and safer live modified virus vaccines. RECENT FINDINGS It has been shown that codon and codon pair deoptimization are rapid and robust methods that can be used for the development of attenuated vaccine candidates. The viruses attenuated by large-scale recoding have the added value that they are extremely genetically stable. However, the exact mechanisms that lead to viral attenuation by recoding are yet to be determined. SUMMARY While the advantages of large-scale recoding (speed, simplicity, potency, and universal applicability) have been known for more than a decade, this approach has been only inadequately explored and the attention was focused on a limited number of RNA viruses. Attenuation of viruses by large-scale recoding should be explored to combat known and future viral threats.
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Affiliation(s)
- Nikolaus Osterrieder
- Institut für Virologie, Zentrum für Infektionsmedizin, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany
| | - Dusan Kunec
- Institut für Virologie, Zentrum für Infektionsmedizin, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany
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152
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Quandt EM, Traverse CC, Ochman H. Local genic base composition impacts protein production and cellular fitness. PeerJ 2018; 6:e4286. [PMID: 29362699 PMCID: PMC5774297 DOI: 10.7717/peerj.4286] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/01/2018] [Indexed: 01/25/2023] Open
Abstract
The maintenance of a G + C content that is higher than the mutational input to a genome provides support for the view that selection serves to increase G + C contents in bacteria. Recent experimental evidence from Escherichia coli demonstrated that selection for increasing G + C content operates at the level of translation, but the precise mechanism by which this occurs is unknown. To determine the substrate of selection, we asked whether selection on G + C content acts across all sites within a gene or is confined to particular genic regions or nucleotide positions. We systematically altered the G + C contents of the GFP gene and assayed its effects on the fitness of strains harboring each variant. Fitness differences were attributable to the base compositional variation in the terminal portion of the gene, suggesting a connection to the folding of a specific protein feature. Variants containing sequence features that are thought to result in rapid translation, such as low G + C content and high levels of codon adaptation, displayed highly reduced growth rates. Taken together, our results show that purifying selection acting against A and T mutations most likely results from their tendency to increase the rate of translation, which can perturb the dynamics of protein folding.
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Affiliation(s)
- Erik M Quandt
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
| | - Charles C Traverse
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
| | - Howard Ochman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
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153
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Ding D, Sun X. Network-Based Methods for Identifying Key Active Proteins in the Extracellular Electron Transfer Process in Shewanella oneidensis MR-1. Genes (Basel) 2018; 9:E41. [PMID: 29337910 PMCID: PMC5793192 DOI: 10.3390/genes9010041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/07/2018] [Accepted: 01/12/2018] [Indexed: 12/22/2022] Open
Abstract
Shewanella oneidensis MR-1 can transfer electrons from the intracellular environment to the extracellular space of the cells to reduce the extracellular insoluble electron acceptors (Extracellular Electron Transfer, EET). Benefiting from this EET capability, Shewanella has been widely used in different areas, such as energy production, wastewater treatment, and bioremediation. Genome-wide proteomics data was used to determine the active proteins involved in activating the EET process. We identified 1012 proteins with decreased expression and 811 proteins with increased expression when the EET process changed from inactivation to activation. We then networked these proteins to construct the active protein networks, and identified the top 20 key active proteins by network centralization analysis, including metabolism- and energy-related proteins, signal and transcriptional regulatory proteins, translation-related proteins, and the EET-related proteins. We also constructed the integrated protein interaction and transcriptional regulatory networks for the active proteins, then found three exclusive active network motifs involved in activating the EET process-Bi-feedforward Loop, Regulatory Cascade with a Feedback, and Feedback with a Protein-Protein Interaction (PPI)-and identified the active proteins involved in these motifs. Both enrichment analysis and comparative analysis to the whole-genome data implicated the multiheme c-type cytochromes and multiple signal processing proteins involved in the process. Furthermore, the interactions of these motif-guided active proteins and the involved functional modules were discussed. Collectively, by using network-based methods, this work reported a proteome-wide search for the key active proteins that potentially activate the EET process.
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Affiliation(s)
- Dewu Ding
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
- Department of Mathematics and Computer Science, Chizhou College, Chizhou 247000, China.
| | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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154
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A set of synthetic versatile genetic control elements for the efficient expression of genes in Actinobacteria. Sci Rep 2018; 8:491. [PMID: 29323285 PMCID: PMC5765039 DOI: 10.1038/s41598-017-18846-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/18/2017] [Indexed: 12/22/2022] Open
Abstract
The design and engineering of secondary metabolite gene clusters that are characterized by complicated genetic organization, require the development of collections of well-characterized genetic control elements that can be reused reliably. Although a few intrinsic terminators and RBSs are used routinely, their translation and termination efficiencies have not been systematically studied in Actinobacteria. Here, we analyzed the influence of the regions surrounding RBSs on gene expression in these bacteria. We demonstrated that inappropriate RBSs can reduce the expression efficiency of a gene to zero. We developed a genetic device – an in vivo RBS-selector – that allows selection of an optimal RBS for any gene of interest, enabling rational control of the protein expression level. In addition, a genetic tool that provides the opportunity for measurement of termination efficiency was developed. Using this tool, we found strong terminators that lead to a 17–100-fold reduction in downstream expression and are characterized by sufficient sequence diversity to reduce homologous recombination when used with other elements. For the first time, a C-terminal degradation tag was employed for the control of protein stability in Streptomyces. Finally, we describe a collection of regulatory elements that can be used to control metabolic pathways in Actinobacteria.
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155
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Brandariz-Núñez A, Zeng F, Lam QN, Jin H. Sbp1 modulates the translation of Pab1 mRNA in a poly(A)- and RGG-dependent manner. RNA (NEW YORK, N.Y.) 2018; 24:43-55. [PMID: 28986506 PMCID: PMC5733569 DOI: 10.1261/rna.062547.117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/29/2017] [Indexed: 05/13/2023]
Abstract
RNA-binding protein Sbp1 facilitates the decapping pathway in mRNA metabolism and inhibits global mRNA translation by an unclear mechanism. Here we report molecular interactions responsible for Sbp1-mediated translation inhibition of mRNA encoding the polyadenosine-binding protein (Pab1), an essential translation factor that stimulates mRNA translation and inhibits mRNA decapping in eukaryotic cells. We demonstrate that the two distal RRMs of Sbp1 bind to the poly(A) sequence in the 5'UTR of the Pab1 mRNA specifically and cooperatively while the central RGG domain of the protein interacts directly with Pab1. Furthermore, methylation of arginines in the RGG domain abolishes the protein-protein interaction and the inhibitory effect of Sbp1 on translation initiation of Pab1 mRNA. Based on these results, the underlying mechanism for Sbp1-specific translational regulation is proposed. The functional differences of Sbp1 and RGG repeats alone on transcript-specific translation were observed, and a comparison of the results suggests the importance of remodeling the 5'UTR by RNA-binding proteins in mRNA translation.
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Affiliation(s)
- Alberto Brandariz-Núñez
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
| | - Fuxing Zeng
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
| | - Quan Ngoc Lam
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
| | - Hong Jin
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
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156
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Płachetka-Bożek A, Chwiałkowska K, Augustyniak M. Molecular changes in vitellogenin gene of Spodoptera exigua after long-time exposure to cadmium - Toxic side effect or microevolution? ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 147:461-470. [PMID: 28898805 DOI: 10.1016/j.ecoenv.2017.08.067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 08/28/2017] [Accepted: 08/30/2017] [Indexed: 06/07/2023]
Abstract
The reproduction of pest insects is a continuously ongoing issue, especially in the environmental pollution context. Natural or artificial stressing factors enforce a kind of trade-off, most often between growth/survival and reproduction, which improves fitness of the organism. Harmful factors, such as cadmium, can affect the vitellogenesis leading to reduction of yolk synthesis and egg production. The aim of this study was to assess whether 130-generational selection to cadmium in food might have induced change in vitellogenesis of Spodoptera exigua. We analyzed the level of Vg gene expression in S. exigua from the control and the cadmium strain at regular time intervals within 48h after eclosion. The full sequence of Vg gene was also compared between strains. The vitellogenin gene expression in both strains was time-dependent. This dependence was more visible in the control strain. In the cadmium strain the vitellogenin expression was significantly lower, comparing with the control strain in the first day after eclosion but increased significantly in the second day. The sequenced CDS (5286bp long) of the control and the cadmium strains were translated into protein sequences containing both 1761 aa. The protein sequences comparison revealed that there is one amino acid change at aa position 1282. Multiple alignments of six orthologous proteins from different species showed that amino acid change is located in the conserved position. Long-lasting exposure to cadmium resulted in permanent mutation in vitellogenin gene. We do not know yet if the mutation can improve fitness of the cadmium-selected insects. However, we can suppose that the mutation is neutral or even beneficial. The mutation and most probably additional effects of cadmium exposure have an influence on the vitellogenin expression. Some modification in the expression of the vitellogenin receptor are also likely to be important.
