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Sciarrino A, Sorba P. Hierarchy of codon usage frequencies from codon-anticodon interaction in the crystal basis model. Biosystems 2024; 235:105102. [PMID: 38092331 DOI: 10.1016/j.biosystems.2023.105102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 12/07/2023] [Accepted: 12/10/2023] [Indexed: 01/06/2024]
Abstract
Analyzing the codon usage frequencies of a specimen of 20 plants, for which the codon-anticodon pattern is known, we have remarked that the hierarchy of the usage frequencies present an almost "universal" behavior. Searching to explain this behavior, we assume that the codon usage probability results from the sum of two contributions: the first dominant term is an almost "universal" one and it depends on the codon-anticodon interaction; the second term is a local one, i.e. depends on the biological species. The codon-anticodon interaction is written as a spin-spin plus a z-spin term in the formalism of the crystal basis model. From general considerations, in particular from the choice of the signs and some constraints on the parameters defining the interaction, we are able to explain most of the observed data.
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Affiliation(s)
| | - P Sorba
- LAPTH, Laboratoire d'Annecy-le-Vieux de Physique Théorique CNRS, Université de Savoie Mont Blanc, Chemin de Bellevue, BP 110, F-74941 Annecy-le-Vieux, France.
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2
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Li P, Zhang Y, Zhao C, Jiang M. Evolution of the Tóxicos en Levadura 63 (TL63) gene family in plants and functional characterization of Arabidopsis thaliana TL63 under oxidative stress. Planta 2023; 258:87. [PMID: 37750983 DOI: 10.1007/s00425-023-04243-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023]
Abstract
MAIN CONCLUSION TL63 orthologs were angiosperm specific and had undergone motifs loss and gain, and increased purifying selection. AtTL63 was involved in the response of yeast and Arabidopsis plants to oxidative stress. The Tóxicos en Levadura (TL) family, a class of E3 ubiquitin ligases with typical RING-H2 type zinc finger structure, plays a pivotal role in mediating physiological processes and responding to stress in plants. However, the evolution and function of TL63 remain unclear. In this study, TL63 homologs were dated roughly back to the origin of land plants and confirmed to have subjected to the gain and loss of motifs and increased purifying selection. Phylogenetic analysis displayed that 279 TL63s could be divided into four main clades (Clade A-D). Notably, the ancestral tandem TL40/41 cluster contributed to the expansion of modern Brassicaceae TL40/41. The substitution rate tests revealed that the TL63 lineage was evidently different from other lineages. The codon usage index exhibited that monocotyledons preferred to use not A3s and T3s, but C3s, G3s, CAI, CBI and Fop. Sequence analysis showed that the TL63 homologs had conserved TM and GLD motifs and RING-H2 domain whose key amino acid residues accounted for the high average abundance. Particularly, Arabidopsis thaliana TL63 (AtTL63) was located in the nuclei, cell membranes and peroxisomes and expressed universally and significantly throughout A. thaliana development. Under H2O2 treatment, low or moderate expression of the AtTL63 held beneficial effects on the growth and viability of yeast cells and the mutation or overexpression of the AtTL63 positively affected the growth of A. thaliana plants. In brief, this study could supply useful insight into the evolution of the plant TL63s and the AtTL63 functions under oxidative stress.
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Affiliation(s)
- Peng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yuxin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Changling Zhao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.
| | - Min Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
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Chen H, Zhang Y, Feng S. Whole-genome and dispersed duplication, including transposed duplication, jointly advance the evolution of TLP genes in seven representative Poaceae lineages. BMC Genomics 2023; 24:290. [PMID: 37254040 DOI: 10.1186/s12864-023-09389-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/18/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND In the evolutionary study of gene families, exploring the duplication mechanisms of gene families helps researchers understand their evolutionary history. The tubby-like protein (TLP) family is essential for growth and development in plants and animals. Much research has been done on its function; however, limited information is available with regard to the evolution of the TLP gene family. Herein, we systematically investigated the evolution of TLP genes in seven representative Poaceae lineages. RESULTS Our research showed that the evolution of TLP genes was influenced not only by whole-genome duplication (WGD) and dispersed duplication (DSD) but also by transposed duplication (TRD), which has been neglected in previous research. For TLP family size, we found an evolutionary pattern of progressive shrinking in the grass family. Furthermore, the evolution of the TLP gene family was at least affected by evolutionary driving forces such as duplication, purifying selection, and base mutations. CONCLUSIONS This study presents the first comprehensive evolutionary analysis of the TLP gene family in grasses. We demonstrated that the TLP gene family is also influenced by a transposed duplication mechanism. Several new insights into the evolution of the TLP gene family are presented. This work provides a good reference for studying gene evolution and the origin of duplication.
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Affiliation(s)
- Huilong Chen
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yingchao Zhang
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.
| | - Shuyan Feng
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
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Pavan-Kumar A, Singh S, Mishra A, Suman S, Gireesh-Babu P, Chaudhari A, Shen KN, Borsa P. Characterization of mitochondrial genome of Indian Ocean blue-spotted maskray, Neotrygon indica and its phylogenetic relationship within Dasyatidae Family. Int J Biol Macromol 2022; 223:458-67. [PMID: 36347369 DOI: 10.1016/j.ijbiomac.2022.10.277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 10/11/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
Abstract
The present study characterized complete mitochondrial genome of Blue-spotted maskray, Neotrygon indica and studied the evolutionary relationship of the species within the Dasyatidae family. The total length of the mitogenome was 17,974 bp including 37 genes and a non-coding control region. The average frequency of nucleotides in protein-coding genes was A: 29.1 %, T: 30.2 %, G: 13.0 % and C: 27.7 % with AT content of 59.3 %. The values of AT and GC skewness were -0.018 and -0.338, respectively. Comparative analyses showed a large number of average synonymous substitutions per synonymous site (Ks) in gene NADH4 (5.07) followed by NADH5 (4.72). High values of average number of non-synonymous substitutions per non-synonymous site (Ka) were observed in genes ATPase8 (0.54) and NADH2 (0.44). Genes NADH4L and NADH2 showed high interspecific genetic distance values of 0.224 ± 0.001 and 0.213 ± 0.002, respectively. Heat map analysis showed variation in codon usage among different species of the Dasyatidae family. The phylogenetic tree showed a sister relationship between the Dasyatinae and the Neotrygoninae subfamilies. Neotrygon indica formed as a sister species to the clade consisting of N. varidens and N. orientalis. Based on the present results, Neotrygon indica could have diverged from the common ancestor of the two latter in the Plio-Pleistocene. The present study showed distinct characteristics of N. indica from its congeners through comparative mitogenomics.
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Oliveira HP, Dos Santos ER, Harrison RL, Ribeiro BM, Ardisson-Araújo DMP. Identification and analysis of putative tRNA genes in baculovirus genomes. Virus Res 2022; 322:198949. [PMID: 36181979 DOI: 10.1016/j.virusres.2022.198949] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 12/24/2022]
Abstract
Transfer RNAs (tRNAs) genes are both coded for and arranged along some viral genomes representing the entire virosphere and seem to play different biological functions during infection, other than transferring the correct amino acid to a growing peptide chain. Baculovirus genome description and annotation has focused mostly on protein-coding genes, microRNA, and homologous regions. Here we carried out a large-scale in silico search for putative tRNA genes in baculovirus genomes. Ninety-six of 257 baculovirus genomes analyzed was found to contain at least one putative tRNA gene. We found great diversity in primary and secondary structure, in location within the genome, in intron presence and size, and in anti-codon identity. In some cases, genes of tRNA-containing genomes were found to have a bias for the codons specified by the tRNAs present in such genomes. Moreover, analysis revealed that most of the putative tRNA genes possessed conserved motifs for tRNA type 2 promoters, including the A-box and B-box motifs with few mismatches from the eukaryotic canonical motifs. From publicly available small RNA deep sequencing datasets of baculovirus-infected insect cells, we found evidence that a putative Autographa californica multiple nucleopolyhedrovirus Gln-tRNA gene was transcribed and modified with the addition of the non-templated 3'-CCA tail found at the end of all tRNAs. Further research is needed to determine the expression and functionality of these viral tRNAs.
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Smith RD. Enhanced effective codon numbers to understand codon usage bias. Biosystems 2022; 220:104734. [PMID: 35842072 DOI: 10.1016/j.biosystems.2022.104734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 11/27/2022]
Abstract
Codon usage bias is a well recognized phenomenon but the relative influence of its major causes: G+C content, mutational biases, and selection, are often difficult to disentangle. This paper presents methods to calculate modified effective codon numbers that allow the investigation of the sources of codon bias and how genes or organisms have their codon biases shaped. In particular, it demonstrates that variation in codon usage bias across organisms is likely driven more by likely mutational forces while the variation in codon usage bias within genomes is likely driven by codon selectional forces.
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Affiliation(s)
- Reginald D Smith
- Ronin Institute 127 Haddon Pl, Montclair, NJ 07043, United States of America; Supreme Vinegar LLC, 3430 Progress Dr. Suite D, Bensalem, PA 19020, United States of America.
