1
|
Ding W, Yu W, Chen Y, Lao L, Fang Y, Fang C, Zhao H, Yang B, Lin S. Rare codon recoding for efficient noncanonical amino acid incorporation in mammalian cells. Science 2024; 384:1134-1142. [PMID: 38843324 DOI: 10.1126/science.adm8143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/03/2024] [Indexed: 06/16/2024]
Abstract
The ability to genetically encode noncanonical amino acids (ncAAs) has empowered proteins with improved or previously unknown properties. However, existing strategies in mammalian cells rely on the introduction of a blank codon to incorporate ncAAs, which is inefficient and limits their widespread applications. In this study, we developed a rare codon recoding strategy that takes advantage of the relative rarity of the TCG codon to achieve highly selective and efficient ncAA incorporation through systematic engineering and big data-model predictions. We highlight the broad utility of this strategy for the incorporation of dozens of ncAAs into various functional proteins at the wild-type protein expression levels, as well as the synthesis of proteins with up to six-site ncAAs or four distinct ncAAs in mammalian cells for downstream applications.
Collapse
Affiliation(s)
- Wenlong Ding
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Wei Yu
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Yulin Chen
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Lihui Lao
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Yu Fang
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Chengzhu Fang
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Hongxia Zhao
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
| | - Bo Yang
- Institute of Pharmacology & Toxicology, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Shixian Lin
- Life Sciences Institute, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
- Department of Medical Oncology, State Key Laboratory of Transvascular Implantation Devices, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| |
Collapse
|
2
|
Bourret J, Borvető F, Bravo IG. Subfunctionalisation of paralogous genes and evolution of differential codon usage preferences: The showcase of polypyrimidine tract binding proteins. J Evol Biol 2023; 36:1375-1392. [PMID: 37667674 DOI: 10.1111/jeb.14212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 09/06/2023]
Abstract
Gene paralogs are copies of an ancestral gene that appear after gene or full genome duplication. When two sister gene copies are maintained in the genome, redundancy may release certain evolutionary pressures, allowing one of them to access novel functions. Here, we focused our study on gene paralogs on the evolutionary history of the three polypyrimidine tract binding protein genes (PTBP) and their concurrent evolution of differential codon usage preferences (CUPrefs) in vertebrate species. PTBP1-3 show high identity at the amino acid level (up to 80%) but display strongly different nucleotide composition, divergent CUPrefs and, in humans and in many other vertebrates, distinct tissue-specific expression levels. Our phylogenetic inference results show that the duplication events leading to the three extant PTBP1-3 lineages predate the basal diversification within vertebrates, and genomic context analysis illustrates that local synteny has been well preserved over time for the three paralogs. We identify a distinct evolutionary pattern towards GC3-enriching substitutions in PTBP1, concurrent with enrichment in frequently used codons and with a tissue-wide expression. In contrast, PTBP2s are enriched in AT-ending, rare codons, and display tissue-restricted expression. As a result of this substitution trend, CUPrefs sharply differ between mammalian PTBP1s and the rest of PTBPs. Genomic context analysis suggests that GC3-rich nucleotide composition in PTBP1s is driven by local substitution processes, while the evidence in this direction is thinner for PTBP2-3. An actual lack of co-variation between the observed GC composition of PTBP2-3 and that of the surrounding non-coding genomic environment would raise an interrogation on the origin of CUPrefs, warranting further research on a putative tissue-specific translational selection. Finally, we communicate an intriguing trend for the use of the UUG-Leu codon, which matches the trends of AT-ending codons. Our results are compatible with a scenario in which a combination of directional mutation-selection processes would have differentially shaped CUPrefs of PTBPs in vertebrates: the observed GC-enrichment of PTBP1 in placental mammals may be linked to genomic location and to the strong and broad tissue-expression, while AT-enrichment of PTBP2 and PTBP3 would be associated with rare CUPrefs and thus, possibly to specialized spatio-temporal expression. Our interpretation is coherent with a gene subfunctionalisation process by differential expression regulation associated with the evolution of specific CUPrefs.
Collapse
Affiliation(s)
- Jérôme Bourret
- Laboratoire MIVEGEC (CNRS IRD Univ Montpellier), Centre National de la Recherche Scientifique (CNRS), Montpellier, France
| | - Fanni Borvető
- Laboratoire MIVEGEC (CNRS IRD Univ Montpellier), Centre National de la Recherche Scientifique (CNRS), Montpellier, France
| | - Ignacio G Bravo
- Laboratoire MIVEGEC (CNRS IRD Univ Montpellier), Centre National de la Recherche Scientifique (CNRS), Montpellier, France
| |
Collapse
|
3
|
McFeely CAL, Shakya B, Makovsky CA, Haney AK, Ashton Cropp T, Hartman MCT. Extensive breaking of genetic code degeneracy with non-canonical amino acids. Nat Commun 2023; 14:5008. [PMID: 37591858 PMCID: PMC10435567 DOI: 10.1038/s41467-023-40529-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 07/26/2023] [Indexed: 08/19/2023] Open
Abstract
Genetic code expansion (GCE) offers many exciting opportunities for the creation of synthetic organisms and for drug discovery methods that utilize in vitro translation. One type of GCE, sense codon reassignment (SCR), focuses on breaking the degeneracy of the 61 sense codons which encode for only 20 amino acids. SCR has great potential for genetic code expansion, but extensive SCR is limited by the post-transcriptional modifications on tRNAs and wobble reading of these tRNAs by the ribosome. To better understand codon-tRNA pairing, here we develop an assay to evaluate the ability of aminoacyl-tRNAs to compete with each other for a given codon. We then show that hyperaccurate ribosome mutants demonstrate reduced wobble reading, and when paired with unmodified tRNAs lead to extensive and predictable SCR. Together, we encode seven distinct amino acids across nine codons spanning just two codon boxes, thereby demonstrating that the genetic code hosts far more re-assignable space than previously expected, opening the door to extensive genetic code engineering.
Collapse
Affiliation(s)
- Clinton A L McFeely
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St., Richmond, VA, 23284, USA
- Massey Cancer Center, Virginia Commonwealth University, 401 College St., Richmond, VA, 23219, USA
| | - Bipasana Shakya
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St., Richmond, VA, 23284, USA
- Massey Cancer Center, Virginia Commonwealth University, 401 College St., Richmond, VA, 23219, USA
| | - Chelsea A Makovsky
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St., Richmond, VA, 23284, USA
- Massey Cancer Center, Virginia Commonwealth University, 401 College St., Richmond, VA, 23219, USA
| | - Aidan K Haney
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St., Richmond, VA, 23284, USA
| | - T Ashton Cropp
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St., Richmond, VA, 23284, USA
| | - Matthew C T Hartman
- Department of Chemistry, Virginia Commonwealth University, 1001 W Main St., Richmond, VA, 23284, USA.
