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Sundar Panja A. The systematic codon usage bias has an important effect on genetic adaption in native species. Gene 2024; 926:148627. [PMID: 38823656 DOI: 10.1016/j.gene.2024.148627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/06/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
Random mutations increase genetic variety and natural selection enhances adaption over generations. Codon usage biases (CUB) provide clues about the genome adaptation mechanisms of native species and extremophile species. Significant numbers of gene (CDS) of nine classes of endangered, native species, including extremophiles and mesophiles were utilised to compute CUB. Codon usage patterns differ among the lineages of endangered and extremophiles with native species. Polymorphic usage of nucleotides with codon burial suggests parallelism of native species within relatively confined taxonomic groups. Utilizing the deviation pattern of CUB of endangered and native species, I present a calculation parameter to estimate the extinction risk of endangered species. Species diversity and extinction risk are both positively associated with the propensity of random mutation in CDS (Coding DNA sequence). Codon bias tenet profoundly selected and it governs to adaptive evolution of native species.
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Affiliation(s)
- Anindya Sundar Panja
- Department of Biotechnology, Molecular Informatics Laboratory, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal 721102, India.
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Majchrzak M, Madej Ł, Łysek-Gładysińska M, Zarębska-Michaluk D, Zegadło K, Dziuba A, Nogal-Nowak K, Kondziołka W, Sufin I, Myszona-Tarnowska M, Jaśkowski M, Kędzierski M, Maciukajć J, Matykiewicz J, Głuszek S, Adamus-Białek W. The RdRp genotyping of SARS-CoV-2 isolated from patients with different clinical spectrum of COVID-19. BMC Infect Dis 2024; 24:281. [PMID: 38439047 PMCID: PMC10913261 DOI: 10.1186/s12879-024-09146-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/16/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND The evolution of SARS-CoV-2 has been observed from the very beginning of the fight against COVID-19, some mutations are indicators of potentially dangerous variants of the virus. However, there is no clear association between the genetic variants of SARS-CoV-2 and the severity of COVID-19. We aimed to analyze the genetic variability of RdRp in correlation with different courses of COVID-19. RESULTS The prospective study included 77 samples of SARS-CoV-2 isolated from outpatients (1st degree of severity) and hospitalized patients (2nd, 3rd and 4th degree of severity). The retrospective analyses included 15,898,266 cases of SARS-CoV-2 genome sequences deposited in the GISAID repository. Single-nucleotide variants were identified based on the four sequenced amplified fragments of SARS-CoV-2. The analysis of the results was performed using appropriate statistical methods, with p < 0.05, considered statistically significant. Additionally, logistic regression analysis was performed to predict the strongest determinants of the observed relationships. The number of mutations was positively correlated with the severity of the COVID-19, and older male patients. We detected four mutations that significantly increased the risk of hospitalization of COVID-19 patients (14676C > T, 14697C > T, 15096 T > C, and 15279C > T), while the 15240C > T mutation was common among strains isolated from outpatients. The selected mutations were searched worldwide in the GISAID database, their presence was correlated with the severity of COVID-19. CONCLUSION Identified mutations have the potential to be used to assess the increased risk of hospitalization in COVID-19 positive patients. Experimental studies and extensive epidemiological data are needed to investigate the association between individual mutations and the severity of COVID-19.
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Affiliation(s)
- Michał Majchrzak
- Institute of Medical Sciences, Jan Kochanowski University, Kielce, Poland
| | - Łukasz Madej
- Institute of Medical Sciences, Jan Kochanowski University, Kielce, Poland
| | | | | | - Katarzyna Zegadło
- Institute of Medical Sciences, Jan Kochanowski University, Kielce, Poland
| | - Anna Dziuba
- Institute of Medical Sciences, Jan Kochanowski University, Kielce, Poland
| | | | | | | | | | | | | | | | | | - Stanisław Głuszek
- Institute of Medical Sciences, Jan Kochanowski University, Kielce, Poland
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Guan X, Pei Y, Song J. DNA-Based Nonviral Gene Therapy─Challenging but Promising. Mol Pharm 2024; 21:427-453. [PMID: 38198640 DOI: 10.1021/acs.molpharmaceut.3c00907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Over the past decades, significant progress has been made in utilizing nucleic acids, including DNA and RNA molecules, for therapeutic purposes. For DNA molecules, although various DNA delivery systems have been established, viral vector systems are the go-to choice for large-scale commercial applications. However, viral systems have certain disadvantages such as immune response, limited payload capacity, insertional mutagenesis and pre-existing immunity. In contrast, nonviral systems are less immunogenic, not size limited, safer, and easier for manufacturing compared with viral systems. What's more, nonviral DNA vectors have demonstrated their capacity to mediate specific protein expression in vivo for diverse therapeutic objectives containing a wide range of diseases such as cancer, rare diseases, neurodegenerative diseases, and infectious diseases, yielding promising therapeutic outcomes. However, exogenous plasmid DNA is prone to degrade and has poor immunogenicity in vivo. Thus, various strategies have been developed: (i) designing novel plasmids with special structures, (ii) optimizing plasmid sequences for higher expression, and (iii) developing more efficient nonviral DNA delivery systems. Based on these strategies, many interesting clinical results have been reported. This Review discusses the development of DNA-based nonviral gene therapy, including novel plasmids, nonviral delivery systems, clinical advances, and prospects. These developments hold great potential for enhancing the efficacy and safety of nonviral gene therapy and expanding its applications in the treatment of various diseases.
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Affiliation(s)
- Xiaocai Guan
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yufeng Pei
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, China
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Oelschlaeger P. Molecular Mechanisms and the Significance of Synonymous Mutations. Biomolecules 2024; 14:132. [PMID: 38275761 PMCID: PMC10813300 DOI: 10.3390/biom14010132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Synonymous mutations result from the degeneracy of the genetic code. Most amino acids are encoded by two or more codons, and mutations that change a codon to another synonymous codon do not change the amino acid in the gene product. Historically, such mutations have been considered silent because they were assumed to have no to very little impact. However, research in the last few decades has produced several examples where synonymous mutations play important roles. These include optimizing expression by enhancing translation initiation and accelerating or decelerating translation elongation via codon usage and mRNA secondary structures, stabilizing mRNA molecules and preventing their breakdown before translation, and faulty protein folding or increased degradation due to enhanced ubiquitination and suboptimal secretion of proteins into the appropriate cell compartments. Some consequences of synonymous mutations, such as mRNA stability, can lead to different outcomes in prokaryotes and eukaryotes. Despite these examples, the significance of synonymous mutations in evolution and in causing disease in comparison to nonsynonymous mutations that do change amino acid residues in proteins remains controversial. Whether the molecular mechanisms described by which synonymous mutations affect organisms can be generalized remains poorly understood and warrants future research in this area.
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Affiliation(s)
- Peter Oelschlaeger
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA
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Wang L, Zhao H, Wang Z, Ding S, Qin L, Jiang R, Deng X, He Z, Li L. An Evolutionary Perspective of Codon Usage Pattern, Dinucleotide Composition and Codon Pair Bias in Prunus Necrotic Ringspot Virus. Genes (Basel) 2023; 14:1712. [PMID: 37761852 PMCID: PMC10530913 DOI: 10.3390/genes14091712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Prunus necrotic ringspot virus (PNRSV) is a significant virus of ornamental plants and fruit trees. It is essential to study this virus due to its impact on the horticultural industry. Several studies on PNRSV diversity and phytosanitary detection technology were reported, but the content on the codon usage bias (CUB), dinucleotide preference and codon pair bias (CPB) of PNRSV is still uncertain. We performed comprehensive analyses on a dataset consisting of 359 coat protein (CP) gene sequences in PNRSV to examine the characteristics of CUB, dinucleotide composition, and CPB. The CUB analysis of PNRSV CP sequences showed that it was not only affected by natural selection, but also affected by mutations, and natural selection played a more significant role compared to mutations as the driving force. The dinucleotide composition analysis showed an over-expression of the CpC/GpA dinucleotides and an under-expression of the UpA/GpC dinucleotides. The dinucleotide composition of the PNRSV CP gene showed a weak association with the viral lineages and hosts, but a strong association with viral codon positions. Furthermore, the CPB of PNRSV CP gene is low and is related to dinucleotide preference and codon usage patterns. This research provides reference for future research on PNRSV genetic diversity and gene evolution mechanism.
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Affiliation(s)
- Lingqi Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China;
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Haiting Zhao
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Zhilei Wang
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Shiwen Ding
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Lang Qin
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Runzhou Jiang
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Xiaolong Deng
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
| | - Zhen He
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.Z.); (Z.W.); (S.D.); (L.Q.); (R.J.); (X.D.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Liangjun Li
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China;
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
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Liu X, Liu H, Wang Y, Li M, Ji L, Wang K, Wei C, Li W, Chen C, Yu L, Zhu X, Hong X. Chromosome-Level Analysis of the Pelochelys cantorii Genome Provides Insights to Its Immunity, Growth and Longevity. BIOLOGY 2023; 12:939. [PMID: 37508370 PMCID: PMC10376104 DOI: 10.3390/biology12070939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/19/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023]
Abstract
The Asian giant soft-shelled turtle, Pelochelys cantorii (Trionychidae), is one of the largest aquatic turtles in China and was designated as a First-Grade Protected Animal in China in 1989. Previous investigation based on a combination of Illumina short-read, PacBio long-read and Hi-C scaffolding technologies acquired a high-quality chromosome-level genome of Pc. cantorii. In this study, comparative genomic analysis between Pc. cantorii and 16 other vertebrate genomes indicated that turtles separated from the ancestor of archosaurians approximately 256.6 (95% highest posterior density interval, 263.6-251.9) million years ago (Mya) (Upper Permian to Triassic) and that Pc. cantorii separated from the ancestor of Pd. sinensis and R. swinhoei approximately 59.3 (95% highest posterior density interval, 64.3-54.3) Mya. Moreover, several candidate genes, such as VWA5A, ABCG2, A2M and IGSF1, associated with tumor suppression, growth and age were expanded, implicating their potential roles in the exceptional longevity of turtles. This new chromosome-level assembly has important scientific value in the study of conservation of Pc. cantorii and also enriches the evolutionary investigation of turtle species.
