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Presenting a codon-optimized palette of fluorescent proteins for use in Candida albicans. Sci Rep 2020; 10:6158. [PMID: 32273559 PMCID: PMC7145796 DOI: 10.1038/s41598-020-63308-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 03/27/2020] [Indexed: 11/20/2022] Open
Abstract
Fluorescent proteins with varying colors are indispensable tools for the life sciences research community. These fluorophores are often developed for use in mammalian systems, with incremental enhancements or new versions published frequently. However, the successful application of these labels in other organisms in the tree of life, such as the fungus Candida albicans, can be difficult to achieve due to the difficulty in engineering constructs for good expression in these organisms. In this contribution, we present a palette of Candida-optimized fluorescent proteins ranging from cyan to red and assess their application potential. We also compare a range of reported expression optimization techniques, and find that none of these strategies is generally applicable, and that even very closely related proteins require the application of different strategies to achieve good expression. In addition to reporting new fluorescent protein variants for applications in Candida albicans, our work highlights the ongoing challenges in optimizing protein expression in heterologous systems.
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Song Y, Gorbatsevych O, Liu Y, Mugavero J, Shen SH, Ward CB, Asare E, Jiang P, Paul AV, Mueller S, Wimmer E. Limits of variation, specific infectivity, and genome packaging of massively recoded poliovirus genomes. Proc Natl Acad Sci U S A 2017; 114:E8731-E8740. [PMID: 28973853 PMCID: PMC5642728 DOI: 10.1073/pnas.1714385114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Computer design and chemical synthesis generated viable variants of poliovirus type 1 (PV1), whose ORF (6,189 nucleotides) carried up to 1,297 "Max" mutations (excess of overrepresented synonymous codon pairs) or up to 2,104 "SD" mutations (randomly scrambled synonymous codons). "Min" variants (excess of underrepresented synonymous codon pairs) are nonviable except for P2Min, a variant temperature-sensitive at 33 and 39.5 °C. Compared with WT PV1, P2Min displayed a vastly reduced specific infectivity (si) (WT, 1 PFU/118 particles vs. P2Min, 1 PFU/35,000 particles), a phenotype that will be discussed broadly. Si of haploid PV presents cellular infectivity of a single genotype. We performed a comprehensive analysis of sequence and structures of the PV genome to determine if evolutionary conserved cis-acting packaging signal(s) were preserved after recoding. We showed that conserved synonymous sites and/or local secondary structures that might play a role in determining packaging specificity do not survive codon pair recoding. This makes it unlikely that numerous "cryptic, sequence-degenerate, dispersed RNA packaging signals mapping along the entire viral genome" [Patel N, et al. (2017) Nat Microbiol 2:17098] play the critical role in poliovirus packaging specificity. Considering all available evidence, we propose a two-step assembly strategy for +ssRNA viruses: step I, acquisition of packaging specificity, either (a) by specific recognition between capsid protein(s) and replication proteins (poliovirus), or (b) by the high affinity interaction of a single RNA packaging signal (PS) with capsid protein(s) (most +ssRNA viruses so far studied); step II, cocondensation of genome/capsid precursors in which an array of hairpin structures plays a role in virion formation.
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Affiliation(s)
- Yutong Song
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794;
| | - Oleksandr Gorbatsevych
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794
| | - Ying Liu
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794
- Pathology and Laboratory Medicine, Staten Island University Hospital, Staten Island, NY 10305
| | - JoAnn Mugavero
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794
| | - Sam H Shen
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794
- Department of Chemistry, University of Iowa, Iowa City, IA 52242
| | - Charles B Ward
- Google, Inc., Mountain View, CA 94043
- Department of Computer Science, Stony Brook University, Stony Brook, NY, 11794
| | - Emmanuel Asare
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794
| | - Ping Jiang
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794
| | - Aniko V Paul
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794
| | - Steffen Mueller
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794
- Codagenix Inc., Stony Brook, NY 11794
| | - Eckard Wimmer
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, 11794;
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Jin Y, Eser U, Struhl K, Churchman LS. The Ground State and Evolution of Promoter Region Directionality. Cell 2017; 170:889-898.e10. [PMID: 28803729 DOI: 10.1016/j.cell.2017.07.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 04/06/2017] [Accepted: 07/07/2017] [Indexed: 01/22/2023]
Abstract
Eukaryotic promoter regions are frequently divergently transcribed in vivo, but it is unknown whether the resultant antisense RNAs are a mechanistic by-product of RNA polymerase II (Pol II) transcription or biologically meaningful. Here, we use a functional evolutionary approach that involves nascent transcript mapping in S. cerevisiae strains containing foreign yeast DNA. Promoter regions in foreign environments lose the directionality they have in their native species. Strikingly, fortuitous promoter regions arising in foreign DNA produce equal transcription in both directions, indicating that divergent transcription is a mechanistic feature that does not imply a function for these transcripts. Fortuitous promoter regions arising during evolution promote bidirectional transcription and over time are purged through mutation or retained to enable new functionality. Similarly, human transcription is more bidirectional at newly evolved enhancers and promoter regions. Thus, promoter regions are intrinsically bidirectional and are shaped by evolution to bias transcription toward coding versus non-coding RNAs.