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Affiliation(s)
- Anna Płachetka-Bożek
- Department of Animal Physiology and Ecotoxicology, University of Silesia in Katowice, Bankowa 9, 40-007 Katowice, Poland.
| | - Karolina Chwiałkowska
- Department of Genetics, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland
| | - Maria Augustyniak
- Department of Animal Physiology and Ecotoxicology, University of Silesia in Katowice, Bankowa 9, 40-007 Katowice, Poland
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157
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Nakajima K, Zhou Y, Tomita A, Hirade Y, Gurumurthy CB, Nakada S. Precise and efficient nucleotide substitution near genomic nick via noncanonical homology-directed repair. Genome Res 2017; 28:223-230. [PMID: 29273627 PMCID: PMC5793786 DOI: 10.1101/gr.226027.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 11/27/2017] [Indexed: 12/12/2022]
Abstract
CRISPR/Cas9, which generates DNA double-strand breaks (DSBs) at target loci, is a powerful tool for editing genomes when codelivered with a donor DNA template. However, DSBs, which are the most deleterious type of DNA damage, often result in unintended nucleotide insertions/deletions (indels) via mutagenic nonhomologous end joining. We developed a strategy for precise gene editing that does not generate DSBs. We show that a combination of single nicks in the target gene and donor plasmid (SNGD) using Cas9D10A nickase promotes efficient nucleotide substitution by gene editing. Nicking the target gene alone did not facilitate efficient gene editing. However, an additional nick in the donor plasmid backbone markedly improved the gene-editing efficiency. SNGD-mediated gene editing led to a markedly lower indel frequency than that by the DSB-mediated approach. We also show that SNGD promotes gene editing at endogenous loci in human cells. Mechanistically, SNGD-mediated gene editing requires long-sequence homology between the target gene and repair template, but does not require CtIP, RAD51, or RAD52. Thus, it is considered that noncanonical homology-directed repair regulates the SNGD-mediated gene editing. In summary, SNGD promotes precise and efficient gene editing and may be a promising strategy for the development of a novel gene therapy approach.
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Affiliation(s)
- Kazuhiro Nakajima
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yue Zhou
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Akiko Tomita
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yoshihiro Hirade
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA.,Developmental Neuroscience, Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Shinichiro Nakada
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.,Institute for Advanced Co-Creation Studies, Osaka University, Suita, Osaka 565-0871, Japan
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158
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Li JJ, Chew GL, Biggin MD. Quantitating translational control: mRNA abundance-dependent and independent contributions and the mRNA sequences that specify them. Nucleic Acids Res 2017; 45:11821-11836. [PMID: 29040683 PMCID: PMC5714229 DOI: 10.1093/nar/gkx898] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 09/25/2017] [Indexed: 11/17/2022] Open
Abstract
Translation rate per mRNA molecule correlates positively with mRNA abundance. As a result, protein levels do not scale linearly with mRNA levels, but instead scale with the abundance of mRNA raised to the power of an ‘amplification exponent’. Here we show that to quantitate translational control, the translation rate must be decomposed into two components. One, TRmD, depends on the mRNA level and defines the amplification exponent. The other, TRmIND, is independent of mRNA amount and impacts the correlation coefficient between protein and mRNA levels. We show that in Saccharomyces cerevisiae TRmD represents ∼20% of the variance in translation and directs an amplification exponent of 1.20 with a 95% confidence interval [1.14, 1.26]. TRmIND constitutes the remaining ∼80% of the variance in translation and explains ∼5% of the variance in protein expression. We also find that TRmD and TRmIND are preferentially determined by different mRNA sequence features: TRmIND by the length of the open reading frame and TRmD both by a ∼60 nucleotide element that spans the initiating AUG and by codon and amino acid frequency. Our work provides more appropriate estimates of translational control and implies that TRmIND is under different evolutionary selective pressures than TRmD.
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Affiliation(s)
- Jingyi Jessica Li
- Department of Statistics and Department of Human Genetics, University of California, Los Angeles, CA 90095, USA
| | - Guo-Liang Chew
- Computational Biology Program, Public Health Sciences and Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mark D Biggin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94708, USA
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159
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Fernandes LD, Moura APSD, Ciandrini L. Gene length as a regulator for ribosome recruitment and protein synthesis: theoretical insights. Sci Rep 2017; 7:17409. [PMID: 29234048 PMCID: PMC5727216 DOI: 10.1038/s41598-017-17618-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/28/2017] [Indexed: 01/14/2023] Open
Abstract
Protein synthesis rates are determined, at the translational level, by properties of the transcript’s sequence. The efficiency of an mRNA can be tuned by varying the ribosome binding sites controlling the recruitment of the ribosomes, or the codon usage establishing the speed of protein elongation. In this work we propose transcript length as a further key determinant of translation efficiency. Based on a physical model that considers the kinetics of ribosomes advancing on the mRNA and diffusing in its surrounding, as well as mRNA circularisation and ribosome drop-off, we explain how the transcript length may play a central role in establishing ribosome recruitment and the overall translation rate of an mRNA. According to our results, the proximity of the 3′ end to the ribosomal recruitment site of the mRNA could induce a feedback in the translation process that would favour the recycling of ribosomes. We also demonstrate how this process may be involved in shaping the experimental ribosome density-gene length dependence. Finally, we argue that cells could exploit this mechanism to adjust and balance the usage of its ribosomal resources.
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Affiliation(s)
- Lucas D Fernandes
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura Luiz de Queiroz - Universidade de São Paulo (USP), 13418-900, Piracicaba/SP, Brazil.,Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Alessandro P S de Moura
- Institute for Complex Systems and Mathematical Biology, University of Aberdeen, Aberdeen, AB24 3UE, UK
| | - Luca Ciandrini
- DIMNP UMR 5235, Université de Montpellier and CNRS, F-34095, Montpellier, France. .,Laboratoire Charles Coulomb UMR5221, Université de Montpellier and CNRS, F-34095, Montpellier, France.
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160
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Zhou M, Xue L, Chen Y, Li H, He Q, Wang B, Meng F, Wang M, Guan MX. A hypertension-associated mitochondrial DNA mutation introduces an m 1G37 modification into tRNA Met, altering its structure and function. J Biol Chem 2017; 293:1425-1438. [PMID: 29222331 DOI: 10.1074/jbc.ra117.000317] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/13/2017] [Indexed: 12/20/2022] Open
Abstract
Defective nucleotide modifications of mitochondrial tRNAs have been associated with several human diseases, but their pathophysiology remains poorly understood. In this report, we investigated the pathogenic molecular mechanism underlying a hypertension-associated 4435A→G mutation in mitochondrial tRNAMet The m.4435A→G mutation affected a highly conserved adenosine at position 37, 3' adjacent to the tRNA's anticodon, which is important for the fidelity of codon recognition and stabilization. We hypothesized that the m.4435A→G mutation introduced an m1G37 modification of tRNAMet, altering its structure and function. Primer extension and methylation activity assays indeed confirmed that the m.4435A→G mutation created a tRNA methyltransferase 5 (TRMT5)-catalyzed m1G37 modification of tRNAMet We found that this mutation altered the tRNAMet structure, indicated by an increased melting temperature and electrophoretic mobility of the mutated tRNA compared with the wildtype molecule. We demonstrated that cybrid cell lines carrying the m.4435A→G mutation exhibited significantly decreased efficiency in aminoacylation and steady-state levels of tRNAMet, as compared with those of control cybrids. The aberrant tRNAMet metabolism resulted in variable decreases in mitochondrial DNA (mtDNA)-encoded polypeptides in the mutant cybrids. Furthermore, we found that the m.4435A→G mutation caused respiratory deficiency, markedly diminished mitochondrial ATP levels and membrane potential, and increased the production of reactive oxygen species in mutant cybrids. These results demonstrated that an aberrant m1G37 modification of mitochondrial tRNAMet affected the structure and function of its tRNA and consequently altered mitochondrial function. Our findings provide critical insights into the pathophysiology of maternally inherited hypertension, which is manifested by the deficient tRNA nucleotide modification.
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Affiliation(s)
- Mi Zhou
- From the Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China.,the Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China
| | - Ling Xue
- the Attardi Institute of Mitochondrial Biomedicine and
| | - Yaru Chen
- the Attardi Institute of Mitochondrial Biomedicine and
| | - Haiying Li
- the Department of Cardiology, the First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325035 Zhejiang, China
| | - Qiufen He
- the Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China
| | - Bibin Wang
- the Attardi Institute of Mitochondrial Biomedicine and
| | - Feilong Meng
- From the Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China.,the Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China
| | - Meng Wang
- From the Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China.,the Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China
| | - Min-Xin Guan
- From the Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China, .,the Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China.,the Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, 310058 Zhejiang, China, and.,the Joining Institute of Genetics and Genomic Medicine between Zhejiang University and University of Toronto, Hangzhou, 310058 Zhejiang, China
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161
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Wan Makhtar WR, Browne G, Karountzos A, Stevens C, Alghamdi Y, Bottrill AR, Mistry S, Smith E, Bushel M, Pringle JH, Sayan AE, Tulchinsky E. Short stretches of rare codons regulate translation of the transcription factor ZEB2 in cancer cells. Oncogene 2017; 36:6640-6648. [PMID: 28783176 PMCID: PMC5681250 DOI: 10.1038/onc.2017.273] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/16/2017] [Accepted: 07/03/2017] [Indexed: 01/14/2023]
Abstract
Two proteins comprising the ZEB family of zinc finger transcription factors, ZEB1 and ZEB2, execute EMT programs in embryonic development and cancer. By studying regulation of their expression, we describe a novel mechanism that limits ZEB2 protein synthesis. A protein motif located at the border of the SMAD-binding domain of ZEB2 protein induces ribosomal pausing and compromises protein synthesis. The function of this protein motif is dependent on stretches of rare codons, Leu(UUA)-Gly(GGU)-Val(GUA). Incorporation of these triplets in the homologous region of ZEB1 does not affect protein translation. Our data suggest that rare codons have a regulatory role only if they are present within appropriate protein structures. We speculate that pools of transfer RNA available for protein translation impact on the configuration of epithelial mesenchymal transition pathways in tumor cells.