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Abdoli R, Mazumder TH, Nematollahian S, Zanjani RS, Mesbah RA, Uddin A. Gaining insights into the compositional constraints and molecular phylogeny of five silkworms mitochondrial genome. Int J Biol Macromol 2022; 206:543-552. [PMID: 35245576 DOI: 10.1016/j.ijbiomac.2022.02.135] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/08/2021] [Accepted: 02/22/2022] [Indexed: 11/28/2022]
Abstract
This study was performed to identify codon usage bias (CUB), genetic similarity and phylogenetic analysis of complete mitochondrial genomes along with separate sequences of 13 protein coding genes per each genome from five types of silkworm including Bombyx mori, Bombyx mandarina, Samia cynthia ricini, Antheraea pernyi and Antheraea assama. Nucleotide composition analysis suggested that AT content was higher than GC content and t-test analysis revealed significance difference (p < 0.01) between AT and GC content. Relative synonymous CUB analysis revealed most over-represented codon ends with A or T. Parity plot analysis revealed both natural selection and mutation pressure influenced CUB of mitochondrial genes while neutrality plot analysis suggested that role of natural selection was higher than mutation pressure. The effective number of codons (ENC) revealed the CUB was low among genes and genomes. In phylogenetic analysis of complete mitochondrial genomes, the B. mori fell in a same cluster with Bombyx mandarina and showed the most similarity (96.7%). In terms of protein coding genes, COX1, COX2 and COX3 showed the most obvious differences. In conclusion, comparative analysis of mitochondrial genomes could be used to identify differences in gene organization, accurate phylogenetic analysis and clustering of different types of silkworms.
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Affiliation(s)
- Ramin Abdoli
- Iran Silk Research Center, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran.
| | | | - Shahla Nematollahian
- Iran Silk Research Center, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Reza Sourati Zanjani
- Iran Silk Research Center, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Rahim Abdollahi Mesbah
- Iran Silk Research Center, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi 788150, Assam, India.
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Singh VK, Nain V, Phanindra MLV, Gothandapani S, Chhapekar SS, Sreevathsa R, Sambasiva Rao KRS, Kumar PA, Kumar A. Rifampicin Increases Expression of Plant Codon-Optimized Bacillus thuringiensis δ-Endotoxin Genes in Escherichia coli. Protein J 2022; 41:327-336. [PMID: 35119603 DOI: 10.1007/s10930-022-10043-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2022] [Indexed: 10/19/2022]
Abstract
Transgenic crops expressing Cry δ-endotoxins of Bacillus thuringiensis for insect resistance have been commercialized worldwide with increased crop productivity and spectacular socioeconomic gains. To attain the enhanced level of protein expression, the cry genes have to be extensively modified for RNA stability and translation efficiency in the plant systems. However, such modifications in nucleotide sequences make it difficult to express the cry genes in Escherichia coli because of the presence of E. coli rare codons. Induction of gene expression through the T7 promoter/lac operator system results in high levels of transcription but limits the availability of activated tRNA corresponding to rare codons that leads to translation stalling at ribosomes. In the present study, an Isopropyl ß-D-1-thiogalactopyranoside (IPTG)/rifampicin combination-based approach was adopted to induce transcription of cry genes through T7 promoter/lac operator while simultaneously inhibiting the transcription of host genes through rifampicin. The results show that the IPTG/rifampicin combination leads to high-level expression of four plant codon-optimized cry genes (cry2Aa, cry1F, cry1Ac, and cry1AcF). Northern blot analysis of the cry gene expressing E. coli samples showed that the RNA expression level in the IPTG-induced samples was higher as compared to that in the IPTG/rifampicin-induced samples. Diet overlay insect bioassay of IPTG/rifampicin-induced Cry toxins with Helicoverpa armigera larvae showed bioactivity (measured as LC50) similar to the previous studies. The experiment has proved that recombinant synthetic gene (plant codon-optimized gene) with the combination of Rifampicin which inhibits DNA-dependent bacterial RNA polymerase and reduces the excessive baggage of translational machinery of the bacterial cell triggers the production of synthetic protein. Purification of protein using high pH buffer increases the solubility of the protein. Further, LC50 analysis shows no reduction of protein activity leads to protein stability. Further, purified cry toxin protein can be used for crop protection against pests and a purified form of the synthetic protein can be used for antibody production and perform the immunoassay for the identification of the transgenic plant. The crystallographic structure of synthetic protein could be used for interaction study with another insect to see insecticidal activity.
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Affiliation(s)
- Vivek Kumar Singh
- ICAR-National Research Centre On Plant Biotechnology, New Delhi, India.,Department of Biotechnology, National Institute of Technology, Raipur, India
| | - Vikrant Nain
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | | | | | | | - Rohini Sreevathsa
- ICAR-National Research Centre On Plant Biotechnology, New Delhi, India
| | | | | | - Awanish Kumar
- Department of Biotechnology, National Institute of Technology, Raipur, India.
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Cappannini A, Forcelloni S, Giansanti A. Evolutionary pressures and codon bias in low complexity regions of plasmodia. Genetica 2021; 149:217-237. [PMID: 34254217 DOI: 10.1007/s10709-021-00126-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 06/30/2021] [Indexed: 11/25/2022]
Abstract
The biological meaning of low complexity regions in the proteins of Plasmodium species is a topic of discussion in evolutionary biology. There is a debate between selectionists and neutralists, who either attribute or do not attribute an effect of low-complexity regions on the fitness of these parasites, respectively. In this work, we comparatively study 22 Plasmodium species to understand whether their low complexity regions undergo a neutral or, rather, a selective and species-dependent evolution. The focus is on the connection between the codon repertoire of the genetic coding sequences and the occurrence of low complexity regions in the corresponding proteins. The first part of the work concerns the correlation between the length of plasmodial proteins and their propensity at embedding low complexity regions. Relative synonymous codon usage, entropy, and other indicators reveal that the incidence of low complexity regions and their codon bias is species-specific and subject to selective evolutionary pressure. We also observed that protein length, a relaxed selective pressure, and a broad repertoire of codons in proteins, are strongly correlated with the occurrence of low complexity regions. Overall, it seems plausible that the codon bias of low-complexity regions contributes to functional innovation and codon bias enhancement of proteins on which Plasmodium species rest as successful evolutionary parasites.
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Affiliation(s)
- Andrea Cappannini
- Department of Physics, Sapienza, University of Rome, P.le A. Moro 5, 00185, Roma, Italy.
| | - Sergio Forcelloni
- Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.,Department of Chemistry, Technical University of Munich, 85748, Garching, Germany
| | - Andrea Giansanti
- Department of Physics, Sapienza, University of Rome, P.le A. Moro 5, 00185, Roma, Italy.,Istituto Nazionale di Fisica Nucleare, INFN, Roma1 section. 00185, Roma, Italy
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Tadi SRR, Nehru G, Sivaprakasam S. Combinatorial approach for improved production of whole-cell 3-aminopropionic acid in recombinant Bacillus megaterium: codon optimization, gene duplication and process optimization. 3 Biotech 2021; 11:333. [PMID: 34221804 DOI: 10.1007/s13205-021-02885-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/06/2021] [Indexed: 12/22/2022] Open
Abstract
In this study, we aimed to develop a Bacillus megaterium based whole-cell biocatalyst for the bio-production of 3-aminopropionic acid (3-APA). l-aspartate-α-decarboxylases (ADC) (EC: 4.1.1.11) from Escherichia coli, B. megaterium, Corynebacterium glutamicum, and Bacillus subtilis were expressed in B. megaterium. B. subtilis derived ADC (panD Bs ) exhibited the highest ADC activity of 0.9 ± 0.02 U/mL in recombinant B. megaterium. Combination of codon optimization and gene duplication strategies resulted in 415.56% enhancement of ADC activity compared to panD Bs . The culture growth conditions of B. megaterium (BMD-7) for 3-APA production were optimized as follows: inducer concentration, 0.5% (w/v); time of induction, 3 h; induction temperature, 37 °C and post-induction incubation time, 8 h. Improvement of the whole-cell biocatalytic process efficiency, was dealt by optimization of reaction temperature, reaction pH, metal ion additives and l-aspartic acid concentration. Shake flask level experiments yielded an enhanced 3-APA titer (16.18 ± 0.26 g/L) and a yield of 0.89 g/g under optimized conditions viz., 45 °C, pH 6.0 and 20 g/L of l-aspartic acid. This study demonstrates the potential of B. megaterium for 3-APA production and paves the scope for the development of 3-APA producing strains in near future. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02885-7.
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Xu Y, Liu K, Han Y, Xing Y, Zhang Y, Yang Q, Zhou M. Codon usage bias regulates gene expression and protein conformation in yeast expression system P. pastoris. Microb Cell Fact 2021; 20:91. [PMID: 33902585 PMCID: PMC8077831 DOI: 10.1186/s12934-021-01580-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/13/2021] [Indexed: 11/30/2022] Open
Abstract
Background Protein synthesis is one of the extremely important anabolic pathways in the yeast expression system Pichia pastoris. Codon optimization is a commonly adopted strategy for improved protein expression, although unexpected failures did appear sometimes waiting for further exploration. Recently codon bias has been studied to regulate protein folding and activity in many other organisms. Results Here the codon bias profile of P. pastoris genome was examined first and a direct correlation between codon translation efficiency and usage frequency was identified. By manipulating the codon choices of both endogenous and heterologous signal peptides, secretion abilities of N-terminal signal peptides were shown to be tolerant towards codon changes. Then two gene candidates with different levels of structural disorder were studied, and full-length codon optimization was found to affect their expression profiles differentially. Finally, more evidences were provided to support possible protein conformation change brought by codon optimization in structurally disordered proteins. Conclusion Our results suggest that codon bias regulates gene expression by modulating several factors including transcription and translation efficiency, protein folding and activity. Because of sequences difference, the extent of affection may be gene specific. For some genes, special codon optimization strategy should be adopted to ensure appropriate expression and conformation. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01580-9.