- Massey Cancer Center, Virginia Commonwealth University, 401 College St., Richmond, VA, 23219, USA.
| |
Collapse
|
4
|
Tietze L, Lale R. Importance of the 5' regulatory region to bacterial synthetic biology applications. Microb Biotechnol 2021; 14:2291-2315. [PMID: 34171170 PMCID: PMC8601185 DOI: 10.1111/1751-7915.13868] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 01/02/2023] Open
Abstract
The field of synthetic biology is evolving at a fast pace. It is advancing beyond single-gene alterations in single hosts to the logical design of complex circuits and the development of integrated synthetic genomes. Recent breakthroughs in deep learning, which is increasingly used in de novo assembly of DNA components with predictable effects, are also aiding the discipline. Despite advances in computing, the field is still reliant on the availability of pre-characterized DNA parts, whether natural or synthetic, to regulate gene expression in bacteria and make valuable compounds. In this review, we discuss the different bacterial synthetic biology methodologies employed in the creation of 5' regulatory regions - promoters, untranslated regions and 5'-end of coding sequences. We summarize methodologies and discuss their significance for each of the functional DNA components, and highlight the key advances made in bacterial engineering by concentrating on their flaws and strengths. We end the review by outlining the issues that the discipline may face in the near future.
Collapse
Affiliation(s)
- Lisa Tietze
- PhotoSynLabDepartment of BiotechnologyFaculty of Natural SciencesNorwegian University of Science and TechnologyTrondheimN‐7491Norway
| | - Rahmi Lale
- PhotoSynLabDepartment of BiotechnologyFaculty of Natural SciencesNorwegian University of Science and TechnologyTrondheimN‐7491Norway
| |
Collapse
|
5
|
Zou Z, Zhang J. Are Nonsynonymous Transversions Generally More Deleterious than Nonsynonymous Transitions? Mol Biol Evol 2021; 38:181-191. [PMID: 32805043 PMCID: PMC7783172 DOI: 10.1093/molbev/msaa200] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
It has been suggested that, due to the structure of the genetic code, nonsynonymous transitions are less likely than transversions to cause radical changes in amino acid physicochemical properties so are on average less deleterious. This view was supported by some but not all mutagenesis experiments. Because laboratory measures of fitness effects have limited sensitivities and relative frequencies of different mutations in mutagenesis studies may not match those in nature, we here revisit this issue using comparative genomics. We extend the standard codon model of sequence evolution by adding the parameter η that quantifies the ratio of the fixation probability of transitional nonsynonymous mutations to that of transversional nonsynonymous mutations. We then estimate η from the concatenated alignment of all protein-coding DNA sequences of two closely related genomes. Surprisingly, η ranges from 0.13 to 2.0 across 90 species pairs sampled from the tree of life, with 51 incidences of η < 1 and 30 incidences of η >1 that are statistically significant. Hence, whether nonsynonymous transversions are overall more deleterious than nonsynonymous transitions is species-dependent. Because the corresponding groups of amino acid replacements differ between nonsynonymous transitions and transversions, η is influenced by the relative exchangeabilities of amino acid pairs. Indeed, an extensive search reveals that the large variation in η is primarily explainable by the recently reported among-species disparity in amino acid exchangeabilities. These findings demonstrate that genome-wide nucleotide substitution patterns in coding sequences have species-specific features and are more variable among evolutionary lineages than are currently thought.
Collapse
Affiliation(s)
- Zhengting Zou
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
- Corresponding author: E-mail: .Associate editor: Jeffrey Townsend
| |
Collapse
|
6
|
Hawthorne-Madell J, Aaron E, Livingston K, Long JH. Embodied Computational Evolution: Feedback Between Development and Evolution in Simulated Biorobots. Front Robot AI 2021; 8:674823. [PMID: 34179109 PMCID: PMC8222576 DOI: 10.3389/frobt.2021.674823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/25/2021] [Indexed: 12/05/2022] Open
Abstract
Given that selection removes genetic variance from evolving populations, thereby reducing exploration opportunities, it is important to find mechanisms that create genetic variation without the disruption of adapted genes and genomes caused by random mutation. Just such an alternative is offered by random epigenetic error, a developmental process that acts on materials and parts expressed by the genome. In this system of embodied computational evolution, simulated within a physics engine, epigenetic error was instantiated in an explicit genotype-to-phenotype map as transcription error at the initiation of gene expression. The hypothesis was that transcription error would create genetic variance by shielding genes from the direct impact of selection, creating, in the process, masquerading genomes. To test this hypothesis, populations of simulated embodied biorobots and their developmental systems were evolved under steady directional selection as equivalent rates of random mutation and random transcriptional error were covaried systematically in an 11 × 11 fully factorial experimental design. In each of the 121 different experimental conditions (unique combinations of mutation and transcription error), the same set of 10 randomly created replicate populations of 60 individuals were evolved. Selection for the improved locomotor behavior of individuals led to increased mean fitness of populations over 100 generations at nearly all levels and combinations of mutation and transcription error. When the effects of both types of error were partitioned statistically, increasing transcription error was shown to increase the final genetic variance of populations, incurring a fitness cost but acting on variance independently and differently from genetic mutation. Thus, random epigenetic errors in development feed back through selection of individuals with masquerading genomes to the population’s genetic variance over generational time. Random developmental processes offer an additional mechanism for exploration by increasing genetic variation in the face of steady, directional selection.