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Affiliation(s)
- Xiaoli Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Haiyang Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yakun Wang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Mingzhi Li
- Guangzhou Bio & Data Technology Co., Ltd., Guangzhou 510555, China
| | - Liqin Ji
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Kaikuo Wang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- College of Life Science and Fisheries, Shanghai Ocean University, Shanghai 201306, China
| | - Chengqing Wei
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Wei Li
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Chen Chen
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Lingyun Yu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Xinping Zhu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- College of Life Science and Fisheries, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaoyou Hong
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
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Pan-cancer analysis of co-occurring mutations in RAD52 and the BRCA1-BRCA2-PALB2 axis in human cancers. PLoS One 2022; 17:e0273736. [PMID: 36107942 PMCID: PMC9477347 DOI: 10.1371/journal.pone.0273736] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/12/2022] [Indexed: 11/19/2022] Open
Abstract
In human cells homologous recombination (HR) is critical for repair of DNA double strand breaks (DSBs) and rescue of stalled or collapsed replication forks. HR is facilitated by RAD51 which is loaded onto DNA by either BRCA2-BRCA1-PALB2 or RAD52. In human culture cells, double-knockdowns of RAD52 and genes in the BRCA1-BRCA2-PALB2 axis are lethal. Mutations in BRCA2, BRCA1 or PALB2 significantly impairs error free HR as RAD51 loading relies on RAD52 which is not as proficient as BRCA2-BRCA1-PALB2. RAD52 also facilitates Single Strand Annealing (SSA) that produces intra-chromosomal deletions. Some RAD52 mutations that affect the SSA function or decrease RAD52 association with DNA can suppress certain BRCA2 associated phenotypes in breast cancers. In this report we did a pan-cancer analysis using data reported on the Catalogue of Somatic Mutations in Cancers (COSMIC) to identify double mutants between RAD52 and BRCA1, BRCA2 or PALB2 that occur in cancer cells. We find that co-occurring mutations are likely in certain cancer tissues but not others. However, all mutations occur in a heterozygous state. Further, using computational and machine learning tools we identified only a handful of pathogenic or driver mutations predicted to significantly affect the function of the proteins. This supports previous findings that co-inactivation of RAD52 with any members of the BRCA2-BRCA1-PALB2 axis is lethal. Molecular modeling also revealed that pathogenic RAD52 mutations co-occurring with mutations in BRCA2-BRCA1-PALB2 axis are either expected to attenuate its SSA function or its interaction with DNA. This study extends previous breast cancer findings to other cancer types and shows that co-occurring mutations likely destabilize HR by similar mechanisms as in breast cancers.
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Tyagi N, Sardar R, Gupta D. Natural selection plays a significant role in governing the codon usage bias in the novel SARS-CoV-2 variants of concern (VOC). PeerJ 2022; 10:e13562. [PMID: 35765592 PMCID: PMC9233899 DOI: 10.7717/peerj.13562] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/19/2022] [Indexed: 01/17/2023] Open
Abstract
The ongoing prevailing COVID-19 pandemic caused by SARS-CoV-2 is becoming one of the major global health concerns worldwide. The SARS-CoV-2 genome encodes spike (S) glycoprotein that plays a very crucial role in viral entry into the host cell via binding of its receptor binding domain (RBD) to the host angiotensin converting enzyme 2 (ACE2) receptor. The continuously evolving SARS-CoV-2 genome results in more severe and transmissible variants characterized by the emergence of novel mutations called 'variants of concern' (VOC). The currently designated alpha, beta, gamma, delta and omicron VOC are the focus of this study due to their high transmissibility, increased virulence, and concerns for decreased effectiveness of the available vaccines. In VOC, the spike (S) gene and other non-structural protein mutations may affect the efficacies of the approved COVID-19 vaccines. To understand the diversity of SARS-CoV-2, several studies have been performed on a limited number of sequences. However, only a few studies have focused on codon usage bias (CUBs) pattern analysis of all the VOC strains. Therefore, to evaluate the evolutionary divergence of all VOC S-genes, we performed CUBs analysis on 300,354 sequences to understand the evolutionary relationship with its adaptation in different hosts, i.e., humans, bats, and pangolins. Base composition and RSCU analysis revealed the presence of 20 preferred AU-ended and 10 under-preferred GC-ended codons. In addition, CpG was found to be depleted, which may be attributable to the adaptive response by viruses to escape from the host defense process. Moreover, the ENC values revealed a higher bias in codon usage in the VOC S-gene. Further, the neutrality plot analysis demonstrated that S-genes analyzed in this study are under 83.93% influence of natural selection, suggesting its pivotal role in shaping the CUBs. The CUBs pattern of S-genes was found to be very similar among all the VOC strains. Interestingly, we observed that VOC strains followed a trend of antagonistic codon usage with respect to the human host. The identified CUBs divergence would help to understand the virus evolution and its host adaptation, thus help design novel vaccine strategies against the emerging VOC strains. To the best of our knowledge, this is the first report for identifying the evolution of CUBs pattern in all the currently identified VOC.
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Affiliation(s)
- Neetu Tyagi
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India, New Delhi, New Delhi, India,Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Rahila Sardar
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India, New Delhi, New Delhi, India,Biochemistry, Jamia Hamdard University, New Delhi, New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India, New Delhi, New Delhi, India
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Mogro EG, Bottero D, Lozano MJ. Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic. Virology 2022; 568:56-71. [PMID: 35134624 PMCID: PMC8808327 DOI: 10.1016/j.virol.2022.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2, the seventh coronavirus known to infect humans, can cause severe life-threatening respiratory pathologies. To better understand SARS-CoV-2 evolution, genome-wide analyses have been made, including the general characterization of its codons usage profile. Here we present a bioinformatic analysis of the evolution of SARS-CoV-2 codon usage over time using complete genomes collected since December 2019. Our results show that SARS-CoV-2 codon usage pattern is antagonistic to, and it is getting farther away from that of the human host. Further, a selection of deoptimized codons over time, which was accompanied by a decrease in both the codon adaptation index and the effective number of codons, was observed. All together, these findings suggest that SARS-CoV-2 could be evolving, at least from the perspective of the synonymous codon usage, to become less pathogenic.
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Affiliation(s)
- Ezequiel G Mogro
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET, CCT-La Plata, Universidad Nacional de La Plata (UNLP), Argentina
| | - Daniela Bottero
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET, CCT-La Plata, Universidad Nacional de La Plata (UNLP), Argentina
| | - Mauricio J Lozano
- Instituto de Biotecnología y Biología Molecular (IBBM), CONICET, CCT-La Plata, Universidad Nacional de La Plata (UNLP), Argentina.
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Nair RR, Mohan M, Rudramurthy GR, Vivekanandam R, Satheshkumar PS. Strategies and Patterns of Codon Bias in Molluscum Contagiosum Virus. Pathogens 2021; 10:1649. [PMID: 34959603 PMCID: PMC8703355 DOI: 10.3390/pathogens10121649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022] Open
Abstract
Trends associated with codon usage in molluscum contagiosum virus (MCV) and factors governing the evolution of codon usage have not been investigated so far. In this study, attempts were made to decipher the codon usage trends and discover the major evolutionary forces that influence the patterns of codon usage in MCV with special reference to sub-types 1 and 2, MCV-1 and MCV-2, respectively. Three hypotheses were tested: (1) codon usage patterns of MCV-1 and MCV-2 are identical; (2) SCUB (synonymous codon usage bias) patterns of MCV-1 and MCV-2 slightly deviate from that of human host to avoid affecting the fitness of host; and (3) translational selection predominantly shapes the SCUB of MCV-1 and MCV-2. Various codon usage indices viz. relative codon usage value, effective number of codons and codon adaptation index were calculated to infer the nature of codon usage. Correspondence analysis and correlation analysis were performed to assess the relative contribution of silent base contents and significance of codon usage indices in defining bias in codon usage. Among the tested hypotheses, only the second and third hypotheses were accepted.