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Affiliation(s)
- W R Wan Makhtar
- Department of Cancer Studies, University of Leicester, Leicester, UK
- MRC Toxicology Unit, Leicester, UK
| | - G Browne
- Department of Cancer Studies, University of Leicester, Leicester, UK
| | - A Karountzos
- Department of Cancer Studies, University of Leicester, Leicester, UK
| | - C Stevens
- Department of Cancer Studies, University of Leicester, Leicester, UK
| | - Y Alghamdi
- Department of Cancer Studies, University of Leicester, Leicester, UK
| | - A R Bottrill
- Protein and Nucleic Acid Chemistry Laboratory (PNACL), University of Leicester, Leicester, UK
| | - S Mistry
- Protein and Nucleic Acid Chemistry Laboratory (PNACL), University of Leicester, Leicester, UK
| | - E Smith
- MRC Toxicology Unit, Leicester, UK
| | - M Bushel
- MRC Toxicology Unit, Leicester, UK
| | - J H Pringle
- Department of Cancer Studies, University of Leicester, Leicester, UK
| | - A E Sayan
- Cancer Sciences Division, University of Southampton, Southampton, UK
| | - E Tulchinsky
- Department of Cancer Studies, University of Leicester, Leicester, UK
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162
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Somatic mutation driven codon transition bias in human cancer. Sci Rep 2017; 7:14204. [PMID: 29079855 PMCID: PMC5660177 DOI: 10.1038/s41598-017-14543-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 10/12/2017] [Indexed: 12/14/2022] Open
Abstract
Accumulation of DNA mutations alters amino acid sequence in the key domains of oncoproteins, leading to cellular malignant transformation. Due to redundancy of the genetic code, the same amino acid alteration can be achieved by multiple distinct genetic mutations, which are considered functionally identical and not actively distinguished in the current cancer genome research. For the first time, we analyzed the distribution of codon level transitions acquired by somatic mutations in human cancers. By analyzing the ~2.5 million nonsynonymous somatic single nucleotide variations (SNVs) found in the COSMIC database, we found 41 recurrent amino acid alterations whose DNA changes are significantly biased toward a specific codon transition. Additional analyses partially identified functional discrepancies between the favored and avoided codon transitions in terms of mutational process, codon usage, alternative splicing, and mRNA stability.
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163
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Wong HE, Huang CJ, Zhang Z. Amino acid misincorporation in recombinant proteins. Biotechnol Adv 2017; 36:168-181. [PMID: 29107148 DOI: 10.1016/j.biotechadv.2017.10.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/12/2017] [Accepted: 10/24/2017] [Indexed: 11/26/2022]
Abstract
Proteins provide the molecular basis for cellular structure, catalytic activity, signal transduction, and molecular transport in biological systems. Recombinant protein expression is widely used to prepare and manufacture novel proteins that serve as the foundation of many biopharmaceutical products. However, protein translation bioprocesses are inherently prone to low-level errors. These sequence variants caused by amino acid misincorporation have been observed in both native and recombinant proteins. Protein sequence variants impact product quality, and their presence can be exacerbated through cellular stress, overexpression, and nutrient starvation. Therefore, the cell line selection process, which is used in the biopharmaceutical industry, is not only directed towards maximizing productivity, but also focuses on selecting clones which yield low sequence variant levels, thereby proactively avoiding potentially inauspicious patient safety and efficacy outcomes. Here, we summarize a number of hallmark studies aimed at understanding the mechanisms of amino acid misincorporation, as well as exacerbating factors, and mitigation strategies. We also describe key advances in analytical technologies in the identification and quantification of sequence variants, and some practical considerations when using LC-MS/MS for detecting sequence variants.
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Affiliation(s)
- H Edward Wong
- Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA 91320, United States
| | - Chung-Jr Huang
- Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA 91320, United States
| | - Zhongqi Zhang
- Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA 91320, United States.
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164
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Sabi R, Volvovitch Daniel R, Tuller T. stAIcalc: tRNA adaptation index calculator based on species-specific weights. Bioinformatics 2017; 33:589-591. [PMID: 27797757 DOI: 10.1093/bioinformatics/btw647] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 10/11/2016] [Indexed: 11/13/2022] Open
Abstract
Summary The tRNA Adaptation Index (tAI) is a tRNA-centric measure of translation efficiency which includes weights that take into account the efficiencies of the different wobble interactions. To enable the calculation of the index based on a species-specific inference of these weights, we created the stAI calc . The calculator includes optimized tAI weights for 100 species from the three domains of life along with a standalone software package that optimizes the weights for new organisms. The tAI with the optimized weights should enable performing large scale studies in disciplines such as molecular evolution, genomics, systems biology and synthetic biology. Availability and Implementation The calculator is publicly available at http://www.cs.tau.ac.il/∼tamirtul/stAIcalc/stAIcalc.html. Contact tamirtul@post.tau.ac.il.
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Affiliation(s)
| | | | - Tamir Tuller
- Department of Biomedical Engineering.,The Sagol School of Neuroscience, Tel Aviv University, Ramat Aviv, 69978, Israel
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165
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Transcription and translation of APOL1 variants. Biosci Rep 2017; 37:BSR20170647. [PMID: 28842513 PMCID: PMC5635210 DOI: 10.1042/bsr20170647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/21/2017] [Accepted: 08/23/2017] [Indexed: 01/05/2023] Open
Abstract
It is highly important to document the molecular alterations existing in normal cells prior to the onset of any disease. Knowledge of genetic mutations and associated molecular mechanisms will be helpful for better diagnosis and management of disease. The major focus of this commentary on providing understanding about the apolipoprotein 1 (APOL1) gene, the protein encoded by this gene (apoL1) and the mechanistic details regarding the role of apoL1 in the lysis of Trypanosoma brucei. Information about APOL1 genetic variants, APOL1G1 and APOL1G2, is provided along with the association of these variants with hypertension-attributed end-stage renal disease (ESRD) and focal segmental glomerulosclerosis (FSGS). Moreover, this commentary presents a brief overview of how the authors of a recent Bioscience Reports article [Haque et al (2017) 37, BSR20160531, doi: 10.1042/BSR20160531] have evaluated the functional impact of G1 and G2 alleles on the transcription and translation of APOL1 mRNA.
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166
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Hanson G, Coller J. Codon optimality, bias and usage in translation and mRNA decay. Nat Rev Mol Cell Biol 2017; 19:20-30. [PMID: 29018283 DOI: 10.1038/nrm.2017.91] [Citation(s) in RCA: 419] [Impact Index Per Article: 59.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The advent of ribosome profiling and other tools to probe mRNA translation has revealed that codon bias - the uneven use of synonymous codons in the transcriptome - serves as a secondary genetic code: a code that guides the efficiency of protein production, the fidelity of translation and the metabolism of mRNAs. Recent advancements in our understanding of mRNA decay have revealed a tight coupling between ribosome dynamics and the stability of mRNA transcripts; this coupling integrates codon bias into the concept of codon optimality, or the effects that specific codons and tRNA concentrations have on the efficiency and fidelity of the translation machinery. In this Review, we first discuss the evidence for codon-dependent effects on translation, beginning with the basic mechanisms through which translation perturbation can affect translation efficiency, protein folding and transcript stability. We then discuss how codon effects are leveraged by the cell to tailor the proteome to maintain homeostasis, execute specific gene expression programmes of growth or differentiation and optimize the efficiency of protein production.
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Affiliation(s)
- Gavin Hanson
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Jeff Coller
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, Ohio 44106, USA
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167
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Growth-Rate Dependent Regulation of tRNA Level and Charging in Bacillus licheniformis. J Mol Biol 2017; 429:3102-3112. [DOI: 10.1016/j.jmb.2017.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 09/09/2017] [Accepted: 09/09/2017] [Indexed: 11/21/2022]
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168
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Machado H, Tuttle RN, Jensen PR. Omics-based natural product discovery and the lexicon of genome mining. Curr Opin Microbiol 2017; 39:136-142. [PMID: 29175703 PMCID: PMC5732065 DOI: 10.1016/j.mib.2017.10.025] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/28/2017] [Indexed: 11/29/2022]
Abstract
Genome sequencing and the application of omic techniques are driving many important advances in the field of microbial natural products research. Despite these gains, there remain aspects of the natural product discovery pipeline where our knowledge remains poor. These include the extent to which biosynthetic gene clusters are transcriptionally active in native microbes, the temporal dynamics of transcription, translation, and natural product assembly, as well as the relationships between small molecule production and detection. Here we touch on a number of these concepts in the context of continuing efforts to unlock the natural product potential revealed in genome sequence data and discuss nomenclatural issues that warrant consideration as the field moves forward.
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Affiliation(s)
- Henrique Machado
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA
| | - Robert N Tuttle
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA; Center for Microbiome Innovation, University of California, San Diego, USA.
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169
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López-Madrigal S, Gil R. Et tu, Brute? Not Even Intracellular Mutualistic Symbionts Escape Horizontal Gene Transfer. Genes (Basel) 2017; 8:genes8100247. [PMID: 28961177 PMCID: PMC5664097 DOI: 10.3390/genes8100247] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/14/2017] [Accepted: 09/22/2017] [Indexed: 01/21/2023] Open
Abstract
Many insect species maintain mutualistic relationships with endosymbiotic bacteria. In contrast to their free-living relatives, horizontal gene transfer (HGT) has traditionally been considered rare in long-term endosymbionts. Nevertheless, meta-omics exploration of certain symbiotic models has unveiled an increasing number of bacteria-bacteria and bacteria-host genetic transfers. The abundance and function of transferred loci suggest that HGT might play a major role in the evolution of the corresponding consortia, enhancing their adaptive value or buffering detrimental effects derived from the reductive evolution of endosymbionts’ genomes. Here, we comprehensively review the HGT cases recorded to date in insect-bacteria mutualistic consortia, and discuss their impact on the evolutionary success of these associations.