Collapse
Affiliation(s)
- Joshua Hawthorne-Madell
- Interdisciplinary Robotics Research Laboratory, Vassar College, Poughkeepsie, NY, United States.,Department of Cognitive Science, Vassar College, Poughkeepsie, NY, United States
| | - Eric Aaron
- Interdisciplinary Robotics Research Laboratory, Vassar College, Poughkeepsie, NY, United States.,Department of Computer Science, Colby College, Waterville, ME, United States
| | - Ken Livingston
- Interdisciplinary Robotics Research Laboratory, Vassar College, Poughkeepsie, NY, United States.,Department of Cognitive Science, Vassar College, Poughkeepsie, NY, United States
| | - John H Long
- Interdisciplinary Robotics Research Laboratory, Vassar College, Poughkeepsie, NY, United States.,Department of Cognitive Science, Vassar College, Poughkeepsie, NY, United States
| |
Collapse
|
7
|
Abstract
Messenger RNAs (mRNAs) consist of a coding region (open reading frame (ORF)) and two untranslated regions (UTRs), 5'UTR and 3'UTR. Ribosomes travel along the coding region, translating nucleotide triplets (called codons) to a chain of amino acids. The coding region was long believed to mainly encode the amino acid content of proteins, whereas regulatory signals reside in the UTRs and in other genomic regions. However, in recent years we have learned that the ORF is expansively populated with various regulatory signals, or codes, which are related to all gene expression steps and additional intracellular aspects. In this paper, we review the current knowledge related to overlapping codes inside the coding regions, such as the influence of synonymous codon usage on translation speed (and, in turn, the effect of translation speed on protein folding), ribosomal frameshifting, mRNA stability, methylation, splicing, transcription and more. All these codes come together and overlap in the ORF sequence, ensuring production of the right protein at the right time.
Collapse
Affiliation(s)
- Shaked Bergman
- Department of Biomedical Engineering, Tel-Aviv University, Tel Aviv, Israel
| | | |
Collapse
|
8
|
Patel U, Gautam S, Chatterji D. Unraveling the Role of Silent Mutation in the ω-Subunit of Escherichia coli RNA Polymerase: Structure Transition Inhibits Transcription. ACS OMEGA 2019; 4:17714-17725. [PMID: 31681877 PMCID: PMC6822122 DOI: 10.1021/acsomega.9b02103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/05/2019] [Indexed: 05/07/2023]
Abstract
The bacterial RNA polymerase is a multi-subunit enzyme complex composed of six subunits, α2ββ'σω. The function of this enzyme is to transcribe the DNA base sequence to the RNA intermediate, which is ultimately translated to protein. Though the contribution of each subunit in RNA synthesis has been clearly elucidated, the role of the smallest ω-subunit is still unclear despite several studies. Recently, a study on a dominant negative mutant of rpoZ has been reported in which the mutant was shown to render the RNA polymerase defective in transcription initiation (ω6, N60D) and gave an insight on the function of ω in RNA polymerase. Serendipitously, we also obtained a silent mutant, and the mutant was found to be lethal during the isolation of toxic mutants. The primary focus of this study is to understand the mechanistic details of this lethality. Isolated ω shows a predominantly unstructured circular dichroism profile and becomes α-helical in the enzyme complex. This structural transition is perhaps the reason for this lack of function. Subsequently, we generated several silent mutants of ω to investigate the role of codon bias and the effect of rare codons with respect to their position in rpoZ. Not all silent mutations affect the structure. RNA polymerase when reconstituted with structurally altered silent mutants of ω is transcriptionally inactive. The CodonPlus strain, which has surplus tRNA, was used to assess for the rescue of the phenotype in lethal silent mutants.
Collapse
Affiliation(s)
| | - Sudhanshu Gautam
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
9
|
Manin BO, Drakeley CJ, Chua TH. Mitochondrial variation in subpopulations of Anopheles balabacensis Baisas in Sabah, Malaysia (Diptera: Culicidae). PLoS One 2018; 13:e0202905. [PMID: 30138386 PMCID: PMC6107281 DOI: 10.1371/journal.pone.0202905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 08/10/2018] [Indexed: 11/19/2022] Open
Abstract
Anopheles balabacensis, the primary vector of Plasmodium knowlesi in Sabah, Malaysia, is both zoophilic and anthropophilic, feeding on macaques as well as humans. It is the dominant Anopheles species found in Kudat Division where it is responsible for all the cases of P. knowlesi. However there is a paucity of basic biological and ecological information on this vector. We investigated the genetic variation of this species using the sequences of cox1 (1,383 bp) and cox2 (685 bp) to gain an insight into the population genetics and inter-population gene flow in Sabah. A total of 71 An. balabacensis were collected from seven districts constituting 14 subpopulations. A total of 17, 10 and 25 haplotypes were detected in the subpopulations respectively using the cox1, cox2 and the combined sequence. Some of the haplotypes were common among the subpopulations due to gene flow occurring between them. AMOVA showed that the genetic variation was high within subpopulations as compared to between subpopulations. Mantel test results showed that the variation between subpopulations was not due to the geographical distance between them. Furthermore, Tajima's D and Fu's Fs tests showed that An. balabacensis in Sabah is experiencing population expansion and growth. High gene flow between the subpopulations was indicated by the low genetic distance and high gene diversity in the cox1, cox2 and the combined sequence. However the population at Lipasu Lama appeared to be isolated possibly due to its higher altitude at 873 m above sea level.
Collapse
Affiliation(s)
- Benny Obrain Manin
- Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Chris J. Drakeley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Tock H. Chua
- Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
- * E-mail:
| |
Collapse
|
10
|
Using the Mutation-Selection Framework to Characterize Selection on Protein Sequences. Genes (Basel) 2018; 9:genes9080409. [PMID: 30104502 PMCID: PMC6115872 DOI: 10.3390/genes9080409] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/02/2018] [Accepted: 08/09/2018] [Indexed: 12/13/2022] Open
Abstract
When mutational pressure is weak, the generative process of protein evolution involves explicit probabilities of mutations of different types coupled to their conditional probabilities of fixation dependent on selection. Establishing this mechanistic modeling framework for the detection of selection has been a goal in the field of molecular evolution. Building on a mathematical framework proposed more than a decade ago, numerous methods have been introduced in an attempt to detect and measure selection on protein sequences. In this review, we discuss the structure of the original model, subsequent advances, and the series of assumptions that these models operate under.