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Affiliation(s)
- Yichun Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Kunshan Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yu Han
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yanzi Xing
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Qiuying Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, 430062, China
| | - Mian Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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Abstract
In each genome, synonymous codons are used with different frequencies; this general phenomenon is known as codon usage bias. It has been previously recognised that codon usage bias could affect the cellular fitness and might be associated with the ecology of microbial organisms. In this exploratory study, we investigated the relationship between codon usage bias, lifestyles (thermophiles vs. mesophiles; pathogenic vs. non-pathogenic; halophilic vs. non-halophilic; aerobic vs. anaerobic and facultative) and habitats (aquatic, terrestrial, host-associated, specialised, multiple) of 615 microbial organisms (544 bacteria and 71 archaea). Principal component analysis revealed that species with given phenotypic traits and living in similar environmental conditions have similar codon preferences, as represented by the relative synonymous codon usage (RSCU) index, and similar spectra of tRNA availability, as gauged by the tRNA gene copy number (tGCN). Moreover, by measuring the average tRNA adaptation index (tAI) for each genome, an index that can be associated with translational efficiency, we observed that organisms able to live in multiple habitats, including facultative organisms, mesophiles and pathogenic bacteria, are characterised by a reduced translational efficiency, consistently with their need to adapt to different environments. Our results show that synonymous codon choices might be under strong translational selection, which modulates the choice of the codons to differently match tRNA availability, depending on the organism’s lifestyle needs. To our knowledge, this is the first large-scale study that examines the role of codon bias and translational efficiency in the adaptation of microbial organisms to the environment in which they live.
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Affiliation(s)
- Davide Arella
- Department of Physics, Sapienza University of Rome, 00185, Rome, Italy.
| | - Maddalena Dilucca
- Department of Physics, Sapienza University of Rome, 001885, Rome, Italy
| | - Andrea Giansanti
- Department of Physics, Sapienza University of Rome, 00185, Rome, Italy
- INFN, Roma1 Unit, 00185, Rome, Italy
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Halder T, Verma SP, Raj J, Pandey S, Singh RK, Sharma V, Joshi D, Das P. Identification & characterization of leucine-rich repeat kinase 2 & parkin RBR E3 ubiquitin protein ligase variants in patients with Parkinson's disease. Indian J Med Res 2021; 152:498-507. [PMID: 33707392 PMCID: PMC8157902 DOI: 10.4103/ijmr.ijmr_730_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background & objectives: Parkinson's disease (PD) is a motor disorder that affects movement. More than 24 loci and 28 associated genes have been identified to be associated with this disease. The present study accounts for the contribution of two candidates, leucine-rich repeat kinase 2 (LRRK2) and parkin RBR E3 ubiquitin protein ligase (PRKN) in the PD patients, and their characterization in silico and in vitro. Methods: A total of 145 sporadic PD cases and 120 ethnically matched healthy controls were enrolled with their informed consent. Mutation screening was performed by direct DNA sequencing of the targeted exons of LRRK2 and all exons flanking introns of PRKN. The effect of the pathogenic PRKN variants on a drug (MG-132) induced loss of mitochondrial membrane potential (△ΨM) was measured by a fluorescent dye tetramethylrhodamine methyl ester (TMRM). Results: Twelve and 20 genetic variants were identified in LRRK2 and PRKN, respectively. Interestingly, five out of seven exonic LRRK2 variants were synonymous. Further assessment in controls confirmed the rarity of two such p.Y1527 and p.V1615. Among the pathogenic missense variations (as predicted in silico) in PRKN, two were selected (p.R42H and p.A82E) for their functional study in vitro, which revealed the reduced fluorescence intensity of TMRM as compared to wild type, in case of p.R42H but not the other. Interpretation & conclusions: About 6.2 per cent of the cases (9/145) in the studied patient cohort were found to carry pathogenic (as predicted in silico) missense variations in PRKN in heterozygous condition but not in case of LRRK2 which was rare. The presence of two rare synonymous variants of LRRK2 (p.Y1527 and p.V1615) may support the phenomenon of codon bias. Functional characterization of selected PRKN variations revealed p.R42H to cause disruption of mitochondrial membrane potential (△ΨM) rendering cells more susceptible to cellular stress.
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Affiliation(s)
- Tamali Halder
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Shiv Prakash Verma
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Janak Raj
- Department of Neurosurgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Sharad Pandey
- Department of Neurosurgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Ranjeet Kumar Singh
- Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Vivek Sharma
- Department of Neurosurgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Deepika Joshi
- Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Parimal Das
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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14
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Guo G, Wang Y, Hu XM, Li ZR, Tan J, Qiao WT. Human Schlafen 11 exploits codon preference discrimination to attenuate viral protein synthesis of prototype foamy virus (PFV). Virology 2020; 555:78-88. [PMID: 33465725 DOI: 10.1016/j.virol.2020.12.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 12/27/2022]
Abstract
Recently, the Schlafen (SLFN) proteins have been identified as a novel interferon-stimulated family with antiviral properties. In this study, we reported that SLFN11 inhibited prototype foamy virus (PFV) replication. Over-expression of human SLFN11 reduced viral production, while knockdown of SLFN11 enhanced viral infectivity. In addition, SLFN11 from cattle and African green monkey also suppressed PFV production. Both the ATPase activity and helicase activity of SLFN11 were required for its inhibitory function. Dephosphorylation activated the antiviral activity of SLFN11. More importantly, SLFN11 inhibited the expression of viral protein, which was rescued by viral gene codon optimization. Together, our results demonstrated that SLFN11 impaired PFV viral protein synthesis by exploiting the distinct codon usage between the virus and the host. These findings further broaden our understanding of the antiviral properties of the SLFN family and the molecular mechanism of PFV latent infection.
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Affiliation(s)
- Ge Guo
- Key Laboratory of Molecular Microbiology and Biotechnology (Ministry of Education) and Key Laboratory of Microbial Functional Genomics (Tianjin), College of Life Sciences, Nankai University, Tianjin, China
| | - Yang Wang
- Key Laboratory of Molecular Microbiology and Biotechnology (Ministry of Education) and Key Laboratory of Microbial Functional Genomics (Tianjin), College of Life Sciences, Nankai University, Tianjin, China
| | - Xiao-Mei Hu
- Key Laboratory of Molecular Microbiology and Biotechnology (Ministry of Education) and Key Laboratory of Microbial Functional Genomics (Tianjin), College of Life Sciences, Nankai University, Tianjin, China
| | - Zhuo-Ran Li
- Key Laboratory of Molecular Microbiology and Biotechnology (Ministry of Education) and Key Laboratory of Microbial Functional Genomics (Tianjin), College of Life Sciences, Nankai University, Tianjin, China
| | - Juan Tan
- Key Laboratory of Molecular Microbiology and Biotechnology (Ministry of Education) and Key Laboratory of Microbial Functional Genomics (Tianjin), College of Life Sciences, Nankai University, Tianjin, China
| | - Wen-Tao Qiao
- Key Laboratory of Molecular Microbiology and Biotechnology (Ministry of Education) and Key Laboratory of Microbial Functional Genomics (Tianjin), College of Life Sciences, Nankai University, Tianjin, China.
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15
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Dasari CM, Bhukya R. Comparative analysis of protein synthesis rate in COVID-19 with other human coronaviruses. Infect Genet Evol 2020; 85:104432. [PMID: 32592845 PMCID: PMC7314694 DOI: 10.1016/j.meegid.2020.104432] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/07/2020] [Accepted: 06/15/2020] [Indexed: 12/24/2022]
Abstract
The genetic code contains information that impacts the efficiency and rate of translation. Translation elongation plays a crucial role in determining the composition of the proteome, errors within a protein contributes towards disease processes. It is important to analyze the novel coronavirus (2019-nCoV) at the codon level to find similarities and variations in hosts to compare with other human coronavirus (CoVs). This requires a comparative and comprehensive study of various human and zoonotic nature CoVs relating to codon usage bias, relative synonymous codon usage (RSCU), proportions of slow codons, and slow di-codons, the effective number of codons (ENC), mutation bias, codon adaptation index (CAI), and codon frequencies. In this work, seven different CoVs were analyzed to determine the protein synthesis rate and the adaptation of these viruses to the host cell. The result reveals that the proportions of slow codons and slow di-codons in human host of 2019-nCoV and SARS-CoV found to be similar and very less compared to the other five coronavirus types, which suggest that the 2019-nCoV and SARS-CoV have faster protein synthesis rate. Zoonotic CoVs have high RSCU and codon adaptation index than human CoVs which implies the high translation rate in zoonotic viruses. All CoVs have more AT% than GC% in genetic codon compositions. The average ENC values of seven CoVs ranged between 38.36 and 49.55, which implies the CoVs are highly conserved and are easily adapted to host cells. The mutation rate of 2019-nCoV is comparatively less than MERS-CoV and NL63 that shows an evidence for genetic diversity. Host-specific codon composition analysis portrays the relation between viral host sequences and the capability of novel virus replication in host cells. Moreover, the analysis provides useful measures for evaluating a virus-host adaptation, transmission potential of novel viruses, and thus contributes to the strategies of anti-viral drug design.
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Affiliation(s)
- Chandra Mohan Dasari
- Department of Computer Science and Engineering, National Institute of Technology, Warangal, Telangana-506004, India.
| | - Raju Bhukya
- Department of Computer Science and Engineering, National Institute of Technology, Warangal, Telangana-506004, India.