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Affiliation(s)
- Rahul Raveendran Nair
- Centre for Evolutionary Ecology, Aushmath Biosciences, Vadavalli Post, Coimbatore 641041, India
| | - Manikandan Mohan
- College of Pharmacy, University of Georgia, Athens, GA 30605, USA;
| | | | - Reethu Vivekanandam
- Department of Biotechnology, Bharathiyar University, Coimbatore 641046, India;
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Nelakurti DD, Rossetti T, Husbands AY, Petreaca RC. Arginine Depletion in Human Cancers. Cancers (Basel) 2021; 13:cancers13246274. [PMID: 34944895 PMCID: PMC8699593 DOI: 10.3390/cancers13246274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/04/2021] [Accepted: 12/09/2021] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Thousands of cancer genomes are now publicly available which has led to new insights into the underlying features of cancers. These include the identification of mutational signatures at both nucleotide and amino acid levels. Here, we discuss C > T transitions as a key nucleotide-level mutational signature that leads to a dramatic overrepresentation of arginine substitutions in cancers. We propose that this underlying C > T mutational signature canalizes possible arginine substitution outcomes, favoring histidine, cysteine, glutamine, and tryptophan. This initial asymmetry is then acted on at the amino acid level by purifying selection. Thus, a model of “sequential selection” could explain the documented bias towards arginine substitutions in multiple cancers. Abstract Arginine is encoded by six different codons. Base pair changes in any of these codons can have a broad spectrum of effects including substitutions to twelve different amino acids, eighteen synonymous changes, and two stop codons. Four amino acids (histidine, cysteine, glutamine, and tryptophan) account for over 75% of amino acid substitutions of arginine. This suggests that a mutational bias, or “purifying selection”, mechanism is at work. This bias appears to be driven by C > T and G > A transitions in four of the six arginine codons, a signature that is universal and independent of cancer tissue of origin or histology. Here, we provide a review of the available literature and reanalyze publicly available data from the Catalogue of Somatic Mutations in Cancer (COSMIC). Our analysis identifies several genes with an arginine substitution bias. These include known factors such as IDH1, as well as previously unreported genes, including four cancer driver genes (FGFR3, PPP6C, MAX, GNAQ). We propose that base pair substitution bias and amino acid physiology both play a role in purifying selection. This model may explain the documented arginine substitution bias in cancers.
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Affiliation(s)
- Devi D. Nelakurti
- Biomedical Science Undergraduate Program, The Ohio State University Medical School, Columbus, OH 43210, USA;
| | - Tiffany Rossetti
- Biology Undergraduate Program, The Ohio State University, Marion, OH 43302, USA;
| | - Aman Y. Husbands
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43215, USA
- Correspondence: (A.Y.H.); (R.C.P.)
| | - Ruben C. Petreaca
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA
- Cancer Biology Program, The Ohio State University James Comprehensive Cancer Center, Columbus, OH 43210, USA
- Correspondence: (A.Y.H.); (R.C.P.)
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Abstract
Codon usage bias is the preferential or non-random use of synonymous codons, a ubiquitous phenomenon observed in bacteria, plants and animals. Different species have consistent and characteristic codon biases. Codon bias varies not only with species, family or group within kingdom, but also between the genes within an organism. Codon usage bias has evolved through mutation, natural selection, and genetic drift in various organisms. Genome composition, GC content, expression level and length of genes, position and context of codons in the genes, recombination rates, mRNA folding, and tRNA abundance and interactions are some factors influencing codon bias. The factors shaping codon bias may also be involved in evolution of the universal genetic code. Codon-usage bias is critical factor determining gene expression and cellular function by influencing diverse processes such as RNA processing, protein translation and protein folding. Codon usage bias reflects the origin, mutation patterns and evolution of the species or genes. Investigations of codon bias patterns in genomes can reveal phylogenetic relationships between organisms, horizontal gene transfers, molecular evolution of genes and identify selective forces that drive their evolution. Most important application of codon bias analysis is in the design of transgenes, to increase gene expression levels through codon optimization, for development of transgenic crops. The review gives an overview of deviations of genetic code, factors influencing codon usage or bias, codon usage bias of nuclear and organellar genes, computational methods to determine codon usage and the significance as well as applications of codon usage analysis in biological research, with emphasis on plants.
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Affiliation(s)
| | - Varatharajalu Udayasuriyan
- Department of Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - Vijaipal Bhadana
- ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, 834010, India
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Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB. Genes (Basel) 2021; 12:genes12081169. [PMID: 34440343 PMCID: PMC8393687 DOI: 10.3390/genes12081169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 12/03/2022] Open
Abstract
Giardia duodenalis, a flagellated parasitic protozoan, the most common cause of parasite-induced diarrheal diseases worldwide. Codon usage bias (CUB) is an important evolutionary character in most species. However, G. duodenalis CUB remains unclear. Thus, this study analyzes codon usage patterns to assess the restriction factors and obtain useful information in shaping G. duodenalis CUB. The neutrality analysis result indicates that G. duodenalis has a wide GC3 distribution, which significantly correlates with GC12. ENC-plot result—suggesting that most genes were close to the expected curve with only a few strayed away points. This indicates that mutational pressure and natural selection played an important role in the development of CUB. The Parity Rule 2 plot (PR2) result demonstrates that the usage of GC and AT was out of proportion. Interestingly, we identified 26 optimal codons in the G. duodenalis genome, ending with G or C. In addition, GC content, gene expression, and protein size also influence G. duodenalis CUB formation. This study systematically analyzes G. duodenalis codon usage pattern and clarifies the mechanisms of G. duodenalis CUB. These results will be very useful to identify new genes, molecular genetic manipulation, and study of G. duodenalis evolution.
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14
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Gil-Gil T, Ochoa-Sánchez LE, Baquero F, Martínez JL. Antibiotic resistance: Time of synthesis in a post-genomic age. Comput Struct Biotechnol J 2021; 19:3110-3124. [PMID: 34141134 PMCID: PMC8181582 DOI: 10.1016/j.csbj.2021.05.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 12/20/2022] Open
Abstract
Antibiotic resistance has been highlighted by international organizations, including World Health Organization, World Bank and United Nations, as one of the most relevant global health problems. Classical approaches to study this problem have focused in infected humans, mainly at hospitals. Nevertheless, antibiotic resistance can expand through different ecosystems and geographical allocations, hence constituting a One-Health, Global-Health problem, requiring specific integrative analytic tools. Antibiotic resistance evolution and transmission are multilayer, hierarchically organized processes with several elements (from genes to the whole microbiome) involved. However, their study has been traditionally gene-centric, each element independently studied. The development of robust-economically affordable whole genome sequencing approaches, as well as other -omic techniques as transcriptomics and proteomics, is changing this panorama. These technologies allow the description of a system, either a cell or a microbiome as a whole, overcoming the problems associated with gene-centric approaches. We are currently at the time of combining the information derived from -omic studies to have a more holistic view of the evolution and spread of antibiotic resistance. This synthesis process requires the accurate integration of -omic information into computational models that serve to analyse the causes and the consequences of acquiring AR, fed by curated databases capable of identifying the elements involved in the acquisition of resistance. In this review, we analyse the capacities and drawbacks of the tools that are currently in use for the global analysis of AR, aiming to identify the more useful targets for effective corrective interventions.
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Affiliation(s)
- Teresa Gil-Gil
- Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Madrid, Spain
| | | | - Fernando Baquero
- Department of Microbiology, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain
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15
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Role of Synonymous Mutations in the Evolution of TEM β-Lactamase Genes. Antimicrob Agents Chemother 2021; 65:AAC.00018-21. [PMID: 33820762 DOI: 10.1128/aac.00018-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/23/2021] [Indexed: 01/25/2023] Open
Abstract
Nonsynonymous mutations are well documented in TEM β-lactamases. The resulting amino acid changes often alter the conferred phenotype from broad spectrum (2b) conferred by TEM-1 to extended spectrum (2be), inhibitor resistant (2br), or both extended spectrum and inhibitor resistant (2ber). The encoding bla TEM genes also deviate in numerous synonymous mutations, which are not well understood. bla TEM-3 (2be), bla TEM-33 (2br), and bla TEM-109 (2ber) were studied in comparison to bla TEM-1 bla TEM-33 was chosen for more detailed studies because it deviates from bla TEM-1 by a single nonsynonymous mutation and three additional synonymous mutations. Genes encoding the enzymes with only nonsynonymous or all (including synonymous) mutations plus all permutations between bla TEM-1 and bla TEM-33 were expressed in Escherichia coli cells. In disc diffusion assays, genes encoding TEM-3, TEM-33, and TEM-109 with all synonymous mutations resulted in higher resistance levels than genes without synonymous mutations. Disc diffusion assays with the 16 genes carrying all possible nucleotide change combinations between bla TEM-1 and bla TEM-33 indicated different susceptibilities for different variants. Nucleotide BLAST searches did not identify genes without synonymous mutations but did identify some without nonsynonymous mutations. Energies of possible secondary mRNA structures calculated with mfold are generally higher with synonymous mutations, suggesting that their role could be to destabilize the mRNA and facilitate its unfolding for efficient translation. In summary, our data indicate that transition from bla TEM-1 to other variant genes by simply acquiring the nonsynonymous mutations is not favored. Instead, synonymous mutations seem to support the transition to other variant genes with nonsynonymous mutations leading to different phenotypes.
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Arias L, Martínez F, González D, Flores-Ríos R, Katz A, Tello M, Moreira S, Orellana O. Modification of Transfer RNA Levels Affects Cyclin Aggregation and the Correct Duplication of Yeast Cells. Front Microbiol 2021; 11:607693. [PMID: 33519754 PMCID: PMC7843576 DOI: 10.3389/fmicb.2020.607693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/21/2020] [Indexed: 11/13/2022] Open
Abstract
Codon usage bias (the preferential use of certain synonymous codons (optimal) over others is found at the organism level (intergenomic) within specific genomes (intragenomic) and even in certain genes. Whether it is the result of genetic drift due to GC/AT content and/or natural selection is a topic of intense debate. Preferential codons are mostly found in genes encoding highly-expressed proteins, while lowly-expressed proteins usually contain a high proportion of rare (lowly-represented) codons. While optimal codons are decoded by highly expressed tRNAs, rare codons are usually decoded by lowly-represented tRNAs. Whether rare codons play a role in controlling the expression of lowly- or temporarily-expressed proteins is an open question. In this work we approached this question using two strategies, either by replacing rare glycine codons with optimal counterparts in the gene that encodes the cell cycle protein Cdc13, or by overexpression the tRNA Gly that decodes rare codons from the fission yeast, Schizosaccharomyces pombe. While the replacement of synonymous codons severely affected cell growth, increasing tRNA levels affected the aggregation status of Cdc13 and cell division. These lead us to think that rare codons in lowly-expressed cyclin proteins are crucial for cell division, and that the overexpression of tRNA that decodes rare codons affects the expression of proteins containing these rare codons. These codons may be the result of the natural selection of codons in genes that encode lowly-expressed proteins.