Collapse
|
11
|
Roy P, Dey S, Nandy A, Basak SC, Das S. Base Distribution in Dengue Nucleotide Sequences Differs Significantly from Other Mosquito-Borne Human-Infecting Flavivirus Members. Curr Comput Aided Drug Des 2018; 15:29-44. [PMID: 30062973 DOI: 10.2174/1573409914666180731090005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/02/2018] [Accepted: 07/25/2018] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Among the mosquito-borne human-infecting flavivirus species that include Zika, West Nile, yellow fever, Japanese encephalitis and Dengue viruses, the Zika virus is found to be closest to Dengue virus, sharing the same clade in the Flavivirus phylogenetic tree. We consider these five flaviviruses and on closer examination in our analyses, the nucleotide sequences of the Dengue viral genes (envelope and NS5) and genomes are seen to be quite widely different from the other four flaviviruses. We consider the extent of this distinction and determine the advantage and/or disadvantage such differences may confer upon the Dengue viral pathogenesis. METHODS We have primarily used a 2D graphical representation technique to show the differences in base distributions in these five flaviviruses and subsequently, obtained quantitative estimates of the differences. Similarity/dissimilarity between the viruses based on the genes were also determined which showed that the differences with the Dengue genes are more pronounced. RESULTS We found that the Dengue viruses compared to the other four flaviviruses spread rapidly worldwide and became endemic in various regions with small alterations in sequence composition relative to the host populations as revealed by codon usage biases and phylogenetic examination. CONCLUSION We conclude that the Dengue genes are indeed more widely separated from the other aforementioned mosquito-borne human-infecting flaviviruses due to excess adenine component, a feature that is sparse in the literature. Such excesses have a bearing on drug and vaccine, especially peptide vaccine, development and should be considered appropriately.
Collapse
Affiliation(s)
- Proyasha Roy
- Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata 700058, India
| | - Sumanta Dey
- Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata 700058, India
| | - Ashesh Nandy
- Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata 700058, India
| | - Subhash C Basak
- Department of Chemistry and Biochemistry, Duluth-Natural Resources Research Institute, University of Minnesota Duluth, 5013 Miller Trunk Highway, Duluth, MN 55811, United States
| | - Sukhen Das
- Department of Physics, Jadavpur University, Jadavpur, Kolkata 700032, India
| |
Collapse
|
12
|
Bertelli S, Barbieri R, Pusch M, Gavazzo P. Gain of function of sporadic/familial hemiplegic migraine-causing SCN1A mutations: Use of an optimized cDNA. Cephalalgia 2018; 39:477-488. [PMID: 29986598 DOI: 10.1177/0333102418788336] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
INTRODUCTION Familial hemiplegic migraine 3 is an autosomal dominant headache disorder associated with aura and transient hemiparesis, caused by mutations of the neuronal voltage-gated sodium channel Nav1.1. While a gain-of function phenotype is generally assumed to underlie familial hemiplegic migraine, this has not been fully explored. Indeed, a major obstacle in studying in vitro neuronal sodium channels is the difficulty in propagating and mutagenizing expression plasmids containing their cDNAs. The aim of this work was to study the functional effect of two previously uncharacterized hemiplegic migraine causing mutations, Leu1670Trp (L1670W) and Phe1774Ser (F1774S). METHODS A novel SCN1A containing-plasmid was designed in silico and synthesized, and migraine mutations were inserted in this background. Whole-cell patch clamp was performed to investigate the functional properties of mutant Nav1.1 transiently expressed in Human Embryonic Kidney 293 cells. RESULTS AND CONCLUSIONS We generated an optimized Nav1.1 expression plasmid that was extremely simple to handle and used the novel plasmid to study the functional effects of two migraine mutations. We observed that L1670W, but not F1774S, reduced current density and that both mutations led to a dramatic increase in persistent sodium currents, a depolarizing shift of the steady state-inactivation voltage-dependence, and a faster recovery from inactivation. The results are consistent with a major gain-of function effect underlying familial hemiplegic migraine 3. Our optimization strategy will help to characterize in an efficient manner the effect in vitro of mutations of neuronal voltage-gated sodium channels.
Collapse
Affiliation(s)
- Sara Bertelli
- 1 Istituto di Biofisica (Biophysics Institute, National Research Council), Genova, Italy.,2 Scuola Internazionale Superiore di Studi Avanzati (SISSA) (International School for Advanced Studies), Trieste, Italy
| | - Raffaella Barbieri
- 1 Istituto di Biofisica (Biophysics Institute, National Research Council), Genova, Italy
| | - Michael Pusch
- 1 Istituto di Biofisica (Biophysics Institute, National Research Council), Genova, Italy
| | - Paola Gavazzo
- 1 Istituto di Biofisica (Biophysics Institute, National Research Council), Genova, Italy
| |
Collapse
|
13
|
Fourie G, Van der Merwe NA, Wingfield BD, Bogale M, Wingfield MJ, Steenkamp ET. Mitochondrial introgression and interspecies recombination in the Fusarium fujikuroi species complex. IMA Fungus 2018; 9:37-48. [PMID: 30018871 PMCID: PMC6048563 DOI: 10.5598/imafungus.2018.09.01.04] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 02/18/2018] [Indexed: 01/31/2023] Open
Abstract
The Fusarium fujikuroi species complex (FFSC) is an economically important monophyletic lineage in the genus Fusarium. Incongruence observed among mitochondrial gene trees, as well as the multiple non-orthologous copies of the internal transcribed spacer region of the ribosomal RNA genes, suggests that the origin and history of this complex likely involved interspecies gene flow. Based on this hypothesis, the mitochondrial genomes of non-conspecific species should harbour signatures of introgression or introgressive hybridization. The aim of this study was therefore to search for recombination between the mitochondrial genomes of different species in the FFSC. Using methods based on mt genome sequence similarity, five significant recombinant regions in both gene and intergenic regions were detected. Using coalescent-based methods and the sequences for individual mt genes, various ancestral recombination events between different lineages of the FFSC were also detected. These findings suggest that interspecies gene flow and introgression are likely to have played key roles in the evolution of the FFSC at both ancient and more recent time scales.
Collapse
Affiliation(s)
- Gerda Fourie
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Nicolaas A Van der Merwe
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Brenda D Wingfield
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Mesfin Bogale
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Michael J Wingfield
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Emma T Steenkamp
- Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| |
Collapse
|
14
|
Yang JR. Does mRNA structure contain genetic information for regulating co-translational protein folding? Zool Res 2018; 38:36-43. [PMID: 28271668 PMCID: PMC5368379 DOI: 10.13918/j.issn.2095-8137.2017.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Currently many facets of genetic information are illdefined. In particular, how protein folding is genetically regulated has been a long-standing issue for genetics and protein biology. And a generic mechanistic model with supports of genomic data is still lacking. Recent technological advances have enabled much needed genome-wide experiments. While putting the effect of codon optimality on debate, these studies have supplied mounting evidence suggesting a role of mRNA structure in the regulation of protein folding by modulating translational elongation rate. In conjunctions with previous theories, this mechanistic model of protein folding guided by mRNA structure shall expand our understandings of genetic information and offer new insights into various biomedical puzzles.