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16
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Hia F, Takeuchi O. The effects of codon bias and optimality on mRNA and protein regulation. Cell Mol Life Sci 2020; 78:1909-1928. [PMID: 33128106 DOI: 10.1007/s00018-020-03685-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/05/2020] [Accepted: 10/12/2020] [Indexed: 12/25/2022]
Abstract
The central dogma of molecular biology entails that genetic information is transferred from nucleic acid to proteins. Notwithstanding retro-transcribing genetic elements, DNA is transcribed to RNA which in turn is translated into proteins. Recent advancements have shown that each stage is regulated to control protein abundances for a variety of essential physiological processes. In this regard, mRNA regulation is essential in fine-tuning or calibrating protein abundances. In this review, we would like to discuss one of several mRNA-intrinsic features of mRNA regulation that has been gaining traction of recent-codon bias and optimality. Specifically, we address the effects of codon bias with regard to codon optimality in several biological processes centred on translation, such as mRNA stability and protein folding among others. Finally, we examine how different organisms or cell types, through this system, are able to coordinate physiological pathways to respond to a variety of stress or growth conditions.
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Affiliation(s)
- Fabian Hia
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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17
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Gonzalez A, Corsini G, Lobos S, Seelenfreund D, Tello M. Metabolic Specialization and Codon Preference of Lignocellulolytic Genes in the White Rot Basidiomycete Ceriporiopsis subvermispora. Genes (Basel) 2020; 11:genes11101227. [PMID: 33092062 PMCID: PMC7588917 DOI: 10.3390/genes11101227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 11/16/2022] Open
Abstract
Ceriporiopsis subvermispora is a white-rot fungus with a high specificity towards lignin mineralization when colonizing dead wood or lignocellulosic compounds. Its lignocellulose degrading system is formed by cellulose hydrolytic enzymes, manganese peroxidases, and laccases that catalyze the efficient depolymerization and mineralization of lignocellulose. To determine if this metabolic specialization has modified codon usage of the lignocellulolytic system, improving its adaptation to the fungal translational machine, we analyzed the adaptation to host codon usage (CAI), tRNA pool (tAI, and AAtAI), codon pair bias (CPB), and the number of effective codons (Nc). These indexes were correlated with gene expression of C. subvermispora, in the presence of glucose and Aspen wood. General gene expression was not correlated with the index values. However, in media containing Aspen wood, the induction of expression of lignocellulose-degrading genes, showed significantly (p < 0.001) higher values of CAI, AAtAI, CPB, tAI, and lower values of Nc than non-induced genes. Cellulose-binding proteins and manganese peroxidases presented the highest adaptation values. We also identified an expansion of genes encoding glycine and glutamic acid tRNAs. Our results suggest that the metabolic specialization to use wood as the sole carbon source has introduced a bias in the codon usage of genes involved in lignocellulose degradation. This bias reduces codon diversity and increases codon usage adaptation to the tRNA pool available in C. subvermispora. To our knowledge, this is the first study showing that codon usage is modified to improve the translation efficiency of a group of genes involved in a particular metabolic process.
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Affiliation(s)
- Alex Gonzalez
- Laboratorio de Microbiología Ambiental y Extremófilos, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de los Lagos, Osorno 5290000, Chile;
| | - Gino Corsini
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8910132, Chile;
| | - Sergio Lobos
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380492, Chile; (S.L.); (D.S.)
| | - Daniela Seelenfreund
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380492, Chile; (S.L.); (D.S.)
| | - Mario Tello
- Laboratorio de Metagenómica Bacteriana, Centro de Biotecnología Acuícola, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9170002, Chile
- Correspondence:
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18
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Dutta R, Buragohain L, Borah P. Analysis of codon usage of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) and its adaptability in dog. Virus Res 2020; 288:198113. [PMID: 32771430 PMCID: PMC7410794 DOI: 10.1016/j.virusres.2020.198113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 01/10/2023]
Abstract
Codon analysis reveal natural selection and other undefined factors dominates the overall codon usage bias in SARS-CoV-2 rather than mutational pressure. The host adaptation potential of SARS-CoV-2 is more in human as compared to dog.
Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is recognized as one of the life-threatening viruses causing the most destructive pandemic in this century. The genesis of this virus is still unknown. To elucidate its molecular evolution and regulation of gene expression, the knowledge of codon usage is a pre-requisite. In this study, an attempt was made to document the genome-wide codon usage profile and the various factors influencing the codon usage patterns of SARS-CoV-2 in human and dog. The SARS-CoV-2 genome showed relative abundance of A and U nucleotides and relative synonymous codon usage analysis revealed that the preferred synonymous codons mostly end with A/U. The analysis of ENc-GC3s, Neutrality and Parity rule 2 plots indicated that natural selection and other undefined factors dominate the overall codon usage bias in SARS-CoV-2 whereas the impact of mutation pressure is comparatively minor. The codon adaptation index and relative codon deoptimization index of SARS-CoV-2 deciphered that human is more favoured host for adaptation compared to dog. These results enhance our understanding of the factors involved in evolution of the novel human SARS-CoV-2 and its adaptability in dog.
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Affiliation(s)
- Rupam Dutta
- Department of Animal Biotechnology, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati 22, Assam, India.
| | - Lukumoni Buragohain
- Department of Animal Biotechnology, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati 22, Assam, India
| | - Probodh Borah
- Department of Animal Biotechnology, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati 22, Assam, India
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19
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Gómez MM, de Mello Volotão E, Assandri IR, Peyrou M, Cristina J. Analysis of codon usage bias in potato virus Y non-recombinant strains. Virus Res 2020; 286:198077. [PMID: 32619560 DOI: 10.1016/j.virusres.2020.198077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 11/30/2022]
Abstract
Potato virus Y (PVY) is a member of the genus Potyvirus, family Potyviridae, is considered one of the most devastating pest affecting economically important crops, such as potato, tobacco, tomato and pepper, representing a serious threat due to high incidence and worldwide distribution. Its economic significance as well as it biological and molecular complexities have aroused great attention, thus several studies have explore it genetic characteristics. However, little is known about PVY codon usage. To shed light on the relation of codon usage among viruses and their hosts is extremely important to understand virus survival, fitness and evolution. In this study, we performed a comprehensive analysis of codon usage and composition of PVY non-recombinant strains (PVYN-NA, PVYEu-N, PVYO, PVYO5, PVYC) based on 130 complete open reading frame sequences extracted from public databases. Furthermore, similarities between the synonymous codon usage of PVY and its main hosts were investigated. The results obtained in the current study suggest that the overall codon usage among PVY genotypes is similar and slightly biased. PVY codon usage is strongly influenced by mutational bias, but also by G + C compositional constraint and dinucleotide composition. Furthermore, similarities among codon usage preferences between PVY strains and analyzed hosts were observed.
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Affiliation(s)
- Mariela Martínez Gómez
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, 11600, Montevideo, Uruguay.
| | - Eduardo de Mello Volotão
- Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, 11600, Montevideo, Uruguay
| | - Isabel Rodríguez Assandri
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, 11600, Montevideo, Uruguay
| | - Mercedes Peyrou
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, 11600, Montevideo, Uruguay
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Igua 4225, 11400, Montevideo, Uruguay
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20
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Abstract
The relationship between patterns of codon usage bias (CUB), the preferential usage of synonimous nucleotide triplets encoding the same amino acid, and radioresistance was investigated int he genomes of 16 taxonomically distinct radioresistant prokaryotic organisms and in a control set of 11 non-radioresistant bacteria. The radioresistant species were found to be strongly biased towards G and C in the third synonimous codon position. ENC and neutrality plots also sugest that CUB in radioresistant bacteria is mainly affected by mutational bias. Furthermore, the availability of tRNA gene copy number was analyzed and it was found that nine radioresistant species have the sam number of tRNA gene copies for each codon. This suggests that tRNA gene copies and codon bias co-evolved in a specific way in radioresistant species.
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Affiliation(s)
| | - Athanasia Pavlopoulou
- Izmir International Biomedicine and Genome Institute (iBG-Izmir), Dokuz Eyll University, 35340, Turkey
| | - Alexandros G Georgakilas
- Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Athens, Greece
| | - Andrea Giansanti
- Physics Department, Sapienza University of Rome, Rome, Italy; INFN Roma1 Unit, Rome, Italy
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21
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Sheikh A, Al-Taher A, Al-Nazawi M, Al-Mubarak AI, Kandeel M. Analysis of preferred codon usage in the coronavirus N genes and their implications for genome evolution and vaccine design. J Virol Methods 2020; 277:113806. [PMID: 31911390 PMCID: PMC7119019 DOI: 10.1016/j.jviromet.2019.113806] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 11/24/2019] [Accepted: 12/20/2019] [Indexed: 02/08/2023]
Abstract
The nucleotide variations among the N genes of 13 different coronaviruses (CoVs) were interpreted. Overall, 18 amino acids observed with varying preferred codons. The effective number of codon values ranged from 40.43 to 53.85, revealing a slight codon bias. A highly significant correlation between GC3s and ENc values was observed in porcine epidemic diarrhea CoV, followed by Middle East respiratory syndrome CoV.
The nucleocapsid (N) protein of a coronavirus plays a crucial role in virus assembly and in its RNA transcription. It is important to characterize a virus at the nucleotide level to discover the virus’s genomic sequence variations and similarities relative to other viruses that could have an impact on the functions of its genes and proteins. This entails a comprehensive and comparative analysis of the viral genomes of interest for preferred nucleotides, codon bias, nucleotide changes at the 3rd position (NT3s), synonymous codon usage and relative synonymous codon usage. In this study, the variations in the N proteins among 13 different coronaviruses (CoVs) were analysed at the nucleotide and amino acid levels in an attempt to reveal how these viruses adapt to their hosts relative to their preferred codon usage in the N genes. The results revealed that, overall, eighteen amino acids had different preferred codons and eight of these were over-biased. The N genes had a higher AT% over GC% and the values of their effective number of codons ranged from 40.43 to 53.85, indicating a slight codon bias. Neutrality plots and correlation analyses showed a very high level of GC3s/GC correlation in porcine epidemic diarrhea CoV (pedCoV), followed by Middle East respiratory syndrome-CoV (MERS CoV), porcine delta CoV (dCoV), bat CoV (bCoV) and feline CoV (fCoV) with r values 0.81, 0.68, -0.47, 0.98 and 0.58, respectively. These data implied a high rate of evolution of the CoV genomes and a strong influence of mutation on evolutionary selection in the CoV N genes. This type of genetic analysis would be useful for evaluating a virus’s host adaptation, evolution and is thus of value to vaccine design strategies.