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Affiliation(s)
- Sergio López-Madrigal
- Biologie Fonctionnelle Insectes et Interactions, UMR203 BF2I, INRA, INSA-Lyon, Université de Lyon, 69100 Villeurbanne, France.
| | - Rosario Gil
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València/CSIC, 46980 Paterna (València), Spain.
- Departament de Genètica, Universitat de València, Dr. Moliner, 50, 46100 Burjassot (València), Spain.
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170
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Espah Borujeni A, Cetnar D, Farasat I, Smith A, Lundgren N, Salis HM. Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences. Nucleic Acids Res 2017; 45:5437-5448. [PMID: 28158713 PMCID: PMC5435973 DOI: 10.1093/nar/gkx061] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/24/2017] [Indexed: 02/06/2023] Open
Abstract
A mRNA's translation rate is controlled by several sequence determinants, including the presence of RNA structures within the N-terminal regions of its coding sequences. However, the physical rules that govern when such mRNA structures will inhibit translation remain unclear. Here, we introduced systematically designed RNA hairpins into the N-terminal coding region of a reporter protein with steadily increasing distances from the start codon, followed by characterization of their mRNA and expression levels in Escherichia coli. We found that the mRNAs' translation rates were repressed, by up to 530-fold, when mRNA structures overlapped with the ribosome's footprint. In contrast, when the mRNA structure was located outside the ribosome's footprint, translation was repressed by <2-fold. By combining our measurements with biophysical modeling, we determined that the ribosomal footprint extends 13 nucleotides into the N-terminal coding region and, when a mRNA structure overlaps or partially overlaps with the ribosomal footprint, the free energy to unfold only the overlapping structure controlled the extent of translation repression. Overall, our results provide precise quantification of the rules governing translation initiation at N-terminal coding regions, improving the predictive design of post-transcriptional regulatory elements that regulate translation rate.
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Affiliation(s)
- Amin Espah Borujeni
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Daniel Cetnar
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Iman Farasat
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ashlee Smith
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Natasha Lundgren
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Howard M Salis
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA.,Department of Biological Engineering, The Pennsylvania State University, University Park, PA 16802, USA
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171
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Pal S, Sarkar I, Roy A, Mohapatra PKD, Mondal KC, Sen A. Comparative evolutionary genomics of Corynebacterium with special reference to codon and amino acid usage diversities. Genetica 2017; 146:13-27. [DOI: 10.1007/s10709-017-9986-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/11/2017] [Indexed: 11/28/2022]
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172
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Thoring L, Dondapati SK, Stech M, Wüstenhagen DA, Kubick S. High-yield production of "difficult-to-express" proteins in a continuous exchange cell-free system based on CHO cell lysates. Sci Rep 2017; 7:11710. [PMID: 28916746 PMCID: PMC5601898 DOI: 10.1038/s41598-017-12188-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 09/06/2017] [Indexed: 11/10/2022] Open
Abstract
Cell-free protein synthesis (CFPS) represents a promising technology for efficient protein production targeting especially so called "difficult-to-express" proteins whose synthesis is challenging in conventional in vivo protein production platforms. Chinese hamster ovary (CHO) cells are one of the most prominent and safety approved cell lines for industrial protein production. In this study we demonstrated the ability to produce high yields of various protein types including membrane proteins and single chain variable fragments (scFv) in a continuous exchange cell-free (CECF) system based on CHO cell lysate that contains endogenous microsomal structures. We showed significant improvement of protein yield compared to batch formatted reactions and proved biological activity of synthesized proteins using various analysis technologies. Optimized CECF reaction conditions led to membrane protein yields up to 980 µg/ml, which is the highest protein yield reached in a microsome containing eukaryotic cell-free system presented so far.
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Affiliation(s)
- Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany
- Institute for Biotechnology, Technical University of Berlin (TUB), Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Srujan K Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany
| | - Doreen A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany.
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173
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Thoring L, Dondapati SK, Stech M, Wüstenhagen DA, Kubick S. High-yield production of "difficult-to-express" proteins in a continuous exchange cell-free system based on CHO cell lysates. Sci Rep 2017; 7:11710. [PMID: 28916746 DOI: 10.1038/s41598-017-12188-12188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 09/06/2017] [Indexed: 05/28/2023] Open
Abstract
Cell-free protein synthesis (CFPS) represents a promising technology for efficient protein production targeting especially so called "difficult-to-express" proteins whose synthesis is challenging in conventional in vivo protein production platforms. Chinese hamster ovary (CHO) cells are one of the most prominent and safety approved cell lines for industrial protein production. In this study we demonstrated the ability to produce high yields of various protein types including membrane proteins and single chain variable fragments (scFv) in a continuous exchange cell-free (CECF) system based on CHO cell lysate that contains endogenous microsomal structures. We showed significant improvement of protein yield compared to batch formatted reactions and proved biological activity of synthesized proteins using various analysis technologies. Optimized CECF reaction conditions led to membrane protein yields up to 980 µg/ml, which is the highest protein yield reached in a microsome containing eukaryotic cell-free system presented so far.
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Affiliation(s)
- Lena Thoring
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany
- Institute for Biotechnology, Technical University of Berlin (TUB), Gustav-Meyer-Allee 25, 13355, Berlin, Germany
| | - Srujan K Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany
| | - Doreen A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, D-14476, Potsdam, Germany.
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174
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Göertz GP, Abbo SR, Fros JJ, Pijlman GP. Functional RNA during Zika virus infection. Virus Res 2017; 254:41-53. [PMID: 28864425 DOI: 10.1016/j.virusres.2017.08.015] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/28/2017] [Accepted: 08/28/2017] [Indexed: 12/24/2022]
Abstract
Zika virus (ZIKV; family Flaviviridae; genus Flavivirus) is a pathogenic mosquito-borne RNA virus that currently threatens human health in the Americas, large parts of Asia and occasionally elsewhere in the world. ZIKV infection is often asymptomatic but can cause severe symptoms including congenital microcephaly and Guillain-Barré syndrome. The positive single-stranded RNA genome of the mosquito-borne ZIKV requires effective replication in two evolutionary distinct hosts - mosquitoes and primates. In addition to some of the viral proteins, the ZIKV genomic RNA and functional RNAs produced thereof aid in the establishment of productive infection and the evasion of host cell antiviral responses. ZIKV has evolved to contain a nucleotide composition and RNA modifications, such as methylation and the formation of G-quadruplexes that allow effective replication in both hosts. Furthermore, a number of host factors interact with the viral genome to modulate RNA replication. Importantly, the ZIKV genome produces non-coding subgenomic flavivirus RNA (sfRNA) due to stalling of host 5'- 3' ribonucleases on viral RNA structures in the 3' untranslated region (UTR). This sfRNA (sfRNA) exerts important proviral functions such as antagonizing the innate interferon response and RNA interference. Here, we discuss the ZIKV genomic RNA and functional RNAs thereof to assess their significance during ZIKV infection. Understanding the details of the ZIKV infection cycle will aid in the development of effective antiviral strategies and safe vaccines.
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Affiliation(s)
- Giel P Göertz
- Laboratory of Virology, Wageningen University & Research, Wageningen, The Netherlands.
| | - Sandra R Abbo
- Laboratory of Virology, Wageningen University & Research, Wageningen, The Netherlands.
| | - Jelke J Fros
- Laboratory of Virology, Wageningen University & Research, Wageningen, The Netherlands; Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK.
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University & Research, Wageningen, The Netherlands.
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175
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Constraints and consequences of the emergence of amino acid repeats in eukaryotic proteins. Nat Struct Mol Biol 2017; 24:765-777. [PMID: 28805808 DOI: 10.1038/nsmb.3441] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/23/2017] [Indexed: 12/21/2022]
Abstract
Proteins with amino acid homorepeats have the potential to be detrimental to cells and are often associated with human diseases. Why, then, are homorepeats prevalent in eukaryotic proteomes? In yeast, homorepeats are enriched in proteins that are essential and pleiotropic and that buffer environmental insults. The presence of homorepeats increases the functional versatility of proteins by mediating protein interactions and facilitating spatial organization in a repeat-dependent manner. During evolution, homorepeats are preferentially retained in proteins with stringent proteostasis, which might minimize repeat-associated detrimental effects such as unregulated phase separation and protein aggregation. Their presence facilitates rapid protein divergence through accumulation of amino acid substitutions, which often affect linear motifs and post-translational-modification sites. These substitutions may result in rewiring protein interaction and signaling networks. Thus, homorepeats are distinct modules that are often retained in stringently regulated proteins. Their presence facilitates rapid exploration of the genotype-phenotype landscape of a population, thereby contributing to adaptation and fitness.