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Affiliation(s)
- Loreto Arias
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Fabián Martínez
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Daniela González
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Rodrigo Flores-Ríos
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Assaf Katz
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Mario Tello
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Sandra Moreira
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Omar Orellana
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
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Identification of New, Functionally Relevant Mutations in the Coding Regions of the Human Fos and Jun Proto-Oncogenes in Rheumatoid Arthritis Synovial Tissue. Life (Basel) 2020; 11:life11010005. [PMID: 33374881 PMCID: PMC7823737 DOI: 10.3390/life11010005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 02/06/2023] Open
Abstract
In rheumatoid arthritis (RA), the expression of many pro-destructive/pro-inflammatory proteins depends on the transcription factor AP-1. Therefore, our aim was to analyze the presence and functional relevance of mutations in the coding regions of the AP-1 subunits of the fos and jun family in peripheral blood (PB) and synovial membranes (SM) of RA and osteoarthritis patients (OA, disease control), as well as normal controls (NC). Using the non-isotopic RNAse cleavage assay, one known polymorphism (T252C: silent; rs1046117; present in RA, OA, and NC) and three novel germline mutations of the cfos gene were detected: (i) C361G/A367G: Gln121Glu/Ile123Val, denoted as “fos121/123”; present only in one OA sample; (ii) G374A: Arg125Lys, “fos125”; and (iii) C217A/G374A: Leu73Met/Arg125Lys, “fos73/125”, the latter two exclusively present in RA. In addition, three novel somatic cjun mutations (604–606ΔCAG: ΔGln202, “jun202”; C706T: Pro236Ser, “jun236”; G750A: silent) were found exclusively in the RA SM. Tansgenic expression of fos125 and fos73/125 mutants in NIH-3T3 cells induced an activation of reporter constructs containing either the MMP-1 (matrix metalloproteinase) promoter (3- and 4-fold, respectively) or a pentameric AP-1 site (approximately 5-fold). Combined expression of these two cfos mutants with cjun wildtype or mutants (jun202, jun236) further enhanced reporter expression of the pentameric AP-1 construct. Finally, genotyping for the novel functionally relevant germline mutations in 298 RA, 288 OA, and 484 NC samples revealed no association with RA. Thus, functional cfos/cjun mutants may contribute to local joint inflammation/destruction in selected patients with RA by altering the transactivation capacity of AP-1 complexes.
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Kanduc D. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): Codon Usage and Replicative Fitness. Glob Med Genet 2020; 7:92-94. [PMID: 33392612 PMCID: PMC7772010 DOI: 10.1055/s-0040-1721080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) codon usage, as shown by the polyprotein coding sequence, shows better translation potential in the human host when compared with human coronavirus OC43 (HCoV-OC43) codon usage. Such translational advantage might facilitate SARS-CoV-2 replication, immunogenicity, and pathogenicity, thus also accounting for the less harmful character of HCoV-OC43 infection.
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Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, Bari, Italy
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19
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Liberles DA, Chang B, Geiler-Samerotte K, Goldman A, Hey J, Kaçar B, Meyer M, Murphy W, Posada D, Storfer A. Emerging Frontiers in the Study of Molecular Evolution. J Mol Evol 2020; 88:211-226. [PMID: 32060574 PMCID: PMC7386396 DOI: 10.1007/s00239-020-09932-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A collection of the editors of Journal of Molecular Evolution have gotten together to pose a set of key challenges and future directions for the field of molecular evolution. Topics include challenges and new directions in prebiotic chemistry and the RNA world, reconstruction of early cellular genomes and proteins, macromolecular and functional evolution, evolutionary cell biology, genome evolution, molecular evolutionary ecology, viral phylodynamics, theoretical population genomics, somatic cell molecular evolution, and directed evolution. While our effort is not meant to be exhaustive, it reflects research questions and problems in the field of molecular evolution that are exciting to our editors.
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Affiliation(s)
- David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.
| | - Belinda Chang
- Department of Ecology and Evolutionary Biology and Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Kerry Geiler-Samerotte
- Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Aaron Goldman
- Department of Biology, Oberlin College and Conservatory, K123 Science Center, 119 Woodland Street, Oberlin, OH, 44074, USA
| | - Jody Hey
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - Betül Kaçar
- Department of Molecular and Cell Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Michelle Meyer
- Department of Biology, Boston College, Chestnut Hill, MA, 02467, USA
| | - William Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | - David Posada
- Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
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20
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Kandeel M, Ibrahim A, Fayez M, Al-Nazawi M. From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes. J Med Virol 2020; 92:660-666. [PMID: 32159237 PMCID: PMC7228358 DOI: 10.1002/jmv.25754] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/09/2020] [Indexed: 12/11/2022]
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is an emerging disease with fatal outcomes. In this study, a fundamental knowledge gap question is to be resolved by evaluating the differences in biological and pathogenic aspects of SARS‐CoV‐2 and the changes in SARS‐CoV‐2 in comparison with the two prior major COV epidemics, SARS and Middle East respiratory syndrome (MERS) coronaviruses. Methods The genome composition, nucleotide analysis, codon usage indices, relative synonymous codons usage, and effective number of codons (ENc) were analyzed in the four structural genes; Spike (S), Envelope (E), membrane (M), and Nucleocapsid (N) genes, and two of the most important nonstructural genes comprising RNA‐dependent RNA polymerase and main protease (Mpro) of SARS‐CoV‐2, Beta‐CoV from pangolins, bat SARS, MERS, and SARS CoVs. Results SARS‐CoV‐2 prefers pyrimidine rich codons to purines. Most high‐frequency codons were ending with A or T, while the low frequency and rare codons were ending with G or C. SARS‐CoV‐2 structural proteins showed 5 to 20 lower ENc values, compared with SARS, bat SARS, and MERS CoVs. This implies higher codon bias and higher gene expression efficiency of SARS‐CoV‐2 structural proteins. SARS‐CoV‐2 encoded the highest number of over‐biased and negatively biased codons. Pangolin Beta‐CoV showed little differences with SARS‐CoV‐2 ENc values, compared with SARS, bat SARS, and MERS CoV. Conclusion Extreme bias and lower ENc values of SARS‐CoV‐2, especially in Spike, Envelope, and Mpro genes, are suggestive for higher gene expression efficiency, compared with SARS, bat SARS, and MERS CoVs.
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Affiliation(s)
- Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf, Egypt.,Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelshikh University, Kafrelshikh, Egypt
| | - Abdelazim Ibrahim
- Department of Pathology, College of Veterinary Medicine, King Faisal University, Al-hofuf, Saudi Arabia.,Department of Pathology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Mahmoud Fayez
- Al Ahsa Veterinary Diagnostic Laboratory, Ministry of Agriculture, Al-Ahsa, Kingdom of Saudi Arabia.,Veterinary Serum and Vaccine Institute, Cairo, Egypt
| | - Mohammed Al-Nazawi
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-hofuf, Egypt
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21
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Hernandez‐Alias X, Benisty H, Schaefer MH, Serrano L. Translational efficiency across healthy and tumor tissues is proliferation-related. Mol Syst Biol 2020; 16:e9275. [PMID: 32149479 PMCID: PMC7061310 DOI: 10.15252/msb.20199275] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/11/2020] [Accepted: 02/11/2020] [Indexed: 12/20/2022] Open
Abstract
Different tissues express genes with particular codon usage and anticodon tRNA repertoires. However, the codon-anticodon co-adaptation in humans is not completely understood, nor is its effect on tissue-specific protein levels. Here, we first validated the accuracy of small RNA-seq for tRNA quantification across five human cell lines. We then analyzed the tRNA abundance of more than 8,000 tumor samples from TCGA, together with their paired mRNA-seq and proteomics data, to determine the Supply-to-Demand Adaptation. We thereby elucidate that the dynamic adaptation of the tRNA pool is largely related to the proliferative state across tissues. The distribution of such tRNA pools over the whole cellular translatome affects the subsequent translational efficiency, which functionally determines a condition-specific expression program both in healthy and tumor states. Furthermore, the aberrant translational efficiency of some codons in cancer, exemplified by ProCCA and GlyGGT, is associated with poor patient survival. The regulation of these tRNA profiles is partly explained by the tRNA gene copy numbers and their promoter DNA methylation.
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Affiliation(s)
- Xavier Hernandez‐Alias
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Hannah Benisty
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Martin H Schaefer
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Department of Experimental OncologyIEO, European Institute of Oncology IRCCSMilanItaly
| | - Luis Serrano
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- ICREABarcelonaSpain
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22
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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] [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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Abstract
Genetic variation is a necessity of all biological systems. Viruses use all known mechanisms of variation; mutation, several forms of recombination, and segment reassortment in the case of viruses with a segmented genome. These processes are intimately connected with the replicative machineries of viruses, as well as with fundamental physical-chemical properties of nucleotides when acting as template or substrate residues. Recombination has been viewed as a means to rescue viable genomes from unfit parents or to produce large modifications for the exploration of phenotypic novelty. All types of genetic variation can act conjointly as blind processes to provide the raw materials for adaptation to the changing environments in which viruses must replicate. A distinction is made between mechanistically unavoidable and evolutionarily relevant mutation and recombination.