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Affiliation(s)
- Abdullah Sheikh
- The Camel Research Center, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia
| | - Abdulla Al-Taher
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia
| | - Mohammed Al-Nazawi
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia
| | - Abdullah I Al-Mubarak
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia
| | - Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Alhofuf, Alahsa 31982, Saudi Arabia; Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
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22
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Shi SL, Xia RX. Codon Usage in the Iflaviridae Family Is Not Diverse Though the Family Members Are Isolated from Diverse Host Taxa. Viruses 2019; 11:E1087. [PMID: 31766648 PMCID: PMC6950266 DOI: 10.3390/v11121087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/17/2019] [Accepted: 11/20/2019] [Indexed: 12/12/2022] Open
Abstract
All iflavirus members belong to the unique genus, Iflavirus, of the family, Iflaviridae. The host taxa and sequence identities of these viruses are diverse. A codon usage bias, maintained by a balance between selection, mutation, and genetic drift, exists in a wide variety of organisms. We characterized the codon usage patterns of 44 iflavirus genomes that were isolated from the classes, Insecta, Arachnida, Mammalia, and Malacostraca. Iflaviruses lack a strong codon usage bias when they are evaluated using an effective number of codons. The odds ratios of the majority of dinucleotides are within the normal range. However, the dinucleotides at the 1st-2nd codon positions are more biased than those at the 2nd-3rd codon positions. Plots of effective numbers of codons, relative neutrality analysis, and PR2 bias analysis all indicate that selection pressure dominates mutations in shaping codon usage patterns in the family, Iflaviridae. When these viruses were grouped into their host taxa, we found that the indices, including the nucleotide composition, effective number of codons, relative synonymous codon usage, and the influencing factors behind the codon usage patterns, all show that there are non-significant differences between the six host-taxa-groups. Our results disagree with our assumption that diverse viruses should possess diverse codon usage patterns, suggesting that the nucleotide composition and codon usage in the family, Iflaviridae, are not host taxa-specific signatures.
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Affiliation(s)
| | - Run-Xi Xia
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China;
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23
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Abstract
BACKGROUND The uneven use of synonymous codons in the transcriptome regulates the efficiency and fidelity of protein translation rates. Yet, the importance of this codon bias in regulating cell state-specific expression programmes is currently debated. Here, we ask whether different codon usage controls gene expression programmes in self-renewing and differentiating embryonic stem cells. RESULTS Using ribosome and transcriptome profiling, we identify distinct codon signatures during human embryonic stem cell differentiation. We find that cell state-specific codon bias is determined by the guanine-cytosine (GC) content of differentially expressed genes. By measuring the codon frequencies at the ribosome active sites interacting with transfer RNAs (tRNA), we further discover that self-renewing cells optimize translation of codons that depend on the inosine tRNA modification in the anticodon wobble position. Accordingly, inosine levels are highest in human pluripotent embryonic stem cells. This effect is conserved in mice and is independent of the differentiation stimulus. CONCLUSIONS We show that GC content influences cell state-specific mRNA levels, and we reveal how translational mechanisms based on tRNA modifications change codon usage in embryonic stem cells.
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Affiliation(s)
- Susanne Bornelöv
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Tommaso Selmi
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Sophia Flad
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Sabine Dietmann
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Michaela Frye
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
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24
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Mirihana Arachchilage G, Hetti Arachchilage M, Venkataraman A, Piontkivska H, Basu S. Stable G-quadruplex enabling sequences are selected against by the context-dependent codon bias. Gene 2019; 696:149-161. [PMID: 30753890 DOI: 10.1016/j.gene.2019.02.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 01/14/2019] [Accepted: 02/05/2019] [Indexed: 12/22/2022]
Abstract
The distributions of secondary structural elements appear to differ between coding regions (CDS) of mRNAs compared to the untranslated regions (UTRs), presumably as a mechanism to fine-tune gene expression, including efficiency of translation. However, a systematic and comprehensive analysis of secondary structure avoidance because of potential bias in codon usage is difficult as some of the common secondary structures, such as, hairpins can be formed by numerous sequence combinations. Using G-quadruplex (GQ) as the model secondary structure we studied the impact of codon bias on GQs within the CDS. Because GQs can be predicted using specific consensus sequence motifs, they provide an excellent platform for investigation of the selectivity of such putative structures at the codon level. Using a bioinformatics approach, we calculated the frequencies of putative GQs within the CDS of a variety of species. Our results suggest that the most stable GQs appear to be significantly underrepresented within the CDS, through the use of specific synonymous codon combinations. Furthermore, we identified many peptide sequence motifs in which silent mutations can potentially alter translation via stable GQ formation. This work not only provides a comprehensive analysis on how stable secondary structures appear to be avoided within the CDS of mRNA, but also broadens the current understanding of synonymous codon usage as they relate to the structure-function relationship of RNA.
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Affiliation(s)
| | | | - Aparna Venkataraman
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, United States of America
| | - Helen Piontkivska
- Department of Biological Sciences, Kent State University, Kent, OH 44242, United States of America
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, United States of America.
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25
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Ballard A, Bieniek S, Carlini DB. The fitness consequences of synonymous mutations in Escherichia coli: Experimental evidence for a pleiotropic effect of translational selection. Gene 2019; 694:111-120. [PMID: 30738968 DOI: 10.1016/j.gene.2019.01.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/21/2018] [Accepted: 01/22/2019] [Indexed: 01/06/2023]
Abstract
Codon usage bias (CUB) is a universal feature of genomes, and in most species CUB of protein coding genes is positively correlated with expression level and degree of evolutionary conservation. There is mounting experimental evidence that CUB is due in part to selection for translational efficiency and/or accuracy, i.e., translational selection. However, there is a paucity of experimental data on whether and how CUB acts in trans - does the usage of preferred codons in a highly expressed gene affect the translation of other genes by freeing up more ribosomes, thereby increasing their availability to translate all mRNA transcripts in the cell? We investigated this question by creating two extreme versions of the highly expressed Escherichia coli β-lactamase (bla) gene, one comprised almost entirely of unpreferred codons, and a second comprised almost entirely of preferred codons. We monitored the fitness effects of these synonymous mutations over hundreds of generations in two selective environments that allowed us to disentangle translational effects acting in cis from those acting in trans. In a selective environment for maximizing translational efficiency in trans of a gene (tetA) encoding a tetracycline resistance protein, unpreferred synonymous mutations had a negative impact on long-term fitness, whereas preferred mutations had a positive impact on long-term fitness, providing strong experimental evidence for a pleiotropic effect of translational selection.
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Affiliation(s)
- Anne Ballard
- Department of Biology, American University, 4400 Massachusetts Avenue, NW, Washington, DC, 20016, United States of America
| | - Sarah Bieniek
- Department of Biology, American University, 4400 Massachusetts Avenue, NW, Washington, DC, 20016, United States of America
| | - David B Carlini
- Department of Biology, American University, 4400 Massachusetts Avenue, NW, Washington, DC, 20016, United States of America.
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26
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Gun L, Haixian P, Yumiao R, Han T, Jingqi L, Liguang Z. Codon usage characteristics of PB2 gene in influenza A H7N9 virus from different host species. Infect Genet Evol 2018; 65:430-435. [PMID: 30179716 DOI: 10.1016/j.meegid.2018.08.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 08/02/2018] [Accepted: 08/30/2018] [Indexed: 12/13/2022]
Abstract
The influenza A H7N9 virus is a highly contagious virus which can only infect poultry before early 2013. But after that time, it widely caused human infections in China and brought Southeast Asia great threaten in the public health area. The coding gene for polymerase basic protein 2 (PB2) in influenza A H7N9 virus encodes the PB2 protein, which is a part of the RNA polymerase. The enzyme lacks a correction function during its own replication process, so the mutation frequency of the influenza A H7N9 virus gene is high and the PB2 gene is also included. To investigate the codon usages characteristics of PB2 gene, gene sequences of 12 kinds of poultry are downloaded form the gene bank (NCBI) and their codon usage characteristics such as the effective number of codons (ENC), the evolutionary relationship of the sequences, the codon adaptation index (CAI), the correspondence analysis (COA), the relative synonymous codon usage (RSCU) and their PR2-bias are compared and studied. The value of these reults showed that there is a low codon usage bias in the PB2 gene. Then, the differences between the codon usages of PB2 gene from 12 kinds of poultry are compared and their potential applications are discussed. These results could lay a foundation for other further study on the evolution of H7N9.