Collapse
Affiliation(s)
- Jian-Rong Yang
- Department of Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.
| |
Collapse
|
15
|
Mioduser O, Goz E, Tuller T. Significant differences in terms of codon usage bias between bacteriophage early and late genes: a comparative genomics analysis. BMC Genomics 2017; 18:866. [PMID: 29132309 PMCID: PMC5683454 DOI: 10.1186/s12864-017-4248-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/31/2017] [Indexed: 11/13/2022] Open
Abstract
Background Viruses undergo extensive evolutionary selection for efficient replication which effects, among others, their codon distribution. In the current study, we aimed at understanding the way evolution shapes the codon distribution in early vs. late viral genes in terms of their expression during different stages in the viral replication cycle. To this end we analyzed 14 bacteriophages and 11 human viruses with available information about the expression phases of their genes. Results We demonstrated evidence of selection for distinct composition of synonymous codons in early and late viral genes in 50% of the analyzed bacteriophages. Among others, this phenomenon may be related to the time specific adaptation of the viral genes to the translation efficiency factors involved at different bacteriophage developmental stages. Specifically, we showed that the differences in codon composition in different temporal gene groups cannot be explained only by phylogenetic proximities between the analyzed bacteriophages, and can be partially explained by differences in the adaptation to the host tRNA pool, nucleotide bias, GC content and more. In contrast, no difference in temporal regulation of synonymous codon usage was observed in human viruses, possibly because of a stronger selection pressure due to a larger effective population size in bacteriophages and their bacterial hosts. Conclusions The codon distribution in large fractions of bacteriophage genomes tend to be different in early and late genes. This phenomenon seems to be related to various aspects of the viral life cycle, and to various intracellular processes. We believe that the reported results should contribute towards better understanding of viral evolution and may promote the development of relevant procedures in synthetic virology. Electronic supplementary material The online version of this article (10.1186/s12864-017-4248-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Oriah Mioduser
- Department of Biomedical Engineering, Tel-Aviv University, Ramat Aviv, Israel
| | - Eli Goz
- Department of Biomedical Engineering, Tel-Aviv University, Ramat Aviv, Israel.,SynVaccineLtd. Ramat Hachayal, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel-Aviv University, Ramat Aviv, Israel. .,SynVaccineLtd. Ramat Hachayal, Tel Aviv, Israel. .,Sagol School of Neuroscience, Tel-Aviv University, Ramat Aviv, Israel.
| |
Collapse
|
16
|
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.
Collapse
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.
| |
Collapse
|
17
|
Diambra LA. Differential bicodon usage in lowly and highly abundant proteins. PeerJ 2017; 5:e3081. [PMID: 28289571 PMCID: PMC5346287 DOI: 10.7717/peerj.3081] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/10/2017] [Indexed: 01/23/2023] Open
Abstract
Degeneracy in the genetic code implies that different codons can encode the same amino acid. Usage preference of synonymous codons has been observed in all domains of life. There is much evidence suggesting that this bias has a major role on protein elongation rate, contributing to differential expression and to co-translational folding. In addition to codon usage bias, other preference variations have been observed such as codon pairs. In this paper, I report that codon pairs have significant different frequency usage for coding either lowly or highly abundant proteins. These usage preferences cannot be explained by the frequency usage of the single codons. The statistical analysis of coding sequences of nine organisms reveals that in many cases bicodon preferences are shared between related organisms. Furthermore, it is observed that misfolding in the drug-transport protein, encoded by MDR1 gene, is better explained by a big change in the pause propensity due to the synonymous bicodon variant, rather than by a relatively small change in codon usage. These findings suggest that codon pair usage can be a more powerful framework to understand translation elongation rate, protein folding efficiency, and to improve protocols to optimize heterologous gene expression.
Collapse
Affiliation(s)
- Luis A. Diambra
- Centro Regional de Estudios Genómicos, Universidad Nacional de La Plata, CONICET, La Plata, Argentina
| |
Collapse
|
18
|
Zhong C, Wei P, Zhang YHP. Enhancing functional expression of codon-optimized heterologous enzymes in Escherichia coli BL21(DE3) by selective introduction of synonymous rare codons. Biotechnol Bioeng 2016; 114:1054-1064. [PMID: 27943233 DOI: 10.1002/bit.26238] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 12/12/2022]
Abstract
Rare codon in a heterologous gene may cause premature termination of protein synthesis, misincorporation of amino acids, and/or slow translation of mRNA, decreasing the heterologous protein expression. However, its hypothetical function pertaining to functional protein folding has been barely reported. Here, we investigated the effects of selective introduction of synonymous rare codons (SRCs) to two codon-optimized (i.e., rare codon-free) genes sucrose phosphorylase (SP) gene from Thermoanaerobacterium thermosaccharolyticum and amidohydrolase gene from Streptomyces caatingaensis on their expression levels in Escherichia coli BL21(DE3). We investigated the introduction of a single SRC to the coding regions of alpha-helix, beta-strand, or linker in the first half of rare codon-free sp and ah gene. The introduction of a single SRC in the beginning of the coding regions of beta-strand greatly enhanced their soluble expression levels as compared to the other regions. Also, we applied directed evolution to test multi-SRC-containing sp gene mutants for enhanced soluble SP expression levels. To easily identify the soluble SP expression level of colonies growing on Petri dishes, mCherry fluorescent protein was used as a SP-folding reporter when it was fused to the 3' end of the sp gene mutant libraries. After three rounds of screening, the best sp gene mutant containing nine SRCs exhibited an approximately six-fold enhancement in soluble protein expression level as compared to the wild-type and rare codon-free sp control. This study suggests that the selective introduction of SRCs can attenuate translation at specific points and such discontinuous attenuation can temporally separate the translation of segments of the peptide chains and actively coordinates their co-translational folding, resulting in enhanced functional protein expression. Biotechnol. Bioeng. 2017;114: 1054-1064. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Chao Zhong
- Department of Biological Systems Engineering, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia, 24061.,College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China
| | - Ping Wei
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, China
| | - Yi-Heng Percival Zhang
- Department of Biological Systems Engineering, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia, 24061.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China
| |
Collapse
|
19
|
Browning CL, Qin Q, Kelly DF, Prakash R, Vanoli F, Jasin M, Wise JP. Prolonged Particulate Hexavalent Chromium Exposure Suppresses Homologous Recombination Repair in Human Lung Cells. Toxicol Sci 2016; 153:70-8. [PMID: 27449664 DOI: 10.1093/toxsci/kfw103] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Genomic instability is one of the primary models of carcinogenesis and a feature of almost all cancers. Homologous recombination (HR) repair protects against genomic instability by maintaining high genomic fidelity during the repair of DNA double strand breaks. The defining step of HR repair is the formation of the Rad51 nucleofilament, which facilitates the search for a homologous sequence and invasion of the template DNA strand. Particulate hexavalent chromium (Cr(VI)), a human lung carcinogen, induces DNA double strand breaks and chromosome instability. Since the loss of HR repair increases Cr(VI)-induced chromosome instability, we investigated the effect of extended Cr(VI) exposure on HR repair. We show acute (24 h) Cr(VI) exposure induces a normal HR repair response. In contrast, prolonged (120 h) exposure to particulate Cr(VI) inhibited HR repair and Rad51 nucleofilament formation. Prolonged Cr(VI) exposure had a profound effect on Rad51, evidenced by reduced protein levels and Rad51 mislocalization to the cytoplasm. The response of proteins involved in Rad51 nuclear import and nucleofilament formation displayed varying responses to prolonged Cr(VI) exposure. BRCA2 formed nuclear foci after prolonged Cr(VI) exposure, while Rad51C foci formation was suppressed. These results suggest that particulate Cr(VI), a major chemical carcinogen, inhibits HR repair by targeting Rad51, causing DNA double strand breaks to be repaired by a low fidelity, Rad51-independent repair pathway. These results further enhance our understanding of the underlying mechanism of Cr(VI)-induced chromosome instability and thus, carcinogenesis.