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176
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Villada JC, Brustolini OJB, Batista da Silveira W. Integrated analysis of individual codon contribution to protein biosynthesis reveals a new approach to improving the basis of rational gene design. DNA Res 2017; 24:419-434. [PMID: 28449100 PMCID: PMC5737324 DOI: 10.1093/dnares/dsx014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 01/21/2023] Open
Abstract
Gene codon optimization may be impaired by the misinterpretation of frequency and optimality of codons. Although recent studies have revealed the effects of codon usage bias (CUB) on protein biosynthesis, an integrated perspective of the biological role of individual codons remains unknown. Unlike other previous studies, we show, through an integrated framework that attributes of codons such as frequency, optimality and positional dependency should be combined to unveil individual codon contribution for protein biosynthesis. We designed a codon quantification method for assessing CUB as a function of position within genes with a novel constraint: the relativity of position-dependent codon usage shaped by coding sequence length. Thus, we propose a new way of identifying the enrichment, depletion and non-uniform positional distribution of codons in different regions of yeast genes. We clustered codons that shared attributes of frequency and optimality. The cluster of non-optimal codons with rare occurrence displayed two remarkable characteristics: higher codon decoding time than frequent-non-optimal cluster and enrichment at the 5'-end region, where optimal codons with the highest frequency are depleted. Interestingly, frequent codons with non-optimal adaptation to tRNAs are uniformly distributed in the Saccharomyces cerevisiae genes, suggesting their determinant role as a speed regulator in protein elongation.
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Affiliation(s)
- Juan C. Villada
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa 36570-900, Brazil
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177
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Abstract
Mistranslation errors compromise fitness by wasting resources on nonfunctional proteins. In order to reduce the cost of mistranslations, natural selection chooses the most accurately translated codons at sites that are particularly important for protein structure and function. We investigated the determinants underlying selection for translational accuracy in several species of plants belonging to three clades: Brassicaceae, Fabidae, and Poaceae. Although signatures of translational selection were found in genes from a wide range of species, the underlying factors varied in nature and intensity. Indeed, the degree of synonymous codon bias at evolutionarily conserved sites varied among plant clades while remaining uniform within each clade. This is unlikely to solely reflect the diversity of tRNA pools because there is little correlation between synonymous codon bias and tRNA abundance, so other factors must affect codon choice and translational accuracy in plant genes. Accordingly, synonymous codon choice at a given site was affected not only by the selection pressure at that site, but also its participation in protein domains or mRNA secondary structures. Although these effects were detected in all the species we analyzed, their impact on translation accuracy was distinct in evolutionarily distant plant clades. The domain effect was found to enhance translational accuracy in dicot and monocot genes with a high GC content, but to oppose the selection of more accurate codons in monocot genes with a low GC content.
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178
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Sabi R, Tuller T. Computational analysis of nascent peptides that induce ribosome stalling and their proteomic distribution in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2017; 23:983-994. [PMID: 28363900 PMCID: PMC5473148 DOI: 10.1261/rna.059188.116] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 03/24/2017] [Indexed: 05/14/2023]
Abstract
Interactions between the ribosomal exit tunnel and the nascent peptide can affect translation elongation rates. While previous studies have already demonstrated the feasibility of such interactions, little is known about the nature of the stalling peptide sequences and their distribution in the proteome. Here we ask which peptide sequences tend to occupy the tunnel of stalled ribosomes and how they are distributed in the proteome. Using computational analysis of ribosome profiling data from S. cerevisiae, we identified for the first time dozens of short stalling peptide sequences and studied their statistical properties. We found that short peptide sequences associated with ribosome stalling tend significantly to be either over- or underrepresented in the proteome. We then showed that the stalling interactions may occur at different positions along the length of the tunnel, prominently close to the P-site. Our findings throw light on the determinants of nascent peptide-mediated ribosome stalling during translation elongation and support the novel conjecture that mRNA translation affects the proteomic distribution of short peptide sequences.
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Affiliation(s)
- Renana Sabi
- Department of Biomedical Engineering, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Ramat Aviv 69978, Israel
- The Sagol School of Neuroscience, Tel Aviv University, Ramat Aviv 69978, Israel
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179
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Grelet S, McShane A, Geslain R, Howe PH. Pleiotropic Roles of Non-Coding RNAs in TGF-β-Mediated Epithelial-Mesenchymal Transition and Their Functions in Tumor Progression. Cancers (Basel) 2017; 9:cancers9070075. [PMID: 28671581 PMCID: PMC5532611 DOI: 10.3390/cancers9070075] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/21/2017] [Accepted: 06/30/2017] [Indexed: 12/12/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a spatially- and temporally-regulated process involved in physiological and pathological transformations, such as embryonic development and tumor progression. While the role of TGF-β as an EMT-inducer has been extensively documented, the molecular mechanisms regulating this transition and their implications in tumor metastasis are still subjects of intensive debates and investigations. TGF-β regulates EMT through both transcriptional and post-transcriptional mechanisms, and recent advances underline the critical roles of non-coding RNAs in these processes. Although microRNAs and lncRNAs have been clearly identified as effectors of TGF-β-mediated EMT, the contributions of other atypical non-coding RNA species, such as piRNAs, snRNAs, snoRNAs, circRNAs, and even housekeeping tRNAs, have only been suggested and remain largely elusive. This review discusses the current literature including the most recent reports emphasizing the regulatory functions of non-coding RNA in TGF-β-mediated EMT, provides original experimental evidence, and advocates in general for a broader approach in the quest of new regulatory RNAs.
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Affiliation(s)
- Simon Grelet
- Department of Biochemistry and Molecular Biology, MUSC, Charleston, SC 29425, USA.
| | - Ariel McShane
- Laboratory of tRNA Biology, Department of Biology, College of Charleston, Charleston, SC 29424, USA.
| | - Renaud Geslain
- Laboratory of tRNA Biology, Department of Biology, College of Charleston, Charleston, SC 29424, USA.
| | - Philip H Howe
- Department of Biochemistry and Molecular Biology, MUSC, Charleston, SC 29425, USA.
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180
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Fu J, Murphy KA, Zhou M, Li YH, Lam VH, Tabuloc CA, Chiu JC, Liu Y. Codon usage affects the structure and function of the Drosophila circadian clock protein PERIOD. Genes Dev 2017; 30:1761-75. [PMID: 27542830 PMCID: PMC5002980 DOI: 10.1101/gad.281030.116] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/15/2016] [Indexed: 11/25/2022]
Abstract
Fu et al. show that Drosophila period (dper) codon usage is important for circadian clock function. Codon optimization of dper resulted in conformational changes of dPER protein, altered dPER phosphorylation profile and stability, and impaired dPER function in the circadian negative feedback loop, which manifests into changes in molecular rhythmicity and abnormal circadian behavioral output. Codon usage bias is a universal feature of all genomes, but its in vivo biological functions in animal systems are not clear. To investigate the in vivo role of codon usage in animals, we took advantage of the sensitivity and robustness of the Drosophila circadian system. By codon-optimizing parts of Drosophila period (dper), a core clock gene that encodes a critical component of the circadian oscillator, we showed that dper codon usage is important for circadian clock function. Codon optimization of dper resulted in conformational changes of the dPER protein, altered dPER phosphorylation profile and stability, and impaired dPER function in the circadian negative feedback loop, which manifests into changes in molecular rhythmicity and abnormal circadian behavioral output. This study provides an in vivo example that demonstrates the role of codon usage in determining protein structure and function in an animal system. These results suggest a universal mechanism in eukaryotes that uses a codon usage “code” within genetic codons to regulate cotranslational protein folding.
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Affiliation(s)
- Jingjing Fu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Katherine A Murphy
- Department of Entomology and Nematology, University of California at Davis, Davis, California 95616, USA
| | - Mian Zhou
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Ying H Li
- Department of Entomology and Nematology, University of California at Davis, Davis, California 95616, USA
| | - Vu H Lam
- Department of Entomology and Nematology, University of California at Davis, Davis, California 95616, USA
| | - Christine A Tabuloc
- Department of Entomology and Nematology, University of California at Davis, Davis, California 95616, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, University of California at Davis, Davis, California 95616, USA
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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181
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Abstract
The elucidation of the genetic code remains among the most influential discoveries in biology. While innumerable studies have validated the general universality of the code and its value in predicting and analyzing protein coding sequences, established and emerging work has also suggested that full genome decryption may benefit from a greater consideration of a codon's neighborhood within an mRNA than has been broadly applied. This Review examines the evidence for context cues in translation, with a focus on several recent studies that reveal broad roles for mRNA context in programming translation start sites, the rate of translation elongation, and stop codon identity.
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182
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Tokizawa M, Kusunoki K, Koyama H, Kurotani A, Sakurai T, Suzuki Y, Sakamoto T, Kurata T, Yamamoto YY. Identification of Arabidopsis genic and non-genic promoters by paired-end sequencing of TSS tags. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:587-605. [PMID: 28214361 DOI: 10.1111/tpj.13511] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 02/02/2017] [Accepted: 02/06/2017] [Indexed: 06/06/2023]
Abstract
Information about transcription start sites (TSSs) provides baseline data for the analysis of promoter architecture. In this paper we used paired- and single-end deep sequencing to analyze Arabidopsis TSS tags from several libraries prepared from roots, shoots, flowers and etiolated seedlings. The clustering of approximately 33 million mapped TSS tags led to the identification of 324 461 promoters that covered 79.7% (21 672/27 206) of protein-coding genes in the Arabidopsis genome. In addition we identified intragenic, antisense and orphan promoters that were not associated with any gene models. Of these, intragenic promoters exhibited unique characteristics regarding dinucleotide sequences at TSSs and core promoter element composition, suggesting that these promoters use different mechanisms of transcriptional initiation. An analysis of base composition with regard to promoter position revealed a low GC content throughout the promoter region and several local strand biases that were evident for TATA-type promoters, but not for Coreless-type promoters. Most observed strand biases coincided with strand biases of single nucleotide polymorphism rate. Our analysis also revealed that transcription of a gene is supported by an average of 2.7 genic promoters, among which one specific promoter, designated as a top promoter, substantially determines the expression level of the gene.