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Affiliation(s)
- Li Gun
- Department of Biomedical Engineering, School of Electronics and Information Engineering, Xi'an Technological University, Xi'an, Shaanxi Province, China.
| | - Pan Haixian
- Department of Biomedical Engineering, School of Electronics and Information Engineering, Xi'an Technological University, Xi'an, Shaanxi Province, China
| | - Ren Yumiao
- Department of Biomedical Engineering, School of Electronics and Information Engineering, Xi'an Technological University, Xi'an, Shaanxi Province, China
| | - Tian Han
- Department of Biomedical Engineering, School of Electronics and Information Engineering, Xi'an Technological University, Xi'an, Shaanxi Province, China
| | - Lu Jingqi
- Department of Biomedical Engineering, School of Electronics and Information Engineering, Xi'an Technological University, Xi'an, Shaanxi Province, China
| | - Zhang Liguang
- Department of Biomedical Engineering, School of Electronics and Information Engineering, Xi'an Technological University, Xi'an, Shaanxi Province, China
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Seward EA, Kelly S. Selection-driven cost-efficiency optimization of transcripts modulates gene evolutionary rate in bacteria. Genome Biol 2018; 19:102. [PMID: 30064467 PMCID: PMC6066932 DOI: 10.1186/s13059-018-1480-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/11/2018] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Most amino acids are encoded by multiple synonymous codons. However, synonymous codons are not used equally, and this biased codon use varies between different organisms. It has previously been shown that both selection acting to increase codon translational efficiency and selection acting to decrease codon biosynthetic cost contribute to differences in codon bias. However, it is unknown how these two factors interact or how they affect molecular sequence evolution. RESULTS Through analysis of 1320 bacterial genomes, we show that bacterial genes are subject to multi-objective selection-driven optimization of codon use. Here, selection acts to simultaneously decrease transcript biosynthetic cost and increase transcript translational efficiency, with highly expressed genes under the greatest selection. This optimization is not simply a consequence of the more translationally efficient codons being less expensive to synthesize. Instead, we show that transfer RNA gene copy number alters the cost-efficiency trade-off of synonymous codons such that, for many species, selection acting on transcript biosynthetic cost and translational efficiency act in opposition. Finally, we show that genes highly optimized to reduce cost and increase efficiency show reduced rates of synonymous and non-synonymous mutation. CONCLUSIONS This analysis provides a simple mechanistic explanation for variation in evolutionary rate between genes that depends on selection-driven cost-efficiency optimization of the transcript. These findings reveal how optimization of resource allocation to messenger RNA synthesis is a critical factor that determines both the evolution and composition of genes.
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Affiliation(s)
- Emily A Seward
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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28
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Dilucca M, Cimini G, Giansanti A. Essentiality, conservation, evolutionary pressure and codon bias in bacterial genomes. Gene 2018; 663:178-188. [PMID: 29678658 DOI: 10.1016/j.gene.2018.04.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 03/25/2018] [Accepted: 04/09/2018] [Indexed: 11/30/2022]
Abstract
Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than on genes that are either nonessential or peculiar to a single or a few species. In order to further assess this expectation, we study here how essentiality of a gene is connected with its degree of conservation among several unrelated bacterial species, each one characterised by its own codon usage bias. Confirming previous results on E. coli, we show the existence of a universal exponential relation between gene essentiality and conservation in bacteria. Moreover, we show that, within each bacterial genome, there are at least two groups of functionally distinct genes, characterised by different levels of conservation and codon bias: i) a core of essential genes, mainly related to cellular information processing; ii) a set of less conserved nonessential genes with prevalent functions related to metabolism. In particular, the genes in the first group are more retained among species, are subject to a stronger purifying conservative selection and display a more limited repertoire of synonymous codons. The core of essential genes is close to the minimal bacterial genome, which is in the focus of recent studies in synthetic biology, though we confirm that orthologs of genes that are essential in one species are not necessarily essential in other species. We also list a set of highly shared genes which, reasonably, could constitute a reservoir of targets for new anti-microbial drugs.
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Affiliation(s)
- Maddalena Dilucca
- Dipartimento di Fisica, "Sapienza" University of Rome, Rome 00185, Italy.
| | - Giulio Cimini
- IMT School for Advanced Studies, Lucca 55100, Italy; Istituto dei Sistemi Complessi (ISC)-CNR, Rome 00185, Italy
| | - Andrea Giansanti
- Dipartimento di Fisica, "Sapienza" University of Rome, Rome 00185, Italy; INFN Roma1 Unit, Rome 00185, Italy
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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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Liu H, Rahman SU, Mao Y, Xu X, Tao S. Codon usage bias in 5' terminal coding sequences reveals distinct enrichment of gene functions. Genomics 2017; 109:506-513. [PMID: 28778539 DOI: 10.1016/j.ygeno.2017.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/24/2017] [Accepted: 07/30/2017] [Indexed: 11/16/2022]
Abstract
Codon bias at the 5' terminal of coding sequence (CDS) is known to be distinct from the rest of the CDS. A number of events occur in this short region to regulate early translation elongation and co-translational translocation. In the genes encoding secretory proteins, there is a special signal sequence which has a higher occurrence of rare codons. In this study, we analyzed codon bias of secretory genes in several eukaryotes. The results showed that secretory genes in the species except mammals had a higher occurrence of rare codons in the 5' terminal of CDS, and the bias was greater than the same region of non-secretory genes. GO analysis revealed that secretory genes containing rare codon clusters in different regions were responsible for various roles in gene functions. Moreover, codon bias in the region encoding the hydrophobic region of protein is similar in secretory and non-secretory genes, indicating that codon bias in secretory genes was partly influenced by amino acid bias. Rare codon clusters are found more frequently in specific regions, and continuous rare codons are not favoured probably because they will increase the probability of ribosome collision and drop-off. Based on ribosome profiling data, there is no significant difference in the average translation efficiencies between rare and optimal codons. Higher ribosomal density in the 5' terminal may result from ribosome pausing which could be involved in different translation events. These findings collectively provided rich information on codon bias in secretory genes, which may shed light on the co-effect of codon bias, mRNA structure and tRNA abundance in translational regulations.
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Affiliation(s)
- Huiling Liu
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Siddiq Ur Rahman
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuanhui Mao
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaodong Xu
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, China.
| | - Shiheng Tao
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, China.
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Franzo G, Tucciarone CM, Cecchinato M, Drigo M. Canine parvovirus type 2 (CPV-2) and Feline panleukopenia virus (FPV) codon bias analysis reveals a progressive adaptation to the new niche after the host jump. Mol Phylogenet Evol 2017; 114:82-92. [PMID: 28603036 DOI: 10.1016/j.ympev.2017.05.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 05/01/2017] [Accepted: 05/21/2017] [Indexed: 10/19/2022]
Abstract
Based on virus dependence from host cell machinery, their codon usage is expected to show a strong relation with the host one. Even if this association has been stated, especially for bacteria viruses, the linkage is considered to be less consistent for more complex organisms and a codon bias adaptation after host jump has never been proven. Canine parvovirus type 2 (CPV-2) was selected as a model because it represents a well characterized case of host jump, originating from Feline panleukopenia virus (FPV). The current study demonstrates that the adaptation to specific tissue and host codon bias affected CPV-2 evolution. Remarkably, FPV and CPV-2 showed a higher closeness toward the codon bias of the tissues they display the higher tropism for. Moreover, after the host jump, a clear and significant trend was evidenced toward a reduction in the distance between CPV-2 and the dog codon bias over time. This evidence was not confirmed for FPV, suggesting that an equilibrium has been reached during the prolonged virus-host co-evolution. Additionally, the presence of an intermediate pattern displayed by some strains infecting wild species suggests that these could have facilitated the host switch also by acting on codon bias.
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Dornburg A, Townsend JP, Brooks W, Spriggs E, Eytan RI, Moore JA, Wainwright PC, Lemmon A, Lemmon EM, Near TJ. New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset. Mol Phylogenet Evol 2017; 110:27-38. [PMID: 28254474 DOI: 10.1016/j.ympev.2017.02.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 02/22/2017] [Accepted: 02/25/2017] [Indexed: 11/17/2022]
Abstract
Percomorph fishes represent over 17,100 species, including several model organisms and species of economic importance. Despite continuous advances in the resolution of the percomorph Tree of Life, resolution of the sister lineage to Percomorpha remains inconsistent but restricted to a small number of candidate lineages. Here we use an anchored hybrid enrichment (AHE) dataset of 132 loci with over 99,000 base pairs to identify the sister lineage of percomorph fishes. Initial analyses of this dataset failed to recover a strongly supported sister clade to Percomorpha, however, scrutiny of the AHE dataset revealed a bias towards high GC content at fast-evolving codon partitions (GC bias). By combining several existing approaches aimed at mitigating the impacts of convergence in GC bias, including RY coding and analyses of amino acids, we consistently recovered a strongly supported clade comprised of Holocentridae (squirrelfishes), Berycidae (Alfonsinos), Melamphaidae (bigscale fishes), Cetomimidae (flabby whalefishes), and Rondeletiidae (redmouth whalefishes) as the sister lineage to Percomorpha. Additionally, implementing phylogenetic informativeness (PI) based metrics as a filtration method yielded this same topology, suggesting PI based approaches will preferentially filter these fast-evolving regions and act in a manner consistent with other phylogenetic approaches aimed at mitigating GC bias. Our results provide a new perspective on a key issue for studies investigating the evolutionary history of more than one quarter of all living species of vertebrates.