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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] [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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25
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Genetic evolution and codon usage analysis of NKX-2.5 gene governing heart development in some mammals. Genomics 2019; 112:1319-1329. [PMID: 31377427 DOI: 10.1016/j.ygeno.2019.07.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/26/2019] [Accepted: 07/31/2019] [Indexed: 11/21/2022]
Abstract
NKX-2.5 gene is responsible for cardiac development and its targeted disruption apprehends cardiac development at the linear heart tube stage. Bioinformatic analysis was employed to investigate the codon usage pattern and dN/dS of mammalian NKX-2.5 gene. The relative synonymous codon usage analysis revealed variation in codon usage and two synonymous codons namely ATA (Ile) and GTA (Val) were absent in NKX-2.5 gene across selected mammalian species suggesting that these two codons were possibly selected against during evolution. Parity rule 2 analysis of two and four fold amino acids showed CT bias whereas six-fold amino acids revealed GA bias. Neutrality analysis suggests that selection played a prominent role while mutation had a minor role. The dN/dS analysis suggests synonymous substitution played a significant role and it negatively correlated with p-distance of the gene. Purifying natural selection played a dominant role in the genetic evolution of NKX-2.5 gene in mammals.
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Sexton NR, Ebel GD. Effects of Arbovirus Multi-Host Life Cycles on Dinucleotide and Codon Usage Patterns. Viruses 2019; 11:v11070643. [PMID: 31336898 PMCID: PMC6669465 DOI: 10.3390/v11070643] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022] Open
Abstract
Arthropod-borne viruses (arboviruses) of vertebrates including dengue, zika, chikungunya, Rift Valley fever, and blue tongue viruses cause extensive morbidity and mortality in humans, agricultural animals, and wildlife across the globe. As obligate intercellular pathogens, arboviruses must be well adapted to the cellular and molecular environment of both their arthropod (invertebrate) and vertebrate hosts, which are vastly different due to hundreds of millions of years of separate evolution. Here we discuss the comparative pressures on arbovirus RNA genomes as a result of a dual host life cycle, focusing on pressures that do not alter amino acids. We summarize what is currently known about arboviral genetic composition, such as dinucleotide and codon usage, and how cyclical infection of vertebrate and invertebrate hosts results in different genetic profiles compared with single-host viruses. To serve as a comparison, we compile what is known about arthropod tRNA, dinucleotide, and codon usages and compare this with vertebrates. Additionally, we discuss the potential roles of genetic robustness in arboviral evolution and how it may vary from other viruses. Overall, both arthropod and vertebrate hosts influence the resulting genetic composition of arboviruses, but a great deal remains to be investigated.
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Affiliation(s)
- Nicole R Sexton
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Gregory D Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.
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Yu H, Meng W, Mao Y, Zhang Y, Sun Q, Tao S. Deciphering the rules of mRNA structure differentiation in Saccharomyces cerevisiae in vivo and in vitro with deep neural networks. RNA Biol 2019; 16:1044-1054. [PMID: 31119975 PMCID: PMC6602416 DOI: 10.1080/15476286.2019.1612692] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The structure of mRNA in vivo is unwound to some extent in response to multiple factors involved in the translation process, resulting in significant differences from the structure of the same mRNA in vitro. In this study, we have proposed a novel application of deep neural networks, named DeepDRU, to predict the degree of mRNA structure unwinding in vivo by fitting five quantifiable features that may affect mRNA folding: ribosome density (RD), minimum folding free energy (MFE), GC content, translation initiation ribosome density (INI) and mRNA structure position (POS). mRNA structures with adjustment of the simulated structural features were designed and then fed into the trained DeepDRU model. We found unique effect regions of these five features on mRNA structure in vivo. Strikingly, INI is the most critical factor affecting the structure of mRNA in vivo, and structural sequence features, including MFE and GC content, have relatively smaller effects. DeepDRU provides a new paradigm for predicting the unwinding capability of mRNA structure in vivo. This improved knowledge about the mechanisms of factors influencing the structural capability of mRNA to unwind will facilitate the design and functional analysis of mRNA structure in vivo.
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Affiliation(s)
- Haopeng Yu
- a College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas , Northwest A&F University , Yangling , Shaanxi , China.,b Bioinformatics Center , Northwest A&F University , Yangling , Shaanxi , China
| | - Wenjing Meng
- a College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas , Northwest A&F University , Yangling , Shaanxi , China.,b Bioinformatics Center , Northwest A&F University , Yangling , Shaanxi , China
| | - Yuanhui Mao
- a College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas , Northwest A&F University , Yangling , Shaanxi , China.,b Bioinformatics Center , Northwest A&F University , Yangling , Shaanxi , China
| | - Yi Zhang
- a College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas , Northwest A&F University , Yangling , Shaanxi , China.,b Bioinformatics Center , Northwest A&F University , Yangling , Shaanxi , China
| | - Qing Sun
- a College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas , Northwest A&F University , Yangling , Shaanxi , China.,b Bioinformatics Center , Northwest A&F University , Yangling , Shaanxi , China
| | - Shiheng Tao
- a College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas , Northwest A&F University , Yangling , Shaanxi , China.,b Bioinformatics Center , Northwest A&F University , Yangling , Shaanxi , China
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Pollo-Oliveira L, de Crécy-Lagard V. Can Protein Expression Be Regulated by Modulation of tRNA Modification Profiles? Biochemistry 2018; 58:355-362. [PMID: 30511849 DOI: 10.1021/acs.biochem.8b01035] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
tRNAs are the central adaptor molecules in translation. Their decoding properties are influenced by post-transcriptional modifications, particularly in the critical anticodon-stem-loop (ASL) region. Synonymous codon choice, also called codon usage bias, affects both translation efficiency and accuracy, and ASL modifications play key roles in both of these processes. In combination with a handful of historical examples, recent studies integrating ribosome profiling, proteomics, codon-usage analyses, and modification quantifications show that levels of tRNA modifications can change under stress, during development, or under specific metabolic conditions and can modulate the expression of specific genes. Deconvoluting the different responses (global or specific) to tRNA modification deficiencies can be difficult because of pleiotropic effects, but, as more cases emerge, it does seem that tRNA modification changes could add another layer of regulation in the transfer of information from DNA to protein.
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Affiliation(s)
- Leticia Pollo-Oliveira
- Department of Microbiology and Cell Science , University of Florida , Gainesville , Florida 32603 , United States
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science , University of Florida , Gainesville , Florida 32603 , United States.,University of Florida Genetics Institute , Gainesville , Florida 32608 , United States
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29
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Barbhuiya PA, Uddin A, Chakraborty S. Compositional properties and codon usage of TP73 gene family. Gene 2018; 683:159-168. [PMID: 30316927 DOI: 10.1016/j.gene.2018.10.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 10/03/2018] [Accepted: 10/11/2018] [Indexed: 12/19/2022]
Abstract
The TP73 gene is considered as one of the members of TP53 gene family and shows much homology to p53 gene. TP73 gene plays a pivotal role in cancer studies in addition to other biological functions. Codon usage bias (CUB) is the phenomenon of unequal usage of synonymous codons for an amino acid wherein some codons are more frequently used than others and it reveals the evolutionary relationship of a gene. Here, we report the pattern of codon usage in TP73 gene using various bioinformatic tools as no work was reported yet. Nucleotide composition analysis suggested that the mean nucleobase C was the highest, followed by G and the gene was GC rich. Correlation analysis between codon usage and GC3 suggested that most of the GC-ending codons showed positive correlation while most of the AT-ending codons showed negative correlation with GC3 in the coding sequences of TP73 gene variants in human. The CUB is moderate in human TP73 gene as evident from intrinsic codon deviation index (ICDI) analysis. Nature selected against two codons namely ATA (isoleucine) and AGA (arginine) in the coding sequences of TP73 gene during the course of evolution. A significant correlation (p < 0.05) was found between overall nucleotide composition and its composition at the 3rd codon position, indicating that both mutation pressure and natural selection might influence the CUB. The correlation analysis between ICDI and biochemical properties of protein suggested that variation of CUB was associated with degree of hydrophobicity and length of protein.
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Affiliation(s)
- Parvin A Barbhuiya
- Departments of Biotechnology, Assam University, Silchar 788011, Assam, India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi 788150, Assam, India
| | - Supriyo Chakraborty
- Departments of Biotechnology, Assam University, Silchar 788011, Assam, India.