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Affiliation(s)
- Yi Jin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Umut Eser
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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Behura SK, Severson DW. Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes. Biol Rev Camb Philos Soc 2012; 88:49-61. [PMID: 22889422 DOI: 10.1111/j.1469-185x.2012.00242.x] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Codon usage bias refers to the phenomenon where specific codons are used more often than other synonymous codons during translation of genes, the extent of which varies within and among species. Molecular evolutionary investigations suggest that codon bias is manifested as a result of balance between mutational and translational selection of such genes and that this phenomenon is widespread across species and may contribute to genome evolution in a significant manner. With the advent of whole-genome sequencing of numerous species, both prokaryotes and eukaryotes, genome-wide patterns of codon bias are emerging in different organisms. Various factors such as expression level, GC content, recombination rates, RNA stability, codon position, gene length and others (including environmental stress and population size) can influence codon usage bias within and among species. Moreover, there has been a continuous quest towards developing new concepts and tools to measure the extent of codon usage bias of genes. In this review, we outline the fundamental concepts of evolution of the genetic code, discuss various factors that may influence biased usage of synonymous codons and then outline different principles and methods of measurement of codon usage bias. Finally, we discuss selected studies performed using whole-genome sequences of different insect species to show how codon bias patterns vary within and among genomes. We conclude with generalized remarks on specific emerging aspects of codon bias studies and highlight the recent explosion of genome-sequencing efforts on arthropods (such as twelve Drosophila species, species of ants, honeybee, Nasonia and Anopheles mosquitoes as well as the recent launch of a genome-sequencing project involving 5000 insects and other arthropods) that may help us to understand better the evolution of codon bias and its biological significance.
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Affiliation(s)
- Susanta K Behura
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA.
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Bernhardt HS, Tate WP. Evidence from glycine transfer RNA of a frozen accident at the dawn of the genetic code. Biol Direct 2008; 3:53. [PMID: 19091122 PMCID: PMC2630981 DOI: 10.1186/1745-6150-3-53] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Accepted: 12/17/2008] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Transfer RNA (tRNA) is the means by which the cell translates DNA sequence into protein according to the rules of the genetic code. A credible proposition is that tRNA was formed from the duplication of an RNA hairpin half the length of the contemporary tRNA molecule, with the point at which the hairpins were joined marked by the canonical intron insertion position found today within tRNA genes. If these hairpins possessed a 3'-CCA terminus with different combinations of stem nucleotides (the ancestral operational RNA code), specific aminoacylation and perhaps participation in some form of noncoded protein synthesis might have occurred. However, the identity of the first tRNA and the initial steps in the origin of the genetic code remain elusive. RESULTS Here we show evidence that glycine tRNA was the first tRNA, as revealed by a vestigial imprint in the anticodon loop sequences of contemporary descendents. This provides a plausible mechanism for the missing first step in the origin of the genetic code. In 448 of 466 glycine tRNA gene sequences from bacteria, archaea and eukaryote cytoplasm analyzed, CCA occurs immediately upstream of the canonical intron insertion position, suggesting the first anticodon (NCC for glycine) has been captured from the 3'-terminal CCA of one of the interacting hairpins as a result of an ancestral ligation. CONCLUSION That this imprint (including the second and third nucleotides of the glycine tRNA anticodon) has been retained through billions of years of evolution suggests Crick's 'frozen accident' hypothesis has validity for at least this very first step at the dawn of the genetic code. REVIEWERS This article was reviewed by Dr Eugene V. Koonin, Dr Rob Knight and Dr David H Ardell.
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Affiliation(s)
- Harold S Bernhardt
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand.
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Tats A, Tenson T, Remm M. Preferred and avoided codon pairs in three domains of life. BMC Genomics 2008; 9:463. [PMID: 18842120 PMCID: PMC2585594 DOI: 10.1186/1471-2164-9-463] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Accepted: 10/08/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alternative synonymous codons are not used with equal frequencies. In addition, the contexts of codons - neighboring nucleotides and neighboring codons - can have certain patterns. The codon context can influence both translational accuracy and elongation rates. However, it is not known how strong or conserved the codon context preferences in different organisms are. We analyzed 138 organisms (bacteria, archaea and eukaryotes) to find conserved patterns of codon pairs. RESULTS After removing the effects of single codon usage and dipeptide biases we discovered a set of neighboring codons for which avoidances or preferences were conserved in all three domains of life. Such biased codon pairs could be divided into subtypes on the basis of the nucleotide patterns that influence the bias. The most frequently avoided type of codon pair was nnUAnn. We discovered that 95.7% of avoided nnUAnn type patterns contain out-frame UAA or UAG triplets on the sense and/or antisense strand. On average, nnUAnn codon pairs are more frequently avoided in ORFeomes than in genomes. Thus we assume that translational selection plays a major role in the avoidance of these codon pairs. Among the preferred codon pairs, nnGCnn was the major type. CONCLUSION Translational selection shapes codon pair usage in protein coding sequences by rules that are common to all three domains of life. The most frequently avoided codon pairs contain the patterns nnUAnn, nnGGnn, nnGnnC, nnCGCn, GUCCnn, CUCCnn, nnCnnA or UUCGnn. The most frequently preferred codon pairs contain the patterns nnGCnn, nnCAnn or nnUnCn.
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Affiliation(s)
- Age Tats
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Riia str. 23, Tartu 51010, Estonia.
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