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Affiliation(s)
- Alex Dornburg
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA.
| | - Jeffrey P Townsend
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Biostatistics, Yale University, New Haven, CT 06510, USA
| | - Willa Brooks
- North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - Elizabeth Spriggs
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
| | - Ron I Eytan
- Marine Biology Department, Texas A&M University at Galveston, Galveston, TX 77554, USA
| | - Jon A Moore
- Florida Atlantic University, Wilkes Honors College, Jupiter, FL 33458, USA; Florida Atlantic University, Harbor Branch Oceanographic Institution, Fort Pierce, FL 34946, USA
| | - Peter C Wainwright
- Department of Evolution & Ecology, University of California, Davis, CA 95616, USA
| | - Alan Lemmon
- Department of Scientific Computing, Florida State University, 400 Dirac Science Library, Tallahassee, FL 32306, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Thomas J Near
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA; Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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Seward EA, Kelly S. Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms. Genome Biol 2016; 17:226. [PMID: 27842572 PMCID: PMC5109750 DOI: 10.1186/s13059-016-1087-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/12/2016] [Indexed: 11/12/2022] Open
Abstract
Background Genomes are composed of long strings of nucleotide monomers (A, C, G and T) that are either scavenged from the organism’s environment or built from metabolic precursors. The biosynthesis of each nucleotide differs in atomic requirements with different nucleotides requiring different quantities of nitrogen atoms. However, the impact of the relative availability of dietary nitrogen on genome composition and codon bias is poorly understood. Results Here we show that differential nitrogen availability, due to differences in environment and dietary inputs, is a major determinant of genome nucleotide composition and synonymous codon use in both bacterial and eukaryotic microorganisms. Specifically, low nitrogen availability species use nucleotides that require fewer nitrogen atoms to encode the same genes compared to high nitrogen availability species. Furthermore, we provide a novel selection-mutation framework for the evaluation of the impact of metabolism on gene sequence evolution and show that it is possible to predict the metabolic inputs of related organisms from an analysis of the raw nucleotide sequence of their genes. Conclusions Taken together, these results reveal a previously hidden relationship between cellular metabolism and genome evolution and provide new insight into how genome sequence evolution can be influenced by adaptation to different diets and environments. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1087-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emily A Seward
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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Prabha R, Singh DP, Sinha S, Ahmad K, Rai A. Genome-wide comparative analysis of codon usage bias and codon context patterns among cyanobacterial genomes. Mar Genomics 2017; 32:31-9. [PMID: 27733306 DOI: 10.1016/j.margen.2016.10.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/11/2016] [Accepted: 10/03/2016] [Indexed: 11/20/2022]
Abstract
With the increasing accumulation of genomic sequence information of prokaryotes, the study of codon usage bias has gained renewed attention. The purpose of this study was to examine codon selection pattern within and across cyanobacterial species belonging to diverse taxonomic orders and habitats. We performed detailed comparative analysis of cyanobacterial genomes with respect to codon bias. Our analysis reflects that in cyanobacterial genomes, A- and/or T-ending codons were used predominantly in the genes whereas G- and/or C-ending codons were largely avoided. Variation in the codon context usage of cyanobacterial genes corresponded to the clustering of cyanobacteria as per their GC content. Analysis of codon adaptation index (CAI) and synonymous codon usage order (SCUO) revealed that majority of genes are associated with low codon bias. Codon selection pattern in cyanobacterial genomes reflected compositional constraints as major influencing factor. It is also identified that although, mutational constraint may play some role in affecting codon usage bias in cyanobacteria, compositional constraint in terms of genomic GC composition coupled with environmental factors affected codon selection pattern in cyanobacterial genomes.
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35
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Doyle F, Leonardi A, Endres L, Tenenbaum SA, Dedon PC, Begley TJ. Gene- and genome-based analysis of significant codon patterns in yeast, rat and mice genomes with the CUT Codon UTilization tool. Methods 2016; 107:98-109. [PMID: 27245397 PMCID: PMC5014648 DOI: 10.1016/j.ymeth.2016.05.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/16/2016] [Accepted: 05/17/2016] [Indexed: 01/09/2023] Open
Abstract
The translation of mRNA in all forms of life uses a three-nucleotide codon and aminoacyl-tRNAs to synthesize a protein. There are 64 possible codons in the genetic code, with codons for the ∼20 amino acids and 3 stop codons having 1- to 6-fold degeneracy. Recent studies have shown that families of stress response transcripts, termed modification tunable transcripts (MoTTs), use distinct codon biases that match specifically modified tRNAs to regulate their translation during a stress. Similarly, translational reprogramming of the UGA stop codon to generate selenoproteins or to perform programmed translational read-through (PTR) that results in a longer protein, requires distinct codon bias (i.e., more than one stop codon) and, in the case of selenoproteins, a specifically modified tRNA. In an effort to identify transcripts that have codon usage patterns that could be subject to translational control mechanisms, we have used existing genome and transcript data to develop the gene-specific Codon UTilization (CUT) tool and database, which details all 1-, 2-, 3-, 4- and 5-codon combinations for all genes or transcripts in yeast (Saccharomyces cerevisiae), mice (Mus musculus) and rats (Rattus norvegicus). Here, we describe the use of the CUT tool and database to characterize significant codon usage patterns in specific genes and groups of genes. In yeast, we demonstrate how the CUT database can be used to identify genes that have runs of specific codons (e.g., AGA, GAA, AAG) linked to translational regulation by tRNA methyltransferase 9 (Trm9). We further demonstrate how groups of genes can be analyzed to find significant dicodon patterns, with the 80 Gcn4-regulated transcripts significantly (P<0.00001) over-represented with the AGA-GAA dicodon. We have also used the CUT database to identify mouse and rat transcripts with internal UGA codons, with the surprising finding of 45 and 120 such transcripts, respectively, which is much larger than expected. The UGA data suggest that there could be many more translationally reprogrammed transcripts than currently reported. CUT thus represents a multi-species codon-counting database that can be used with mRNA-, translation- and proteomics-based results to better understand and model translational control mechanisms.
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Affiliation(s)
- Frank Doyle
- State University of New York – SUNY Polytechnic Institute, College of Nanoscale Science and Engineering, Albany, NY
| | - Andrea Leonardi
- State University of New York – SUNY Polytechnic Institute, College of Nanoscale Science and Engineering, Albany, NY
| | - Lauren Endres
- State University of New York – SUNY Polytechnic Institute, College of Arts and Sciences, Utica, NY
| | - Scott A. Tenenbaum
- State University of New York – SUNY Polytechnic Institute, College of Nanoscale Science and Engineering, Albany, NY
| | - Peter C. Dedon
- Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA
- Singapore-MIT Alliance for Research and Technology, Singapore
| | - Thomas J. Begley
- State University of New York – SUNY Polytechnic Institute, College of Nanoscale Science and Engineering, Albany, NY
- RNA Institute, University at Albany, State University of New York
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Choi JY, Aquadro CF. Recent and Long-Term Selection Across Synonymous Sites in Drosophila ananassae. J Mol Evol 2016; 83:50-60. [PMID: 27481397 DOI: 10.1007/s00239-016-9753-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 07/23/2016] [Indexed: 11/28/2022]
Abstract
In Drosophila, many studies have examined the short- or long-term evolution occurring across synonymous sites. Few, however, have examined both the recent and long-term evolution to gain a complete view of this selection. Here we have analyzed Drosophila ananassae DNA polymorphism and divergence data using several different methods, and have identified evidence of positive selection favoring preferred codons in both recent and long-term evolutionary time scale. Further in D. ananassae, the strength of selection for preferred codons was stronger on the X chromosome compared to the autosomes. We show that this stronger selection is not due to higher gene expression of X-linked genes. Analysis of the selectively neutral introns indicated that the X chromosome also had a preference for GC over AT nucleotides, potentially from GC-biased gene conversions (gcBGCs) that can also affect the base composition of synonymous sites. Thus selection for preferred codons and gcBGC both seem to be partially responsible for shaping the D. ananassae synonymous site evolution.
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Affiliation(s)
- Jae Young Choi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, USA.
| | - Charles F Aquadro
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, USA
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Cristina J, Fajardo A, Soñora M, Moratorio G, Musto H. A detailed comparative analysis of codon usage bias in Zika virus. Virus Res 2016; 223:147-52. [PMID: 27449601 DOI: 10.1016/j.virusres.2016.06.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 06/08/2016] [Accepted: 06/14/2016] [Indexed: 12/01/2022]
Abstract
Zika virus (ZIKV) is a member of the family Flaviviridae and its genome consists of a single-stranded positive sense RNA molecule with 10,794 nucleotides. Clinical manifestations of disease caused by ZIKV infection range from asymptomatic cases to an influenza-like syndrome. There is an increasing concern about the possible relation among microcephaly and ZIKV infection. To get insight into the relation of codon usage among viruses and their hosts is extremely important to understand virus survival, fitness, evasion from host's immune system and evolution. In this study, we performed a comprehensive analysis of codon usage and composition of ZIKV. The overall codon usage among ZIKV strains is similar and slightly biased. Different codon preferences in ZIKV genes in relation to codon usage of human, Aedes aegypti and Aedes albopictus genes were found. Most of the highly frequent codons are A-ending, which strongly suggests that mutational bias is the main force shaping codon usage in this virus. G+C compositional constraint as well as dinucleotide composition also influence the codon usage of ZIKV. The results of these studies suggest that the emergence of ZIKV outside Africa, in the Pacific and the Americas may also be reflected in ZIKV codon usage. No significant differences were found in codon usage among strains isolated from microcephaly cases and the rest of strains from the Asian cluster enrolled in these studies.