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Accounting for Programmed Ribosomal Frameshifting in the Computation of Codon Usage Bias Indices. G3-GENES GENOMES GENETICS 2018; 8:3173-3183. [PMID: 30111621 PMCID: PMC6169388 DOI: 10.1534/g3.118.200185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Experimental evidence shows that synonymous mutations can have important consequences on genetic fitness. Many organisms display codon usage bias (CUB), where synonymous codons that are translated into the same amino acid appear with distinct frequency. Within genomes, CUB is thought to arise from selection for translational efficiency and accuracy, termed the translational efficiency hypothesis (TEH). Indeed, CUB indices correlate with protein expression levels, which is widely interpreted as evidence for translational selection. However, these tests neglect -1 programmed ribosomal frameshifting (-1 PRF), an important translational disruption effect found across all organisms of the tree of life. Genes that contain -1 PRF signals should cost more to express than genes without. Thus, CUB indices that do not consider -1 PRF may overestimate genes’ true adaptation to translational efficiency and accuracy constraints. Here, we first investigate whether -1 PRF signals do indeed carry such translational cost. We then propose two corrections for CUB indices for genes containing -1 PRF signals. We retest the TEH in Saccharomyces cerevisiae under these corrections. We find that the correlation between corrected CUB index and protein expression remains intact for most levels of uniform -1 PRF efficiencies, and tends to increase when these efficiencies decline with protein expression. We conclude that the TEH is strengthened and that -1 PRF events constitute a promising and useful tool to examine the relationships between CUB and selection for translation efficiency and accuracy.
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31
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Mauro VP. Codon Optimization in the Production of Recombinant Biotherapeutics: Potential Risks and Considerations. BioDrugs 2018; 32:69-81. [PMID: 29392566 DOI: 10.1007/s40259-018-0261-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biotherapeutics are increasingly becoming the mainstay in the treatment of a variety of human conditions, particularly in oncology and hematology. The production of therapeutic antibodies, cytokines, and fusion proteins have markedly accelerated these fields over the past decade and are probably the major contributor to improved patient outcomes. Today, most protein therapeutics are expressed as recombinant proteins in mammalian cell lines. An expression technology commonly used to increase protein levels involves codon optimization. This approach is possible because degeneracy of the genetic code enables most amino acids to be encoded by more than one synonymous codon and because codon usage can have a pronounced influence on levels of protein expression. Indeed, codon optimization has been reported to increase protein expression by > 1000-fold. The primary tactic of codon optimization is to increase the rate of translation elongation by overcoming limitations associated with species-specific differences in codon usage and transfer RNA (tRNA) abundance. However, in mammalian cells, assumptions underlying codon optimization appear to be poorly supported or unfounded. Moreover, because not all synonymous codon mutations are neutral, codon optimization can lead to alterations in protein conformation and function. This review discusses codon optimization for therapeutic protein production in mammalian cells.
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Guan DL, Ma LB, Khan MS, Zhang XX, Xu SQ, Xie JY. Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints. BMC Genomics 2018; 19:542. [PMID: 30016953 PMCID: PMC6050667 DOI: 10.1186/s12864-018-4937-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 07/10/2018] [Indexed: 02/07/2023] Open
Abstract
Background Hirudinaria manillensis is an ephemeral, blood-sucking ectoparasite, possessing anticoagulant capacities with potential medical applications. Analysis of codon usage patterns would contribute to our understanding of the evolutionary mechanisms and genetic architecture of H. manillensis, which in turn would provide insight into the characteristics of other leeches. We analysed codon usage and related indices using 18,000 coding sequences (CDSs) retrieved from H. manillensis RNA-Seq data. Results We identified four highly preferred codons in H. manillensis that have G/C-endings. Points generated in an effective number of codons (ENC) plot distributed below the standard curve and the slope of a neutrality plot was less than 1. Highly expressed CDSs had lower ENC content and higher GC content than weakly expressed CDSs. Principal component analysis conducted on relative synonymous codon usage (RSCU) values divided CDSs according to GC content and divided codons according to ending bases. Moreover, by determining codon usage, we found that the majority of blood-diet related genes have undergone less adaptive evolution in H. manillensis, except for those with homologous sequences in the host species. Conclusions Codon usage in H. manillensis had an overall preference toward C-endings and indicated that codon usage patterns are mediated by differential expression, GC content, and biological function. Although mutation pressure effects were also notable, the majority of genetic evolution in H. manillensis was driven by natural selection. Electronic supplementary material The online version of this article (10.1186/s12864-018-4937-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- De-Long Guan
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China
| | - Li-Bin Ma
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China
| | - Muhammad Salabat Khan
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China
| | - Xiu-Xiu Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China
| | - Sheng-Quan Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China.
| | - Juan-Ying Xie
- School of Computer Science, Shaanxi Normal University, Xi'an, 710119, Shaanxi, People's Republic of China.
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The genetic background of antibiotic resistance among clinical uropathogenic Escherichia coli strains. Mol Biol Rep 2018; 45:1055-1065. [PMID: 30008141 PMCID: PMC6156760 DOI: 10.1007/s11033-018-4254-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/10/2018] [Indexed: 01/07/2023]
Abstract
The spreading mechanisms of antibiotic resistance are related to many bacterial and environment factors. The overuse of antibiotics is leading to an unceasing emergence of new multidrug resistant strains. This problem also concerns uropathogenic Escherichia coli strains, which is the most common pathogen causing urinary tract infections. The aim of this study was the genetic analysis of antibiotic resistance in comparison to the phenotypic background of E. coli strains. The characterized collection of E. coli strains isolated 10 years ago from the urine samples of patients with urinary tract infections was used for antimicrobial susceptibility testing (the disc diffusion method) and analysis of antibiotic resistance genes (PCR reaction, sequencing). Additionally, the presence of ESBL strains was analyzed. Fourteen genes were associated with resistance to beta-lactams, aminoglycosides, sulfonamides and quinolones. The genetic analysis revealed that blaTEM-1 and sul2 were present in almost all of the studied strains. Other drug-resistance genes were very rare or non-existent. Otherwise, the phenotypic resistance to fluoroquinolones was well correlated with the genotypic background of the studied bacteria. The presence of particular genes and specific mutations indicate a high bacterial potential to multidrug resistance. On the other hand, it needs to be emphasized that the standard disk diffusion test for the routine antimicrobial susceptibility analysis is still the best way to estimate the current situation of bacterial drug-resistance.
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Lin D, Li L, Xie T, Yin Q, Saksena N, Wu R, Li W, Dai G, Ma J, Zhou X, Chen X. Codon usage variation of Zika virus: The potential roles of NS2B and NS4A in its global pandemic. Virus Res 2018; 247:71-83. [PMID: 29428601 DOI: 10.1016/j.virusres.2018.01.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 12/18/2022]
Abstract
A comprehensive demonstration of Zika virus (ZIKV) molecular evolution is essential for understanding its adaptation and expansion in its recent pandemics. Despite several studies on mutations and codon usage in ZIKVs, the variations in codon usage patterns across individual genes and their biological implication remains unclear. Here, we performed a gene-by-gene comparison of the codon usage variation in ZIKVs of the African and Asian lineages. We found that besides the evidence of positive selection (Ka/Ks >1) in the Asian lineage of the ZIKV genome, codon usage patterns were gene-specific and codon usage variation of ZIKV genes, was possibly constrained by their individual functional features, such as transmembrane domains, or antigenicity. In particular, the NS2B and NS4A genes showed distinct codon usage patterns, clearly separating them from the clusters of other genes in the correspondence analysis (CA). In the Asian lineage, the NS2B and NS4A genes showed the highest codon usage bias (ENC values: 51.01 ± 0.72 and 48.89 ± 0.99 respectively), and were subjected to the highest translation selection (ENCobs/ENCexp ratio: 0.847 ± 0.0297 and 0.828 ± 0.0233 respectively) in comparison to the African lineages of ZIKV. The CpG frequency of the NS2B showed a gradual ascending trend in the Asian ZIKV lineages, while in NS4A it was constrained along with the expansion of the Asian lineage. Furthermore, between the African and Asian lineages, differentiated and specific over-represented codons were more prominent in the NS2B and NS4A. Together, our study implies that ZIKVs are in the process of evolutionary fine tuning their codon as seen in the recent pandemics, and NS2B and NS4A could have played a potential role in the molecular evolution of the Asian lineage and their establishment.
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Affiliation(s)
- Dechun Lin
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, Guangdong, China; BGI-Shenzhen, Shenzhen 518083, Guangdong, China; China National Genebank, BGI-Shenzhen, Shenzhen 518083, Guangdong, China.
| | - Liqiang Li
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; China National Genebank, BGI-Shenzhen, Shenzhen 518083, Guangdong, China.
| | - Tian Xie
- Department of Pathogen Biology, Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, Guangdong, China.
| | - Qingqing Yin
- Department of Pathogen Biology, Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, Guangdong, China.
| | - Nitin Saksena
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; China National Genebank, BGI-Shenzhen, Shenzhen 518083, Guangdong, China.
| | - Rangke Wu
- The School of Foreign Studies, Southern Medical University, Guangzhou 510515, Guangdong, China.
| | - Wanyu Li
- Department of Pathogen Biology, Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, Guangdong, China.
| | - Geyang Dai
- Department of Pathogen Biology, Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, Guangdong, China.
| | - Jinmin Ma
- BGI-Shenzhen, Shenzhen 518083, Guangdong, China; China National Genebank, BGI-Shenzhen, Shenzhen 518083, Guangdong, China; Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Xiaohong Zhou
- Department of Pathogen Biology, Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, Guangdong, China.
| | - Xiaoguang Chen
- Department of Pathogen Biology, Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, Guangdong, China.
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35
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Mauro VP, Chappell SA. Considerations in the Use of Codon Optimization for Recombinant Protein Expression. Methods Mol Biol 2018; 1850:275-288. [PMID: 30242693 DOI: 10.1007/978-1-4939-8730-6_18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Codon optimization is a gene engineering approach that is commonly used for enhancing recombinant protein expression. This approach is possible because (1) degeneracy of the genetic code enables most amino acids to be encoded by multiple codons and (2) different mRNAs encoding the same protein can vary dramatically in the amount of protein expressed. However, because codon optimization potentially disrupts overlapping information encoded in mRNA coding regions, protein structure and function may be altered. This chapter discusses the use of codon optimization for various applications in mammalian cells as well as potential consequences, so that informed decisions can be made on the appropriateness of using this approach in each case.