Collapse
Affiliation(s)
- Cynthia L Browning
- *Wise Laboratory of Environmental and Genetic Toxicology, Portland, Maine 04104 Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine 04469
| | - Qin Qin
- *Wise Laboratory of Environmental and Genetic Toxicology, Portland, Maine 04104 Virginia Tech Carilion Research Institute, Roanoke, Virginia 24016
| | - Deborah F Kelly
- Virginia Tech Carilion Research Institute, Roanoke, Virginia 24016
| | - Rohit Prakash
- Memorial Sloan Kettering Cancer Center, New York 10065, New York
| | - Fabio Vanoli
- Memorial Sloan Kettering Cancer Center, New York 10065, New York
| | - Maria Jasin
- Memorial Sloan Kettering Cancer Center, New York 10065, New York
| | - John Pierce Wise
- *Wise Laboratory of Environmental and Genetic Toxicology, Portland, Maine 04104 Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine 04469
| |
Collapse
|
20
|
Novel Rhizosphere Soil Alleles for the Enzyme 1-Aminocyclopropane-1-Carboxylate Deaminase Queried for Function with an In Vivo Competition Assay. Appl Environ Microbiol 2015; 82:1050-9. [PMID: 26637602 PMCID: PMC4751833 DOI: 10.1128/aem.03074-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 11/21/2015] [Indexed: 11/20/2022] Open
Abstract
Metagenomes derived from environmental microbiota encode a vast diversity of protein homologs. How this diversity impacts protein function can be explored through selection assays aimed to optimize function. While artificially generated gene sequence pools are typically used in selection assays, their usage may be limited because of technical or ethical reasons. Here, we investigate an alternative strategy, the use of soil microbial DNA as a starting point. We demonstrate this approach by optimizing the function of a widely occurring soil bacterial enzyme, 1-aminocyclopropane-1-carboxylate (ACC) deaminase. We identified a specific ACC deaminase domain region (ACCD-DR) that, when PCR amplified from the soil, produced a variant pool that we could swap into functional plasmids carrying ACC deaminase-encoding genes. Functional clones of ACC deaminase were selected for in a competition assay based on their capacity to provide nitrogen to Escherichia coli in vitro. The most successful ACCD-DR variants were identified after multiple rounds of selection by sequence analysis. We observed that previously identified essential active-site residues were fixed in the original unselected library and that additional residues went to fixation after selection. We identified a divergent essential residue whose presence hints at the possible use of alternative substrates and a cluster of neutral residues that did not influence ACCD performance. Using an artificial ACCD-DR variant library generated by DNA oligomer synthesis, we validated the same fixation patterns. Our study demonstrates that soil metagenomes are useful starting pools of protein-coding-gene diversity that can be utilized for protein optimization and functional characterization when synthetic libraries are not appropriate.
Collapse
|
21
|
Muto Y, Morton J, Palmer D. Investigation of biochemical changes of the ovine calpain 3 exon-10 polymorphism. Mol Cell Probes 2015; 29:382-388. [PMID: 26363096 DOI: 10.1016/j.mcp.2015.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 08/24/2015] [Accepted: 09/07/2015] [Indexed: 11/28/2022]
Abstract
Calpain 3 (CAPN3) is a tissue specific calpain, and its mRNA is the most expressed calpain isoform in skeletal muscles. Many mutations and polymorphisms within the human CAPN3 gene have been reported and related to limb-girdle muscular dystrophy. Several reports link CAPN3 polymorphisms and meat quality. An association between three allele variants in exon-10 of ovine CAPN3 and the yield of fat trimmed meat cuts has been reported. This research investigated the biochemical significance of polymorphic variation in CAPN3. CAPN3 mRNA sequences were obtained from muscle samples collected from lambs which were homozygous for each of the three alleles. Four single base substitutions were found besides those in exon-10, but none of them, including the variations within exon-10, caused a change in amino acid sequence. The expression of CAPN3 mRNA and the amounts of CAPN3 protein were also compared among genotypes, and no significant differences were found. These results suggest that the reported association of specific allele variants within CAPN3 exon-10 to phenotype variations were not direct effects of CAPN3 polymorphisms. Interspecies analyses of the CAPN3 sequences indicated that the sequence reported here is more likely to be the correct common ovine CAPN3 sequence than the reference sequence.