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Affiliation(s)
- Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay.
| | - Alvaro Fajardo
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay
| | - Martín Soñora
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay
| | - Gonzalo Moratorio
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay; Viral Populations and Pathogenesis laboratory. Institut Pasteur, CNRS UMR 3569, Paris, France
| | - Héctor Musto
- Laboratorio de Organización y Evolución del Genoma, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
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Trotta E. Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage. BMC Genomics 2016; 17:366. [PMID: 27188984 PMCID: PMC4869280 DOI: 10.1186/s12864-016-2692-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/05/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The three stop codons UAA, UAG, and UGA signal the termination of mRNA translation. As a result of a mechanism that is not adequately understood, they are normally used with unequal frequencies. RESULTS In this work, we showed that selective forces and mutational biases drive stop codon usage in the human genome. We found that, in respect to sense codons, stop codon usage was affected by stronger selective forces but was less influenced by neutral mutational biases. UGA is the most frequent termination codon in human genome. However, UAA was the preferred stop codon in genes with high breadth of expression, high level of expression, AT-rich coding sequences, housekeeping functions, and in gene ontology categories with the largest deviation from expected stop codon usage. Selective forces associated with the breadth and the level of expression favoured AT-rich sequences in the mRNA region including the stop site and its proximal 3'-UTR, but acted with scarce effects on sense codons, generating two regions, upstream and downstream of the stop codon, with strongly different base composition. By favouring low levels of GC-content, selection promoted labile local secondary structures at the stop site and its proximal 3'-UTR. The compositional and structural context favoured by selection was surprisingly emphasized in the class of ribosomal proteins and was consistent with sequence elements that increase the efficiency of translational termination. Stop codons were also heterogeneously distributed among chromosomes by a mechanism that was strongly correlated with the GC-content of coding sequences. CONCLUSIONS In human genome, the nucleotide composition and the thermodynamic stability of stop codon site and its proximal 3'-UTR are correlated with the GC-content of coding sequences and with the breadth and the level of gene expression. In highly expressed genes stop codon usage is compositionally and structurally consistent with highly efficient translation termination signals.
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Affiliation(s)
- Edoardo Trotta
- Institute of Translational Pharmacology, Consiglio Nazionale delle Ricerche (CNR), Rome, 00133, Italy.
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Boehm CR, Ueda M, Nishimura Y, Shikanai T, Haseloff J. A Cyan Fluorescent Reporter Expressed from the Chloroplast Genome of Marchantia polymorpha. Plant Cell Physiol 2016; 57:291-9. [PMID: 26634291 PMCID: PMC4788411 DOI: 10.1093/pcp/pcv160] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 10/21/2015] [Indexed: 05/10/2023]
Abstract
Recently, the liverwort Marchantia polymorpha has received increasing attention as a basal plant model for multicellular studies. Its ease of handling, well-characterized plastome and proven protocols for biolistic plastid transformation qualify M. polymorpha as an attractive platform to study the evolution of chloroplasts during the transition from water to land. In addition, chloroplasts of M. polymorpha provide a convenient test-bed for the characterization of genetic elements involved in plastid gene expression due to the absence of mechanisms for RNA editing. While reporter genes have proven valuable to the qualitative and quantitative study of gene expression in chloroplasts, expression of green fluorescent protein (GFP) in chloroplasts of M. polymorpha has proven problematic. We report the design of a codon-optimized gfp varian, mturq2cp, which allowed successful expression of a cyan fluorescent protein under control of the tobacco psbA promoter from the chloroplast genome of M. polymorpha. We demonstrate the utility of mturq2cp in (i) early screening for transplastomic events following biolistic transformation of M. polymorpha spores; (ii) visualization of stromules as elements of plastid structure in Marchantia; and (iii) quantitative microscopy for the analysis of promoter activity.
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Affiliation(s)
- Christian R Boehm
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Minoru Ueda
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan Present address: RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045 Japan
| | - Yoshiki Nishimura
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Toshiharu Shikanai
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan CREST, Japan Science and Technology Agency, Chiyoda-ku, Tokyo, 102-0076 Japan
| | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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Abstract
Inequalities between codon usage probabilities for quartets of codons are derived using a minimum principle for codon-anticodon interaction and a probability sum rule in the framework of the Crystal Basis Model of the genetic code. Performing this study separately for the Early and for the Eukaryotic Genetic Code, we observe a consistency in the obtained results for the two codes as well as a good agreement with data from Kasuza Codon Usage Database. Then we analyze the coherent changes of sign occurring, in the evolution from the Early to the Eukaryotic code, in the two parameters regulating the codon-anticodon interaction potential.
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Affiliation(s)
- A Sciarrino
- I.N.F.N., Sezione di Napoli, Complesso Universitario di Monte S. Angelo, Via Cinthia, I-80126 Napoli, Italy.
| | - P Sorba
- Laboratoire d'Annecy-le-Vieux de Physique Théorique LAPTH, CNRS, UMR 5108, associée à l'Université de Savoie, BP 110, F-74941 Annecy-le-Vieux Cedex, France.
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Saini J, Hershberg U. B cell variable genes have evolved their codon usage to focus the targeted patterns of somatic mutation on the complementarity determining regions. Mol Immunol 2015; 65:157-67. [PMID: 25660968 DOI: 10.1016/j.molimm.2015.01.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/29/2014] [Accepted: 01/02/2015] [Indexed: 01/19/2023]
Abstract
The exceptional ability of B cells to diversify through somatic mutation and improve affinity of the repertoire toward the antigens is the cornerstone of adaptive immunity. Somatic mutation is not evenly distributed and exhibits certain micro-sequence specificities. We show here that the combination of somatic mutation targeting and the codon usage in human B cell receptor (BCR) Variable (V) genes create expected patterns of mutation and post mutation changes that are focused on their complementarity determining regions (CDR). T cell V genes are also skewed in targeting mutations but to a lesser extent and are lacking the codon usage bias observed in BCRs. This suggests that the observed skew in T cell receptors is due to their amino acid usage, which is similar to that of BCRs. The mutation targeting and the codon bias allow B cell CDRs to diversify by specifically accumulating nonconservative changes. We counted the distribution of mutations to CDR in 4 different human datasets. In all four cases we found that the number of actual mutations in the CDR correlated significantly with the V gene mutation biases to the CDR predicted by our models. Finally, it appears that the mutation bias in V genes indeed relates to their long-term survival in actual human repertoires. We observed that resting repertoires of B cells overexpressed V genes that were especially biased toward focused mutation and change in the CDR. This bias in V gene usage was somewhat relaxed at the height of the immune response to a vaccine, presumably because of the need for a wider diversity in a primary response. However, older patients did not retain this flexibility and were biased toward using only highly skewed V genes at all stages of their response.
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Affiliation(s)
- Jasmine Saini
- School of Biomedical Engineering Sciences and Health Systems, Drexel University, Philadelphia, PA 19104, United States
| | - Uri Hershberg
- School of Biomedical Engineering Sciences and Health Systems, Drexel University, Philadelphia, PA 19104, United States; Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA 19104, United States.
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Whittaker MM, Whittaker JW. Expression and purification of recombinant Saccharomyces cerevisiae mitochondrial carrier protein YGR257Cp (Mtm1p). Protein Expr Purif 2013; 93:77-86. [PMID: 24184947 DOI: 10.1016/j.pep.2013.10.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 09/11/2013] [Accepted: 10/23/2013] [Indexed: 12/27/2022]
Abstract
The Saccharomyces cerevisiae mitochondrial carrier YGR257Cp (Mtm1p) is an integral membrane protein that plays an essential role in mitochondrial iron homeostasis and respiratory functions, but its carrier substrate has not previously been identified. Large amounts of pure protein are required for biochemical characterization, including substrate screening. Functional complementation of a Saccharomyces knockout by expression of TwinStrep tagged YGR257Cp demonstrates that an affinity tag does not interfere with protein function, but the expression level is very low. Heterologous expression in Pichia pastoris improves the yield but the product is heterogeneous. Expression has been screened in several Escherichia coli hosts, optimizing yield by modifying induction conditions and supplementing with rare tRNAs to overcome codon bias in the eukaryotic gene. Detection of an additional N-terminal truncation product in E. coli reveals the presence of a secondary intracistronic translation initiation site, which can be eliminated by silent mutagenesis of an alternative (Leu) initiation codon, resulting in production of a single, full-length polypeptide (∼30% of the total protein) as insoluble inclusion bodies. Purified inclusion bodies were successfully refolded and affinity purified, yielding approximately 40mg of pure, soluble product per liter of culture. Refolded YGR257Cp binds pyridoxal 5'-phosphate tightly (KD<1μM), supporting a new hypothesis that the mitochondrial carrier YGR237Cp and its homologs function as high affinity PLP transporters in mitochondria, providing the first evidence for this essential transport function in eukaryotes.
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Affiliation(s)
- Mei M Whittaker
- Institute for Environmental Health, Division of Environmental and Biomolecular Systems, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239-3098, United States
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Mahdi RN, Rouchka EC. Codon usage bias as a function of generation time and life expectancy. Bioinformation 2012; 8:158-62. [PMID: 22368389 PMCID: PMC3283889 DOI: 10.6026/97320630008158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Accepted: 01/27/2012] [Indexed: 11/23/2022] Open
Abstract
It has recently been demonstrated that human natural codon usage bias is optimized towards a higher buffering capacity to mutations (measured as the tendency of single point mutations in a DNA sequence to yield the same or similar amino acids) compared to random sequences. In this work, we investigate this phenomenon further by analyzing the natural DNA of four different species (human, mouse, zebrafish and fruit fly) to determine whether such a tolerance to mutations is correlated with the life span and age of sexual maturation for the corresponding organisms. We also propose a new measure to quantify the buffering capacity of a DNA sequence to mutations that takes into account the observed mutation rates within every genome and the effect of the corresponding mutation.Our results suggest there is a propensity for tolerance to mutations that is positively correlated with the life expectancy of the considered organisms. Moreover, random sequences that are constrained to produce the same protein as the naturally occurring sequences are found to be more buffered than completely random sequences while being less buffered than the natural sequences. These results suggest that optimization toward protective mechanisms tolerant to mutations is correlated with both life expectancy and age to sexual maturity at both the levels of codon usage bias and the bias of the natural sequence of codons itself.
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Affiliation(s)
- Rami N Mahdi
- Weill Cornell Medical College, Department of Genetic Medicine, New York, NY USA 10065
| | - Eric C Rouchka
- University of Louisville, Speed
School of Engineering, Department of Computer Engineering and Computer Science, Duthie Center Room 208, Louisville, KY USA 40292
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