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36
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Gajbhiye S, Patra P, Yadav MK. New insights into the factors affecting synonymous codon usage in human infecting Plasmodium species. Acta Trop 2017; 176:29-33. [PMID: 28751162 DOI: 10.1016/j.actatropica.2017.07.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/18/2017] [Accepted: 07/21/2017] [Indexed: 02/07/2023]
Abstract
Codon usage bias is due to the non-random usage of synonymous codons for coding amino acids. The synonymous sites are under weak selection, and codon usage bias is maintained by the equilibrium in mutational bias, genetic drift and selection pressure. The differential codon usage choices are also relevant to human infecting Plasmodium species. Recently, P. knowlesi switches its natural host, long-tailed macaques, and starts infecting humans. This review focuses on the comparative analysis of codon usage choices among human infecting P. falciparum and P. vivax along with P. knowlesi species taking their coding sequence data. The variation in GC content, amino acid frequencies, effective number of codons and other factors plays a crucial role in determining synonymous codon choices. Within species codon choices are more similar for P. vivax and P. knowlesi in comparison with P. falciparum species. This study suggests that synonymous codon choice modulates the gene expression level, mRNA stability, ribosome speed, protein folding, translation efficiency and its accuracy in Plasmodium species, and provides a valuable information regarding the codon usage pattern to facilitate gene cloning as well as expression and transfection studies for malaria causing species.
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Kanduc D. Rare Human Codons and HCMV Translational Regulation. J Mol Microbiol Biotechnol 2017; 27:213-216. [PMID: 28858877 DOI: 10.1159/000478093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/06/2017] [Indexed: 11/19/2022] Open
Abstract
Restriction of protein synthesis characterizes human cytomegalovirus (HCMV) latency in the human host. In analyzing the molecular factors that hinder HCMV expression, the present study shows that HCMV genes frequently use 6 rare codons, i.e., GCG (Ala), CCG (Pro), CGT (Arg), CGC (Arg), TCG (Ser), and ACG (Thr). In some instances, the rare host codons are clustered along viral nucleotide sequences and represent the majority in sequences encoding short alanine and proline repeats. Given the positive correlation between codon usage, tRNA content, and protein production, the results support the hypothesis that HCMV usage of rare human codons might hinder HCMV protein synthesis, in this way leading to HCMV latency.
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Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
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38
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Agris PF, Narendran A, Sarachan K, Väre VYP, Eruysal E. The Importance of Being Modified: The Role of RNA Modifications in Translational Fidelity. Enzymes 2017; 41:1-50. [PMID: 28601219 DOI: 10.1016/bs.enz.2017.03.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The posttranscriptional modifications of tRNA's anticodon stem and loop (ASL) domain represent a third level, a third code, to the accuracy and efficiency of translating mRNA codons into the correct amino acid sequence of proteins. Modifications of tRNA's ASL domain are enzymatically synthesized and site specifically located at the anticodon wobble position-34 and 3'-adjacent to the anticodon at position-37. Degeneracy of the 64 Universal Genetic Codes and the limitation in the number of tRNA species require some tRNAs to decode more than one codon. The specific modification chemistries and their impact on the tRNA's ASL structure and dynamics enable one tRNA to decode cognate and "wobble codons" or to expand recognition to synonymous codons, all the while maintaining the translational reading frame. Some modified nucleosides' chemistries prestructure tRNA to read the two codons of a specific amino acid that shares a twofold degenerate codon box, and other chemistries allow a different tRNA to respond to all four codons of a fourfold degenerate codon box. Thus, tRNA ASL modifications are critical and mutations in genes for the modification enzymes and tRNA, the consequences of which is a lack of modification, lead to mistranslation and human disease. By optimizing tRNA anticodon chemistries, structure, and dynamics in all organisms, modifications ensure translational fidelity of mRNA transcripts.
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Affiliation(s)
- Paul F Agris
- The RNA Institute, State University of New York, Albany, NY, United States.
| | - Amithi Narendran
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Kathryn Sarachan
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Ville Y P Väre
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Emily Eruysal
- The RNA Institute, State University of New York, Albany, NY, United States
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Leichsenring J, Volckmar AL, Magios N, Morais de Oliveira CM, Penzel R, Brandt R, Kirchner M, Bozorgmehr F, Thomas M, Schirmacher P, Warth A, Endris V, Stenzinger A. Synonymous EGFR variant p.Q787Q is neither prognostic nor predictive in patients with lung adenocarcinoma. Genes Chromosomes Cancer 2016; 56:214-220. [PMID: 27750395 DOI: 10.1002/gcc.22427] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/23/2016] [Accepted: 10/10/2016] [Indexed: 01/05/2023] Open
Abstract
Patients with non-small cell lung cancer (NSCLC) harboring activating mutations in the Epidermal Growth Factor Receptor (EGFR) benefit from targeted therapies. A synonymous polymorphism (rs1050171, p.Q787Q) was shown to be associated with improved overall survival (OS) in colorectal cancer patients. As data in NSCLC are limited, we retrospectively analyzed associations of p.Q787Q with clinicopathological parameters including clinical response and outcome in patients with lung adenocarcinoma (ADC) who received tyrosine kinase inhibitor (TKI) therapy. Of 642 ADC patients whose tumors were profiled by next generation sequencing, 102 (15.9%) carried EGFR mutations targetable by TKIs (30.4% male patients, median age 65.1 y, 19.6% smokers with 12.8 median pack years). Seventy-nine patients (77.5%) received TKI therapy either as a first- or second-line therapy. Of the 102 EGFR-mutant tumors, 72 (70.6%) exhibited the p.Q787Q polymorphism and another 12 (11.8%) cases with p.Q787Q harbored an additional TKI insensitive mutation (p.T790M). The polymorphism was neither associated with classic clinicopathological parameters nor with overall survival (21.1 months vs. 20.1 months; P-value = 0.91) or clinical response (P-value = 0.122). The patients with p.T790M had worse survival compared to EGFR activating mutation carriers with and without p.Q787Q when analyzed as a separate group (27.5 months, P-value = 0.02). In conclusion, p.Q787Q is neither a suitable prognostic nor predictive biomarker for ADC patients receiving anti-EGFR therapy in first- or second-line of therapy. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Jonas Leichsenring
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Anna-Lena Volckmar
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Nikolaus Magios
- Thoracic Oncology, Thoraxklinik, University of Heidelberg, Translational Lung Research Center, Heidelberg, Germany
| | | | - Roland Penzel
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Regine Brandt
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Martina Kirchner
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Farastuk Bozorgmehr
- Thoracic Oncology, Thoraxklinik, University of Heidelberg, Translational Lung Research Center, Heidelberg, Germany
| | - Michael Thomas
- Thoracic Oncology, Thoraxklinik, University of Heidelberg, Translational Lung Research Center, Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Arne Warth
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
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40
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Influenza Virus Susceptibility of Wild-Derived CAST/EiJ Mice Results from Two Amino Acid Changes in the MX1 Restriction Factor. J Virol 2016; 90:10682-10692. [PMID: 27654285 DOI: 10.1128/jvi.01213-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/11/2016] [Indexed: 12/27/2022] Open
Abstract
The interferon-regulated Mx1 gene of the A2G mouse strain confers a high degree of resistance against influenza A and Thogoto viruses. Most other laboratory inbred mouse strains carry truncated nonfunctional Mx1 alleles and, consequently, exhibit high virus susceptibility. Interestingly, CAST/EiJ mice, derived from wild Mus musculus castaneus, possess a seemingly intact Mx1 gene but are highly susceptible to influenza A virus challenge. To determine whether the enhanced influenza virus susceptibility is due to intrinsically reduced antiviral activity of the CAST-derived Mx1 allele, we generated a congenic C57BL/6J mouse line that carries the Mx locus of CAST/EiJ mice. Adult animals of this line were almost as susceptible to influenza virus challenge as standard C57BL/6J mice lacking functional Mx1 alleles but exhibited far more pronounced resistance to Thogoto virus. Sequencing revealed that CAST-derived MX1 differs from A2G-derived MX1 by two amino acids (G83R and A222V) in the GTPase domain. Especially the A222V mutation reduced GTPase activity of purified MX1 and diminished the inhibitory effect of MX1 in influenza A virus polymerase activity assays. Further, MX1 protein was substantially less abundant in organs of interferon-treated mice carrying the CAST Mx1 allele than in those of mice carrying the A2G Mx1 allele. We found that the CAST-specific mutations reduced the metabolic stability of the MX1 protein although Mx1 mRNA levels were unchanged. Thus, the enhanced influenza virus susceptibility of CAST/EiJ mice can be explained by minor alterations in the MX1 restriction factor that negatively affect its enzymatic activity and reduce its half-life. IMPORTANCE Although the crystal structure of the prototypic human MXA protein is known, the importance of specific protein domains for antiviral activity is still incompletely understood. Novel insights might come from studying naturally occurring MX protein variants with altered antiviral activity. Here we identified two seemingly minor amino acid changes in the GTPase domain that negatively affect the enzymatic activity and metabolic stability of murine MX1 and thus dramatically reduce the influenza virus resistance of the respective mouse inbred strain. These observations highlight our current inability to predict the biological consequences of previously uncharacterized MX mutations in mice. Since this is probably also true for naturally occurring mutations in Mx genes of humans, careful experimental analysis of any natural MXA variants for altered activity is necessary in order to assess possible consequences of such mutations on innate antiviral immunity.