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Affiliation(s)
- Mutsutomo Tokizawa
- United Graduate School of Agriculture, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan
| | - Kazutaka Kusunoki
- United Graduate School of Agriculture, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan
| | - Hiroyuki Koyama
- United Graduate School of Agriculture, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan
- Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan
| | - Atsushi Kurotani
- RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Tetsuya Sakurai
- RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yutaka Suzuki
- Institute of Medical Science, University of Tokyo, Shiroganedai 4-6-1, Minato-ku, Tokyo, 108-8639, Japan
| | - Tomoaki Sakamoto
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayam-cho 8916-5, Ikoma, Nara, 630-0192, Japan
| | - Tetsuya Kurata
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayam-cho 8916-5, Ikoma, Nara, 630-0192, Japan
| | - Yoshiharu Y Yamamoto
- United Graduate School of Agriculture, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan
- Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan
- RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- JST ALCA, Tokyo, Japan
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183
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Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast. Cell Syst 2017; 4:495-504.e5. [PMID: 28365149 DOI: 10.1016/j.cels.2017.03.003] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 01/31/2017] [Accepted: 03/01/2017] [Indexed: 11/22/2022]
Abstract
Protein synthesis is the most energy-consuming process in a proliferating cell, and understanding what controls protein abundances represents a key question in biology and biotechnology. We quantified absolute abundances of 5,354 mRNAs and 2,198 proteins in Saccharomyces cerevisiae under ten environmental conditions and protein turnover for 1,384 proteins under a reference condition. The overall correlation between mRNA and protein abundances across all conditions was low (0.46), but for differentially expressed proteins (n = 202), the median mRNA-protein correlation was 0.88. We used these data to model translation efficiencies and found that they vary more than 400-fold between genes. Non-linear regression analysis detected that mRNA abundance and translation elongation were the dominant factors controlling protein synthesis, explaining 61% and 15% of its variance. Metabolic flux balance analysis further showed that only mitochondrial fluxes were positively associated with changes at the transcript level. The present dataset represents a crucial expansion to the current resources for future studies on yeast physiology.
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184
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Yi JS, Kim MW, Kim M, Jeong Y, Kim EJ, Cho BK, Kim BG. A Novel Approach for Gene Expression Optimization through Native Promoter and 5' UTR Combinations Based on RNA-seq, Ribo-seq, and TSS-seq of Streptomyces coelicolor. ACS Synth Biol 2017; 6:555-565. [PMID: 27966890 DOI: 10.1021/acssynbio.6b00263] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Streptomycetes are Gram-positive mycelial bacteria, which synthesize a wide range of natural products including over two-thirds of the currently available antibiotics. However, metabolic engineering in Streptomyces species to overproduce a vast of natural products are hampered by a limited number of genetic tools. Here, two promoters and four 5' UTR sequences showing constant strengths were selected based upon multiomics data sets from Streptomyces coelicolor M145, including RNA-seq, Ribo-seq, and TSS-seq, for controllable transcription and translation. A total eight sets of promoter/5' UTR combinations, with minimal interferences of promoters on translation, were constructed using the transcription start site information, and evaluated with the GusA system. Expression of GusA could be controlled to various strengths in three different media, in a range of 0.03- to 2.4-fold, compared to that of the control, ermE*P/Shine-Dalgarno sequence. This method was applied to engineer three previously reported promoters to enhance gene expressions. The expressions of ActII-ORF4 and MetK were also tuned for actinorhodin overproductions in S. coelicolor as examples. In summary, we provide a novel approach and tool for optimizations of gene expressions in Streptomyces coelicolor.
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Affiliation(s)
| | | | | | - Yujin Jeong
- Department
of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | | | - Byung-Kwan Cho
- Department
of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Intelligent Synthetic
Biology Center, Daejeon 34141, Republic of Korea
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185
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McCarthy C, Carrea A, Diambra L. Bicodon bias can determine the role of synonymous SNPs in human diseases. BMC Genomics 2017; 18:227. [PMID: 28288557 PMCID: PMC5347174 DOI: 10.1186/s12864-017-3609-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 03/04/2017] [Indexed: 01/09/2023] Open
Abstract
Background For a long time synonymous single nucleotide polymorphisms were considered as silent mutations. However, nowadays it is well known that they can affect protein conformation and function, leading to altered disease susceptibilities, differential prognosis and/or drug responses, among other clinically relevant genetic traits. This occurs through different mechanisms: by disrupting the splicing signals of precursor mRNAs, affecting regulatory binding-sites of transcription factors and miRNAs, or by modifying the secondary structure of mRNAs. Results In this paper we considered 22 human genetic diseases or traits, linked to 35 synonymous single nucleotide polymorphisms in 27 different genes. We performed a local sequence context analysis in terms of the ribosomal pause propensity affected by synonymous single nucleotide polymorphisms. We found that synonymous mutations related to the above mentioned mechanisms presented small pause propensity changes, whereas synonymous mutations that were not related to those mechanisms presented large pause propensity changes. On the other hand, we did not observe large variations in the codon usage of codons associated with these mutations. Furthermore, we showed that the changes in the pause propensity associated with benign sSNPs are significantly lower than the pause propensity changes related to sSNPs associated to diseases. Conclusions These results suggest that the genetic diseases or traits related to synonymous mutations with large pause propensity changes, could be the consequence of another mechanism underlying non-silent synonymous mutations. Namely, alternative protein configuration related, in turn, to alterations in the ribosome-mediated translational attenuation program encoded by pairs of consecutive codons, not codons. These findings shed light on the latter mechanism based on the perturbation of the co-translational folding process. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3609-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christina McCarthy
- Centro Regional de Estudio Génomicos, Universidad Nacional de La Plata, Boulevard 120, La Plata, Argentina.,CONICET, Buenos Aires, Argentina.,Departamento de Informática y Tecnología, Escuela de Ciencias Agrarias, Naturales y Ambientales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Pergamino, Argentina
| | - Alejandra Carrea
- Centro Regional de Estudio Génomicos, Universidad Nacional de La Plata, Boulevard 120, La Plata, Argentina.,CONICET, Buenos Aires, Argentina
| | - Luis Diambra
- Centro Regional de Estudio Génomicos, Universidad Nacional de La Plata, Boulevard 120, La Plata, Argentina. .,CONICET, Buenos Aires, Argentina.
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186
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Cenik C, Chua HN, Singh G, Akef A, Snyder MP, Palazzo AF, Moore MJ, Roth FP. A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification. RNA (NEW YORK, N.Y.) 2017; 23:270-283. [PMID: 27994090 PMCID: PMC5311483 DOI: 10.1261/rna.059105.116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/14/2016] [Indexed: 06/01/2023]
Abstract
Introns are found in 5' untranslated regions (5'UTRs) for 35% of all human transcripts. These 5'UTR introns are not randomly distributed: Genes that encode secreted, membrane-bound and mitochondrial proteins are less likely to have them. Curiously, transcripts lacking 5'UTR introns tend to harbor specific RNA sequence elements in their early coding regions. To model and understand the connection between coding-region sequence and 5'UTR intron status, we developed a classifier that can predict 5'UTR intron status with >80% accuracy using only sequence features in the early coding region. Thus, the classifier identifies transcripts with 5' proximal-intron-minus-like-coding regions ("5IM" transcripts). Unexpectedly, we found that the early coding sequence features defining 5IM transcripts are widespread, appearing in 21% of all human RefSeq transcripts. The 5IM class of transcripts is enriched for non-AUG start codons, more extensive secondary structure both preceding the start codon and near the 5' cap, greater dependence on eIF4E for translation, and association with ER-proximal ribosomes. 5IM transcripts are bound by the exon junction complex (EJC) at noncanonical 5' proximal positions. Finally, N1-methyladenosines are specifically enriched in the early coding regions of 5IM transcripts. Taken together, our analyses point to the existence of a distinct 5IM class comprising ∼20% of human transcripts. This class is defined by depletion of 5' proximal introns, presence of specific RNA sequence features associated with low translation efficiency, N1-methyladenosines in the early coding region, and enrichment for noncanonical binding by the EJC.
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Affiliation(s)
- Can Cenik
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Hon Nian Chua
- Donnelly Centre, Department of Molecular Genetics, and Department of Computer Science, University of Toronto, Toronto M5S 3E1, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto M5G 1X5, Ontario, Canada
- DataRobot, Inc., Boston, Massachusetts 02109, USA
| | - Guramrit Singh
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- Department of Molecular Genetics, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Abdalla Akef
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alexander F Palazzo
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Melissa J Moore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Frederick P Roth
- Donnelly Centre, Department of Molecular Genetics, and Department of Computer Science, University of Toronto, Toronto M5S 3E1, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto M5G 1X5, Ontario, Canada
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston 02215, Massachusetts, USA
- The Canadian Institute for Advanced Research, Toronto M5G 1Z8, Ontario, Canada
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187
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Role of Eukaryotic Initiation Factors during Cellular Stress and Cancer Progression. J Nucleic Acids 2016; 2016:8235121. [PMID: 28083147 PMCID: PMC5204094 DOI: 10.1155/2016/8235121] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 11/14/2016] [Indexed: 12/12/2022] Open
Abstract
Protein synthesis can be segmented into distinct phases comprising mRNA translation initiation, elongation, and termination. Translation initiation is a highly regulated and rate-limiting step of protein synthesis that requires more than 12 eukaryotic initiation factors (eIFs). Extensive evidence shows that the transcriptome and corresponding proteome do not invariably correlate with each other in a variety of contexts. In particular, translation of mRNAs specific to angiogenesis, tumor development, and apoptosis is altered during physiological and pathophysiological stress conditions. In cancer cells, the expression and functions of eIFs are hampered, resulting in the inhibition of global translation and enhancement of translation of subsets of mRNAs by alternative mechanisms. A precise understanding of mechanisms involving eukaryotic initiation factors leading to differential protein expression can help us to design better strategies to diagnose and treat cancer. The high spatial and temporal resolution of translation control can have an immediate effect on the microenvironment of the cell in comparison with changes in transcription. The dysregulation of mRNA translation mechanisms is increasingly being exploited as a target to treat cancer. In this review, we will focus on this context by describing both canonical and noncanonical roles of eIFs, which alter mRNA translation.