Collapse
Affiliation(s)
- Yukiyo Muto
- Wine Food and Molecular Biosciences Department, Lincoln University, P.O Box84 Lincoln 7647 New Zealand.
| | - Jim Morton
- Wine Food and Molecular Biosciences Department, Lincoln University, P.O Box84 Lincoln 7647 New Zealand.
| | - David Palmer
- Wine Food and Molecular Biosciences Department, Lincoln University, P.O Box84 Lincoln 7647 New Zealand.
| |
Collapse
|
22
|
Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding. Mol Cell 2015; 59:744-54. [PMID: 26321254 DOI: 10.1016/j.molcel.2015.07.018] [Citation(s) in RCA: 353] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 04/08/2015] [Accepted: 07/20/2015] [Indexed: 12/20/2022]
Abstract
Codon usage bias is a universal feature of eukaryotic and prokaryotic genomes and has been proposed to regulate translation efficiency, accuracy, and protein folding based on the assumption that codon usage affects translation dynamics. The roles of codon usage in translation, however, are not clear and have been challenged by recent ribosome profiling studies. Here we used a Neurospora cell-free translation system to directly monitor the velocity of mRNA translation. We demonstrated that the preferred codons enhance the rate of translation elongation, whereas non-optimal codons slow elongation. Codon usage also controls ribosome traffic on mRNA. These conclusions were supported by ribosome profiling results in vitro and in vivo with template mRNAs designed to increase the signal-to-noise ratio. Finally, we demonstrate that codon usage regulates protein function by affecting co-translational protein folding. These results resolve a long-standing fundamental question and suggest the existence of a codon usage code for protein folding.
Collapse
|
23
|
Rudorf S, Lipowsky R. Protein Synthesis in E. coli: Dependence of Codon-Specific Elongation on tRNA Concentration and Codon Usage. PLoS One 2015; 10:e0134994. [PMID: 26270805 PMCID: PMC4535986 DOI: 10.1371/journal.pone.0134994] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/15/2015] [Indexed: 11/18/2022] Open
Abstract
To synthesize a protein, a ribosome moves along a messenger RNA (mRNA), reads it codon by codon, and takes up the corresponding ternary complexes which consist of aminoacylated transfer RNAs (aa-tRNAs), elongation factor Tu (EF-Tu), and GTP. During this process of translation elongation, the ribosome proceeds with a codon-specific rate. Here, we present a general theoretical framework to calculate codon-specific elongation rates and error frequencies based on tRNA concentrations and codon usages. Our theory takes three important aspects of in-vivo translation elongation into account. First, non-cognate, near-cognate and cognate ternary complexes compete for the binding sites on the ribosomes. Second, the corresponding binding rates are determined by the concentrations of free ternary complexes, which must be distinguished from the total tRNA concentrations as measured in vivo. Third, for each tRNA species, the difference between total tRNA and ternary complex concentration depends on the codon usages of the corresponding cognate and near-cognate codons. Furthermore, we apply our theory to two alternative pathways for tRNA release from the ribosomal E site and show how the mechanism of tRNA release influences the concentrations of free ternary complexes and thus the codon-specific elongation rates. Using a recently introduced method to determine kinetic rates of in-vivo translation from in-vitro data, we compute elongation rates for all codons in Escherichia coli. We show that for some tRNA species only a few tRNA molecules are part of ternary complexes and, thus, available for the translating ribosomes. In addition, we find that codon-specific elongation rates strongly depend on the overall codon usage in the cell, which could be altered experimentally by overexpression of individual genes.
Collapse
Affiliation(s)
- Sophia Rudorf
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- * E-mail: (SR); (RL)
| | - Reinhard Lipowsky
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- * E-mail: (SR); (RL)
| |
Collapse
|
24
|
Biryukov J, Meyers C. Papillomavirus Infectious Pathways: A Comparison of Systems. Viruses 2015; 7:4303-25. [PMID: 26247955 PMCID: PMC4576184 DOI: 10.3390/v7082823] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 06/06/2015] [Accepted: 07/23/2015] [Indexed: 12/19/2022] Open
Abstract
The HPV viral lifecycle is tightly linked to the host cell differentiation, causing difficulty in growing virions in culture. A system that bypasses the need for differentiating epithelium has allowed for generation of recombinant particles, such as virus-like particles (VLPs), pseudovirions (PsV), and quasivirions (QV). Much of the research looking at the HPV life cycle, infectivity, and structure has been generated utilizing recombinant particles. While recombinant particles have proven to be invaluable, allowing for a rapid progression of the HPV field, there are some significant differences between recombinant particles and native virions and very few comparative studies using native virions to confirm results are done. This review serves to address the conflicting data in the HPV field regarding native virions and recombinant particles.
Collapse
Affiliation(s)
- Jennifer Biryukov
- Department of Microbiology and Immunology, The Pennsylvania State University, 500 University Drive, Hershey, PA 17033, USA.
| | - Craig Meyers
- Department of Microbiology and Immunology, The Pennsylvania State University, 500 University Drive, Hershey, PA 17033, USA.
| |
Collapse
|
25
|
Tanaka T, Hori N, Takada S. How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations. PLoS Comput Biol 2015; 11:e1004356. [PMID: 26158498 PMCID: PMC4497635 DOI: 10.1371/journal.pcbi.1004356] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/22/2015] [Indexed: 11/18/2022] Open
Abstract
Co-translational folding (CTF) facilitates correct folding in vivo, but its precise mechanism remains elusive. For the CTF of a three-domain protein SufI, it was reported that the translational attenuation is obligatory to acquire the functional state. Here, to gain structural insights on the underlying mechanisms, we performed comparative molecular simulations of SufI that mimic CTF as well as refolding schemes. A CTF scheme that relied on a codon-based prediction of translational rates exhibited folding probability markedly higher than that by the refolding scheme. When the CTF schedule is speeded up, the success rate dropped. These agree with experiments. Structural investigation clarified that misfolding of the middle domain was much more frequent in the refolding scheme than that in the codon-based CTF scheme. The middle domain is less stable and can fold via interactions with the folded N-terminal domain. Folding pathway networks showed the codon-based CTF gives narrower pathways to the native state than the refolding scheme. Proteins are synthesized in vivo by ribosome from their N-termini. When N-terminal fragments of nascent proteins get out of the ribosome exit, they start folding, which is called co-translational folding. It has been suggested that well-scheduled co-translational folding schemes would facilitate correct acquisition of their native structures for some multi-domain proteins. In particular, an un-ambiguous experiment was recently reported for a model protein, SufI where pauses at certain positions in the translational elongation are obligatory for efficient folding. Here, for the first time to our knowledge, we performed molecular dynamics simulations of SufI with co-translational folding as well as re-folding schemes. We found a co-translational folding shceme with rare codon-based pauses indeed increased the success ratio of folding, which is consistent with recent experiments. On top, molecular simulations provided much of structural insights on the folding routes and misfolding in the case of re-folding scheme. This explains why pauses in the translational elongation rescue SufI from misfolding.