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Brbić M, Piškorec M, Vidulin V, Kriško A, Šmuc T, Supek F. The landscape of microbial phenotypic traits and associated genes. Nucleic Acids Res 2016; 44:10074-10090. [PMID: 27915291 PMCID: PMC5137458 DOI: 10.1093/nar/gkw964] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 09/21/2016] [Accepted: 10/11/2016] [Indexed: 12/31/2022] Open
Abstract
Bacteria and Archaea display a variety of phenotypic traits and can adapt to diverse ecological niches. However, systematic annotation of prokaryotic phenotypes is lacking. We have therefore developed ProTraits, a resource containing ∼545 000 novel phenotype inferences, spanning 424 traits assigned to 3046 bacterial and archaeal species. These annotations were assigned by a computational pipeline that associates microbes with phenotypes by text-mining the scientific literature and the broader World Wide Web, while also being able to define novel concepts from unstructured text. Moreover, the ProTraits pipeline assigns phenotypes by drawing extensively on comparative genomics, capturing patterns in gene repertoires, codon usage biases, proteome composition and co-occurrence in metagenomes. Notably, we find that gene synteny is highly predictive of many phenotypes, and highlight examples of gene neighborhoods associated with spore-forming ability. A global analysis of trait interrelatedness outlined clusters in the microbial phenotype network, suggesting common genetic underpinnings. Our extended set of phenotype annotations allows detection of 57 088 high confidence gene-trait links, which recover many known associations involving sporulation, flagella, catalase activity, aerobicity, photosynthesis and other traits. Over 99% of the commonly occurring gene families are involved in genetic interactions conditional on at least one phenotype, suggesting that epistasis has a major role in shaping microbial gene content.
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Affiliation(s)
- Maria Brbić
- Division of Electronics, Ruder Boskovic Institute, 10000 Zagreb, Croatia
| | - Matija Piškorec
- Division of Electronics, Ruder Boskovic Institute, 10000 Zagreb, Croatia
| | - Vedrana Vidulin
- Division of Electronics, Ruder Boskovic Institute, 10000 Zagreb, Croatia
| | - Anita Kriško
- Mediterranean Institute of Life Sciences, 21000 Split, Croatia
| | - Tomislav Šmuc
- Division of Electronics, Ruder Boskovic Institute, 10000 Zagreb, Croatia
| | - Fran Supek
- Division of Electronics, Ruder Boskovic Institute, 10000 Zagreb, Croatia .,EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
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42
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Shi SL, Jiang YR, Yang RS, Wang Y, Qin L. Codon usage in Alphabaculovirus and Betabaculovirus hosted by the same insect species is weak, selection dominated and exhibits no more similar patterns than expected. INFECTION GENETICS AND EVOLUTION 2016; 44:412-417. [PMID: 27484795 PMCID: PMC7106102 DOI: 10.1016/j.meegid.2016.07.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 07/16/2016] [Accepted: 07/29/2016] [Indexed: 11/26/2022]
Abstract
Mutations shape synonymous codon usage bias in certain organism genomes, while selection shapes it in others. Lepidopteran-specific Alphabaculovirus and Betabaculovirus are two large genera in the family of Baculoviridae. In this study, we analyzed the codon usage patterns in 17 baculoviruses, including 10 alphabaculoviruses and 7 betabaculoviruses, which were isolated from seven insect species, and we characterized the codon usage patterns between Alphabaculovirus and Betabaculovirus. Our results show that all the baculoviruses possessed a general weak trend of codon bias. The differences of ENc (effective number of codons) values, nucleotide contents and the impacts of nucleotide content on ENc value within alpha-/betabaculovirus pairs were independent of whether the host species are the same or different. Furthermore, the majority of amino acid sequences adopted codons unequally in all viruses, but the numbers of common preferred codons between alpha- and betabaculoviruses hosted by the same insect species were not significantly different from the differences observed between alpha- and betabaculoviruses hosted by different insect species. In addition, the amino acids that adopt the same synonymous codon composition between alpha- and betabaculoviruses hosted by the same insect species were statistically as few as those between alpha- and betabaculoviruses hosted by different insect species. Correspondence analysis revealed that no major factors resulted in the codon bias in these baculoviruses, implying multiple minor influential factors exist. Neutrality plot analysis indicated that selection pressure dominated mutations in shaping the codon usage. However, the levels of selection pressure were not significantly different among viruses hosted by the same insect species. We expect that evolution would cause the alpha- and betabaculoviruses hosted by the same insect species to share more patterns, but this effect was not observed.
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Affiliation(s)
- Sheng-Lin Shi
- Insect Resource Engineering Research Center of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China.
| | - Yi-Ren Jiang
- Insect Resource Engineering Research Center of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China.
| | - Rui-Sheng Yang
- Insect Resource Engineering Research Center of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China.
| | - Yong Wang
- Insect Resource Engineering Research Center of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China.
| | - Li Qin
- Insect Resource Engineering Research Center of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China.
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43
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Rudolph KLM, Schmitt BM, Villar D, White RJ, Marioni JC, Kutter C, Odom DT. Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States. PLoS Genet 2016; 12:e1006024. [PMID: 27166679 PMCID: PMC4864286 DOI: 10.1371/journal.pgen.1006024] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/12/2016] [Indexed: 11/19/2022] Open
Abstract
Whether codon usage fine-tunes mRNA translation in mammals remains controversial, with recent papers suggesting that production of proteins in specific Gene Ontological (GO) pathways can be regulated by actively modifying the codon and anticodon pools in different cellular conditions. In this work, we compared the sequence content of genes in specific GO categories with the exonic genome background. Although a substantial fraction of variability in codon usage could be explained by random sampling, almost half of GO sets showed more variability in codon usage than expected by chance. Nevertheless, by quantifying translational efficiency in healthy and cancerous tissues in human and mouse, we demonstrated that a given tRNA pool can equally well translate many different sets of mRNAs, irrespective of their cell-type specificity. This disconnect between variations in codon usage and the stability of translational efficiency is best explained by differences in GC content between gene sets. GC variation across the mammalian genome is most likely a result of the interplay between genome repair and gene duplication mechanisms, rather than selective pressures caused by codon-driven translational rates. Consequently, codon usage differences in mammalian transcriptomes are most easily explained by well-understood mutational biases acting on the underlying genome.
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Affiliation(s)
- Konrad L. M. Rudolph
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - Bianca M. Schmitt
- University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Diego Villar
- University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Robert J. White
- University of York, Department of Biology, York, United Kingdom
| | - John C. Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
- University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Claudia Kutter
- University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
- Science for Life Laboratory, Karolinska Institute, Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
| | - Duncan T. Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
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Yan Q, Philmus B, Hesse C, Kohen M, Chang JH, Loper JE. The Rare Codon AGA Is Involved in Regulation of Pyoluteorin Biosynthesis in Pseudomonas protegens Pf-5. Front Microbiol 2016; 7:497. [PMID: 27148187 PMCID: PMC4836200 DOI: 10.3389/fmicb.2016.00497] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/27/2016] [Indexed: 11/24/2022] Open
Abstract
The soil bacterium Pseudomonas protegens Pf-5 can colonize root and seed surfaces of many plants, protecting them from infection by plant pathogenic fungi and oomycetes. The capacity to suppress disease is attributed to Pf-5's production of a large spectrum of antibiotics, which is controlled by complex regulatory circuits operating at the transcriptional and post-transcriptional levels. In this study, we analyzed the genomic sequence of Pf-5 for codon usage patterns and observed that the six rarest codons in the genome are present in all seven known antibiotic biosynthesis gene clusters. In particular, there is an abundance of rare codons in pltR, which encodes a member of the LysR transcriptional regulator family that controls the expression of pyoluteorin biosynthetic genes. To test the hypothesis that rare codons in pltR influence pyoluteorin production, we generated a derivative of Pf-5 in which 23 types of rare codons in pltR were substituted with synonymous preferred codons. The resultant mutant produced pyoluteorin at levels 15 times higher than that of the wild-type Pf-5. Accordingly, the promoter activity of the pyoluteorin biosynthetic gene pltL was 20 times higher in the codon-modified stain than in the wild-type. pltR has six AGA codons, which is the rarest codon in the Pf-5 genome. Substitution of all six AGA codons with preferred Arg codons resulted in a variant of pltR that conferred increased pyoluteorin production and pltL promoter activity. Furthermore, overexpression of tRNAUCUArg, the cognate tRNA for the AGA codon, significantly increased pyoluteorin production by Pf-5. A bias in codon usage has been linked to the regulation of many phenotypes in eukaryotes and prokaryotes but, to our knowledge, this is the first example of the role of a rare codon in the regulation of antibiotic production by a Gram-negative bacterium.
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Affiliation(s)
- Qing Yan
- Department of Botany and Plant Pathology, Oregon State University Corvallis, OR, USA
| | | | - Cedar Hesse
- Horticultural Crops Research Laboratory, US Department of Agriculture, Agricultural Research Service Corvallis, OR, USA
| | - Max Kohen
- Department of Botany and Plant Pathology, Oregon State University Corvallis, OR, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University Corvallis, OR, USA
| | - Joyce E Loper
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA; Horticultural Crops Research Laboratory, US Department of Agriculture, Agricultural Research ServiceCorvallis, OR, USA
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