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188
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Frumkin I, Schirman D, Rotman A, Li F, Zahavi L, Mordret E, Asraf O, Wu S, Levy SF, Pilpel Y. Gene Architectures that Minimize Cost of Gene Expression. Mol Cell 2016; 65:142-153. [PMID: 27989436 DOI: 10.1016/j.molcel.2016.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/10/2016] [Accepted: 11/01/2016] [Indexed: 11/30/2022]
Abstract
Gene expression burdens cells by consuming resources and energy. While numerous studies have investigated regulation of expression level, little is known about gene design elements that govern expression costs. Here, we ask how cells minimize production costs while maintaining a given protein expression level and whether there are gene architectures that optimize this process. We measured fitness of ∼14,000 E. coli strains, each expressing a reporter gene with a unique 5' architecture. By comparing cost-effective and ineffective architectures, we found that cost per protein molecule could be minimized by lowering transcription levels, regulating translation speeds, and utilizing amino acids that are cheap to synthesize and that are less hydrophobic. We then examined natural E. coli genes and found that highly expressed genes have evolved more forcefully to minimize costs associated with their expression. Our study thus elucidates gene design elements that improve the economy of protein expression in natural and heterologous systems.
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Affiliation(s)
- Idan Frumkin
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Dvir Schirman
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Aviv Rotman
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Fangfei Li
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Liron Zahavi
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ernest Mordret
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Omer Asraf
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Song Wu
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Sasha F Levy
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel.
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189
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Incarnato D, Oliviero S. The RNA Epistructurome: Uncovering RNA Function by Studying Structure and Post-Transcriptional Modifications. Trends Biotechnol 2016; 35:318-333. [PMID: 27988057 DOI: 10.1016/j.tibtech.2016.11.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/11/2016] [Accepted: 11/21/2016] [Indexed: 01/15/2023]
Abstract
A large fraction of higher metazoan genomes transcribe RNA molecules whose functions extend far beyond carrying instructions for protein synthesis. Although RNA is apparently a simple molecule, the ways in which it performs many of its functions have remained highly elusive for decades. As learned from studying ribosomal and transfer RNAs, two of the key features influencing the function of RNA are its structure and post-transcriptional modifications. A deep understanding of RNA function therefore requires rapid and straightforward approaches to study the complex and intricate landscape of RNA structures and modifications. In this review we summarize and discuss the most recent methods and findings in the field of RNA biology, with an eye toward new frontiers and open questions.
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Affiliation(s)
- Danny Incarnato
- Human Genetics Foundation (HuGeF), Via Nizza 52, 10126 Torino, Italy; Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, Torino, Italy.
| | - Salvatore Oliviero
- Human Genetics Foundation (HuGeF), Via Nizza 52, 10126 Torino, Italy; Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, Torino, Italy.
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190
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RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq. Cell Syst 2016; 3:563-571.e6. [PMID: 28009265 DOI: 10.1016/j.cels.2016.11.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 05/25/2016] [Accepted: 11/08/2016] [Indexed: 01/30/2023]
Abstract
Synonymous codon choices at the beginning of genes optimize 5' RNA structures for enhanced translation initiation, but less is known about mechanisms that drive codon optimization downstream within the gene. To understand what determines codon choices across a gene, we generated 12,726 in situ codon mutants in the Escherichia coli essential gene infA and measured their fitness by combining multiplex automated genome engineering mutagenesis with amplicon deep sequencing (MAGE-seq). Correlating predicted 5' RNA structure with fitness revealed that codons even far from the start of the gene are deleterious if they disrupt the native 5' RNA conformation. These long-range structural interactions generate context-dependent rules that constrain codon choices beyond intrinsic codon preferences. Genome-wide RNA folding predictions confirm that natural codon choices far from the start codon are optimized in part to prevent disruption of native structures near the 5' UTR. Our results shed light on natural codon distributions and should improve engineering of gene expression for synthetic biology applications.
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191
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Inoo K, Inagaki R, Fujiwara K, Sasawatari S, Kamigaki T, Nakagawa S, Okada N. Immunological quality and performance of tumor vessel-targeting CAR-T cells prepared by mRNA-EP for clinical research. MOLECULAR THERAPY-ONCOLYTICS 2016; 3:16024. [PMID: 27909701 PMCID: PMC5111575 DOI: 10.1038/mto.2016.24] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 08/14/2016] [Accepted: 08/27/2016] [Indexed: 01/03/2023]
Abstract
We previously reported that tumor vessel-redirected T cells, which were genetically engineered with chimeric antigen receptor (CAR) specific for vascular endothelial growth factor receptor 2 (VEGFR2), demonstrated significant antitumor effects in various murine solid tumor models. In the present study, we prepared anti-VEGFR2 CAR-T cells by CAR-coding mRNA electroporation (mRNA-EP) and analyzed their immunological characteristics and functions for use in clinical research. The expression of anti-VEGFR2 CAR on murine and human T cells was detected with approximately 100% efficiency for a few days, after peaking 6-12 hours after mRNA-EP. Triple transfer of murine anti-VEGFR2 CAR-T cells into B16BL6 tumor-bearing mice demonstrated an antitumor effect comparable to that for the single transfer of CAR-T cells engineered with retroviral vector. The mRNA-EP did not cause any damage or defects to human T-cell characteristics, as determined by viability, growth, and phenotypic parameters. Additionally, two kinds of human anti-VEGFR2 CAR-T cells, which expressed different CAR construction, differentiated to effector phase with cytokine secretion and cytotoxic activity in antigen-specific manner. These results indicate that our anti-VEGFR2 CAR-T cells prepared by mRNA-EP have the potential in terms of quality and performance to offer the prospect of safety and efficacy in clinical research as cellular medicine.
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Affiliation(s)
- Kanako Inoo
- Laboratory of Biotechnology and Therapeutics, Graduate School of Pharmaceutical Sciences, Osaka University , Osaka, Japan
| | - Ryo Inagaki
- Laboratory of Biotechnology and Therapeutics, Graduate School of Pharmaceutical Sciences, Osaka University , Osaka, Japan
| | - Kento Fujiwara
- Laboratory of Biotechnology and Therapeutics, Graduate School of Pharmaceutical Sciences, Osaka University , Osaka, Japan
| | | | - Takashi Kamigaki
- MEDINET Co., Ltd., Kanagawa, Japan; Seta Clinic Group, Tokyo, Japan
| | - Shinsaku Nakagawa
- Laboratory of Biotechnology and Therapeutics, Graduate School of Pharmaceutical Sciences, Osaka University , Osaka, Japan
| | - Naoki Okada
- Laboratory of Biotechnology and Therapeutics, Graduate School of Pharmaceutical Sciences, Osaka University , Osaka, Japan
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192
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Depletion of Shine-Dalgarno Sequences Within Bacterial Coding Regions Is Expression Dependent. G3-GENES GENOMES GENETICS 2016; 6:3467-3474. [PMID: 27605518 PMCID: PMC5100845 DOI: 10.1534/g3.116.032227] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Efficient and accurate protein synthesis is crucial for organismal survival in competitive environments. Translation efficiency (the number of proteins translated from a single mRNA in a given time period) is the combined result of differential translation initiation, elongation, and termination rates. Previous research identified the Shine-Dalgarno (SD) sequence as a modulator of translation initiation in bacterial genes, while codon usage biases are frequently implicated as a primary determinant of elongation rate variation. Recent studies have suggested that SD sequences within coding sequences may negatively affect translation elongation speed, but this claim remains controversial. Here, we present a metric to quantify the prevalence of SD sequences in coding regions. We analyze hundreds of bacterial genomes and find that the coding sequences of highly expressed genes systematically contain fewer SD sequences than expected, yielding a robust correlation between the normalized occurrence of SD sites and protein abundances across a range of bacterial taxa. We further show that depletion of SD sequences within ribosomal protein genes is correlated with organismal growth rates, supporting the hypothesis of strong selection against the presence of these sequences in coding regions and suggesting their association with translation efficiency in bacteria.