Collapse
Affiliation(s)
- Tomohiro Tanaka
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Naoto Hori
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
- * E-mail:
| |
Collapse
|
26
|
Exploring codon context bias for synthetic gene design of a thermostable invertase in Escherichia coli. Enzyme Microb Technol 2015; 75-76:57-63. [DOI: 10.1016/j.enzmictec.2015.04.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/31/2015] [Accepted: 04/22/2015] [Indexed: 02/07/2023]
|
27
|
Du J, Dungan SZ, Sabouhanian A, Chang BSW. Selection on synonymous codons in mammalian rhodopsins: a possible role in optimizing translational processes. BMC Evol Biol 2014; 14:96. [PMID: 24884412 PMCID: PMC4021273 DOI: 10.1186/1471-2148-14-96] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 04/11/2014] [Indexed: 01/21/2023] Open
Abstract
Background Synonymous codon usage can affect many cellular processes, particularly those associated with translation such as polypeptide elongation and folding, mRNA degradation/stability, and splicing. Highly expressed genes are thought to experience stronger selection pressures on synonymous codons. This should result in codon usage bias even in species with relatively low effective population sizes, like mammals, where synonymous site selection is thought to be weak. Here we use phylogenetic codon-based likelihood models to explore patterns of codon usage bias in a dataset of 18 mammalian rhodopsin sequences, the protein mediating the first step in vision in the eye, and one of the most highly expressed genes in vertebrates. We use these patterns to infer selection pressures on key translational mechanisms including polypeptide elongation, protein folding, mRNA stability, and splicing. Results Overall, patterns of selection in mammalian rhodopsin appear to be correlated with post-transcriptional and translational processes. We found significant evidence for selection at synonymous sites using phylogenetic mutation-selection likelihood models, with C-ending codons found to have the highest relative fitness, and to be significantly more abundant at conserved sites. In general, these codons corresponded with the most abundant tRNAs in mammals. We found significant differences in codon usage bias between rhodopsin loops versus helices, though there was no significant difference in mean synonymous substitution rate between these motifs. We also found a significantly higher proportion of GC-ending codons at paired sites in rhodopsin mRNA secondary structure, and significantly lower synonymous mutation rates in putative exonic splicing enhancer (ESE) regions than in non-ESE regions. Conclusions By focusing on a single highly expressed gene we both distinguish synonymous codon selection from mutational effects and analytically explore underlying functional mechanisms. Our results suggest that codon bias in mammalian rhodopsin arises from selection to optimally balance high overall translational speed, accuracy, and proper protein folding, especially in structurally complicated regions. Selection at synonymous sites may also be contributing to mRNA stability and splicing efficiency at exonic-splicing-enhancer (ESE) regions. Our results highlight the importance of investigating highly expressed genes in a broader phylogenetic context in order to better understand the evolution of synonymous substitutions.
Collapse
Affiliation(s)
| | | | | | - Belinda S W Chang
- Department of Ecology & Evolutionary Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada.
| |
Collapse
|
28
|
Dammeyer T, Tinnefeld P. Engineered fluorescent proteins illuminate the bacterial periplasm. Comput Struct Biotechnol J 2012; 3:e201210013. [PMID: 24688673 PMCID: PMC3962181 DOI: 10.5936/csbj.201210013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/02/2012] [Accepted: 11/12/2012] [Indexed: 12/21/2022] Open
Abstract
The bacterial periplasm is of special interest whenever cell factories are designed and engineered. Recombinantely produced proteins are targeted to the periplasmic space of Gram negative bacteria to take advantage of the authentic N-termini, disulfide bridge formation and easy accessibility for purification with less contaminating cellular proteins. The oxidizing environment of the periplasm promotes disulfide bridge formation - a prerequisite for proper folding of many proteins into their active conformation. In contrast, the most popular reporter protein in all of cell biology, Green Fluorescent Protein (GFP), remains inactive if translocated to the periplasmic space prior to folding. Here, the self-catalyzed chromophore maturation is blocked by formation of covalent oligomers via interchain disulfide bonds in the oxidizing environment. However, different protein engineering approaches addressing folding and stability of GFP resulted in improved proteins with enhanced folding properties. Recent studies describe GFP variants that are not only active if translocated in their folded form via the twin-arginine translocation (Tat) pathway, but actively fold in the periplasm following general secretory pathway (Sec) and signal recognition particle (SRP) mediated secretion. This mini-review highlights the progress that enables new insights into bacterial export and periplasmic protein organization, as well as new biotechnological applications combining the advantages of the periplasmic production and the Aequorea-based fluorescent reporter proteins.
Collapse
Affiliation(s)
- Thorben Dammeyer
- Institut für Physikalische und Theoretische Chemie, NanoBioSciences, Technische Universität Braunschweig, Hans Sommer Str. 10, 38106 Braunschweig, Germany
| | - Philip Tinnefeld
- Institut für Physikalische und Theoretische Chemie, NanoBioSciences, Technische Universität Braunschweig, Hans Sommer Str. 10, 38106 Braunschweig, Germany
| |
Collapse
|
29
|
Silent substitutions predictably alter translation elongation rates and protein folding efficiencies. J Mol Biol 2012; 422:328-35. [PMID: 22705285 DOI: 10.1016/j.jmb.2012.06.010] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Revised: 05/31/2012] [Accepted: 06/02/2012] [Indexed: 11/23/2022]
Abstract
Genetic code redundancy allows most amino acids to be encoded by multiple codons that are non-randomly distributed along coding sequences. An accepted theory explaining the biological significance of such non-uniform codon selection is that codons are translated at different speeds. Thus, varying codon placement along a message may confer variable rates of polypeptide emergence from the ribosome, which may influence the capacity to fold toward the native state. Previous studies report conflicting results regarding whether certain codons correlate with particular structural or folding properties of the encoded protein. This is partly due to different criteria traditionally utilized for predicting translation speeds of codons, including their usage frequencies and the concentration of tRNA species capable of decoding them, which do not always correlate. Here, we developed a metric to predict organism-specific relative translation rates of codons based on the availability of tRNA decoding mechanisms: Watson-Crick, non-Watson-Crick or both types of interactions. We determine translation rates of messages by pulse-chase analyses in living Escherichia coli cells and show that sequence engineering based on these concepts predictably modulates translation rates in a manner that is superior to codon usage frequency, which occur during the elongation phase, and significantly impacts folding of the encoded polypeptide. Finally, we demonstrate that sequence harmonization based on expression host tRNA pools, designed to mimic ribosome movement of the original organism, can significantly increase the folding of the encoded polypeptide. These results illuminate how genetic code degeneracy may function to specify properties beyond amino acid encoding, including folding.
Collapse
|