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193
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Huang C, Wang Y, Fan H, Ma X, Tang R, Huan X, Zhu Y, Xu Z, Xu H, Yang L. Association analysis of DACT1 genetic variants and gastric cancer risk in a Chinese Han population: a case-control study. Onco Targets Ther 2016; 9:5975-5983. [PMID: 27729806 PMCID: PMC5047710 DOI: 10.2147/ott.s109899] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Purpose Disheveled-binding antagonist of beta-catenin 1 (DACT1) is involved in tumorigenesis through influencing cell apoptosis and proliferation. We aimed to investigate the effect of three tag single-nucleotide polymorphisms (SNPs) in DACT1 (rs863091 C>T, rs17832998 C>T, and rs167481 C>T) on the occurrence of gastric cancer (GC), their association with specific clinical characteristics, and consideration of the functional relevance of GC-related SNPs. Subjects and methods In this hospital-based case–control study, the genotypes were acquired using the TaqMan-MGB method consisting of 602 cases and 602 controls. DACT1 messenger RNA level was evaluated in 76 paired tumoral and normal tissues using quantitative reverse transcription–polymerase chain reaction. Logistic regression was used to evaluate the associations among the DACT1 SNPs and GC. Results We found a significant association between the variant genotypes of rs863091 and decreased risk of GC (TT vs CC: P=0.009, adjusted odds ratio =0.34, 95% confidence interval =0.15–0.77; CT + TT vs CC: P=0.030, adjusted odds ratio =0.74, 95% confidence interval =0.57–0.97). In further stratified analyses, rs863091 variant genotypes were associated with a reduced risk of GC in younger individuals (<60 years) and males. No overall significant association with GC risk was observed in SNP rs17832998 or rs167481. Additionally, we assessed DACT1 messenger RNA levels in GC and found that DACT1 expressions of individuals carrying CT and TT genotypes were much higher than those with CC genotype. Conclusion Our findings suggest that the DACT1 rs863091 C>T polymorphism may be associated with a decreased risk of GC in the Chinese Han population and influence DACT1 expression.
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Affiliation(s)
- Chi Huang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University
| | - Younan Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University
| | - Hao Fan
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University
| | - Xiang Ma
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University
| | - Ran Tang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University
| | - Xiangkun Huan
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University
| | - Yi Zhu
- Institute of Tumor Biology, Jiangsu Province Academy of Clinical Medicine, Nanjing, People's Republic of China
| | - Zekuan Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University
| | - Hao Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University
| | - Li Yang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University
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194
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Codon usage is an important determinant of gene expression levels largely through its effects on transcription. Proc Natl Acad Sci U S A 2016; 113:E6117-E6125. [PMID: 27671647 DOI: 10.1073/pnas.1606724113] [Citation(s) in RCA: 252] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Codon usage biases are found in all eukaryotic and prokaryotic genomes, and preferred codons are more frequently used in highly expressed genes. The effects of codon usage on gene expression were previously thought to be mainly mediated by its impacts on translation. Here, we show that codon usage strongly correlates with both protein and mRNA levels genome-wide in the filamentous fungus Neurospora Gene codon optimization also results in strong up-regulation of protein and RNA levels, suggesting that codon usage is an important determinant of gene expression. Surprisingly, we found that the impact of codon usage on gene expression results mainly from effects on transcription and is largely independent of mRNA translation and mRNA stability. Furthermore, we show that histone H3 lysine 9 trimethylation is one of the mechanisms responsible for the codon usage-mediated transcriptional silencing of some genes with nonoptimal codons. Together, these results uncovered an unexpected important role of codon usage in ORF sequences in determining transcription levels and suggest that codon biases are an adaptation of protein coding sequences to both transcription and translation machineries. Therefore, synonymous codons not only specify protein sequences and translation dynamics, but also help determine gene expression levels.
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195
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Corley M, Laederach A. Selecting against accidental RNA interactions. eLife 2016; 5. [PMID: 27642846 PMCID: PMC5028187 DOI: 10.7554/elife.20686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 09/07/2016] [Indexed: 11/13/2022] Open
Abstract
Random base-pairing interactions between messenger RNAs and noncoding RNAs can reduce translation efficiency.
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Affiliation(s)
- Meredith Corley
- Department of Biology, University of North Carolina, Chapel Hill, United States
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, United States
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196
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Radhakrishnan A, Chen YH, Martin S, Alhusaini N, Green R, Coller J. The DEAD-Box Protein Dhh1p Couples mRNA Decay and Translation by Monitoring Codon Optimality. Cell 2016; 167:122-132.e9. [PMID: 27641505 DOI: 10.1016/j.cell.2016.08.053] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/25/2016] [Accepted: 08/19/2016] [Indexed: 01/01/2023]
Abstract
A major determinant of mRNA half-life is the codon-dependent rate of translational elongation. How the processes of translational elongation and mRNA decay communicate is unclear. Here, we establish that the DEAD-box protein Dhh1p is a sensor of codon optimality that targets an mRNA for decay. First, we find mRNAs whose translation elongation rate is slowed by inclusion of non-optimal codons are specifically degraded in a Dhh1p-dependent manner. Biochemical experiments show Dhh1p is preferentially associated with mRNAs with suboptimal codon choice. We find these effects on mRNA decay are sensitive to the number of slow-moving ribosomes on an mRNA. Moreover, we find Dhh1p overexpression leads to the accumulation of ribosomes specifically on mRNAs (and even codons) of low codon optimality. Lastly, Dhh1p physically interacts with ribosomes in vivo. Together, these data argue that Dhh1p is a sensor for ribosome speed, targeting an mRNA for repression and subsequent decay.
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Affiliation(s)
- Aditya Radhakrishnan
- Program in Molecular Biophysics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Ying-Hsin Chen
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sophie Martin
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Najwa Alhusaini
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
| | - Jeff Coller
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106, USA.
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197
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Gotea V, Gartner JJ, Qutob N, Elnitski L, Samuels Y. The functional relevance of somatic synonymous mutations in melanoma and other cancers. Pigment Cell Melanoma Res 2016; 28:673-84. [PMID: 26300548 DOI: 10.1111/pcmr.12413] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 08/19/2015] [Indexed: 01/07/2023]
Abstract
Recent technological advances in sequencing have flooded the field of cancer research with knowledge about somatic mutations for many different cancer types. Most cancer genomics studies focus on mutations that alter the amino acid sequence, ignoring the potential impact of synonymous mutations. However, accumulating experimental evidence has demonstrated clear consequences for gene function, leading to a widespread recognition of the functional role of synonymous mutations and their causal connection to various diseases. Here, we review the evidence supporting the direct impact of synonymous mutations on gene function via gene splicing; mRNA stability, folding, and translation; protein folding; and miRNA-based regulation of expression. These results highlight the functional contribution of synonymous mutations to oncogenesis and the need to further investigate their detection and prioritization for experimental assessment.
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Affiliation(s)
- Valer Gotea
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Jared J Gartner
- Surgery Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Nouar Qutob
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Laura Elnitski
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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198
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Sagi D, Rak R, Gingold H, Adir I, Maayan G, Dahan O, Broday L, Pilpel Y, Rechavi O. Tissue- and Time-Specific Expression of Otherwise Identical tRNA Genes. PLoS Genet 2016; 12:e1006264. [PMID: 27560950 PMCID: PMC4999229 DOI: 10.1371/journal.pgen.1006264] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 07/27/2016] [Indexed: 11/18/2022] Open
Abstract
Codon usage bias affects protein translation because tRNAs that recognize synonymous codons differ in their abundance. Although the current dogma states that tRNA expression is exclusively regulated by intrinsic control elements (A- and B-box sequences), we revealed, using a reporter that monitors the levels of individual tRNA genes in Caenorhabditis elegans, that eight tryptophan tRNA genes, 100% identical in sequence, are expressed in different tissues and change their expression dynamically. Furthermore, the expression levels of the sup-7 tRNA gene at day 6 were found to predict the animal's lifespan. We discovered that the expression of tRNAs that reside within introns of protein-coding genes is affected by the host gene's promoter. Pairing between specific Pol II genes and the tRNAs that are contained in their introns is most likely adaptive, since a genome-wide analysis revealed that the presence of specific intronic tRNAs within specific orthologous genes is conserved across Caenorhabditis species.
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Affiliation(s)
- Dror Sagi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Roni Rak
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Hila Gingold
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Idan Adir
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Gadi Maayan
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Orna Dahan
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Limor Broday
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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199
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Faure G, Ogurtsov AY, Shabalina SA, Koonin EV. Role of mRNA structure in the control of protein folding. Nucleic Acids Res 2016; 44:10898-10911. [PMID: 27466388 PMCID: PMC5159526 DOI: 10.1093/nar/gkw671] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/12/2016] [Accepted: 07/14/2016] [Indexed: 11/13/2022] Open
Abstract
Specific structures in mRNA modulate translation rate and thus can affect protein folding. Using the protein structures from two eukaryotes and three prokaryotes, we explore the connections between the protein compactness, inferred from solvent accessibility, and mRNA structure, inferred from mRNA folding energy (ΔG). In both prokaryotes and eukaryotes, the ΔG value of the most stable 30 nucleotide segment of the mRNA (ΔGmin) strongly, positively correlates with protein solvent accessibility. Thus, mRNAs containing exceptionally stable secondary structure elements typically encode compact proteins. The correlations between ΔG and protein compactness are much more pronounced in predicted ordered parts of proteins compared to the predicted disordered parts, indicative of an important role of mRNA secondary structure elements in the control of protein folding. Additionally, ΔG correlates with the mRNA length and the evolutionary rate of synonymous positions. The correlations are partially independent and were used to construct multiple regression models which explain about half of the variance of protein solvent accessibility. These findings suggest a model in which the mRNA structure, particularly exceptionally stable RNA structural elements, act as gauges of protein co-translational folding by reducing ribosome speed when the nascent peptide needs time to form and optimize the core structure.
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Affiliation(s)
- Guilhem Faure
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Aleksey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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200
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Uddin A, Chakraborty S. Codon usage trend in mitochondrial CYB gene. Gene 2016; 586:105-14. [DOI: 10.1016/j.gene.2016.04.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 03/11/2016] [Accepted: 04/02/2016] [Indexed: 11/25/2022]
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