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Xu Q, Cao J, Rai KR, Zhu B, Liu D, Wan C. Codon usage bias of goose circovirus and its adaptation to host. Poult Sci 2024; 103:103775. [PMID: 38713985 PMCID: PMC11091504 DOI: 10.1016/j.psj.2024.103775] [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: 02/25/2024] [Revised: 04/03/2024] [Accepted: 04/13/2024] [Indexed: 05/09/2024] Open
Abstract
Goose circovirus (GoCV), a potential immunosuppressive virus possessing a circular single-stranded DNA genome, is widely distributed in both domesticated and wild geese. This virus infection causes significant economic losses in the waterfowl industry. The codon usage patterns of viruses reflect the evolutionary history and genetic architecture, allowing them to adapt quickly to changes in the external environment, particularly to their hosts. In this study, we retrieved the coding sequences (Rep and Cap) and the genome of GoCV from GenBank, conducting comprehensive research to explore the codon usage patterns in 144 GoCV strains. The overall codon usage of the GoCV strains was relatively similar and exhibited a slight bias. The effective number of codons (ENC) indicated a low overall extent of codon usage bias (CUB) in GoCV. Combined with the base composition and relative synonymous codon usage (RSCU) analysis, the results revealed a bias toward A- and G-ending codons in the overall codon usage. Analysis of the ENC-GC3s plot and neutrality plot suggested that natural selection plays an important role in shaping the codon usage pattern of GoCV, with mutation pressure having a minor influence. Furthermore, the correlations between ENC and relative indices, as well as correspondence analysis (COA), showed that hydrophobicity and geographical distribution also contribute to codon usage variation in GoCV, suggesting the possible involvement of natural selection. In conclusion, GoCV exhibits comparatively slight CUB, with natural selection being the major factor shaping the codon usage pattern of GoCV. Our research contributes to a deeper understanding of GoCV evolution and its host adaptation, providing valuable insights for future basic studies and vaccine design related to GoCV.
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Affiliation(s)
- Quanming Xu
- Scientific Research and Experiment Center, Fujian Police College, Fuzhou 350007, China
| | - Jie Cao
- Scientific Research and Experiment Center, Fujian Police College, Fuzhou 350007, China
| | - Kul Raj Rai
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Binling Zhu
- Department of Forensic Science, Fujian Police College, Fuzhou 350007, China
| | - Dan Liu
- China Institute of Veterinary Drug Control, Beijing, 100081, China
| | - Chunhe Wan
- Institute of Animal Husbandry and Veterinary Medicine/Fujian Key Laboratory for Avian Diseases Control and Prevention/Fujian Animal Diseases Control Technology Development Centre, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China.
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Tamer C, Ulrich K, Di Paola N, Kurucay HN, Albayrak H, Weidmann M. Evolution of an Extended Pathogenicity Motif in VP2 of Infectious Pancreatic Necrosis Virus Isolates from Farmed Rainbow Trout in Turkey. Viruses 2024; 16:994. [PMID: 38932285 PMCID: PMC11209135 DOI: 10.3390/v16060994] [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: 05/13/2024] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Infectious pancreatic necrosis virus (IPNV) causes economic losses with a highly variable mortality rate worldwide, especially in rainbow trout. The virus has a double-stranded bi-partite RNA genome designated segment A and B. New complete genome sequences of nine rainbow trout isolates from Turkey were determined and subjected to phylogenetic analysis, identifying all as genotype 5 (serotype Sp). A time-dependent change in the extended pathogenicity motif of VP2 from P217T221A247 (PTA) to PTE P217T221E247 over a period of 10 years was identified. A wider analysis of 99 IPNV sequences from Turkey and Iran revealed the emergence of the motif PTE from 2007 to 2017, inducing significant morbidity in fry by 2013. In fact, displacement of the PTA motif, by the PTE motif in IPNV isolates appeared to be connected to a production peak of rainbow trout in 2013. An additional CAI analysis provided more evidence, indicating that rainbow trout culture in Turkey has an influence on the evolution of IPNV.
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Affiliation(s)
- Cuneyt Tamer
- Department of Virology, Faculty of Veterinary Medicine, Ondokuz Mayıs University, 55139 Samsun, Turkey; (C.T.); (H.N.K.)
| | - Kristina Ulrich
- Institute of Aquaculture, University of Stirling, Scotland FK9 4LA, UK;
| | - Nicholas Di Paola
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD 21702-5011, USA;
| | - Hanne Nur Kurucay
- Department of Virology, Faculty of Veterinary Medicine, Ondokuz Mayıs University, 55139 Samsun, Turkey; (C.T.); (H.N.K.)
| | - Harun Albayrak
- Department of Virology, Faculty of Veterinary Medicine, Ondokuz Mayıs University, 55139 Samsun, Turkey; (C.T.); (H.N.K.)
| | - Manfred Weidmann
- Medizinische Hochschule Brandenburg Theodor Fontane, 01968 Senftenberg, Germany
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S. Celina S, Černý J. Genetic background of adaptation of Crimean-Congo haemorrhagic fever virus to the different tick hosts. PLoS One 2024; 19:e0302224. [PMID: 38662658 PMCID: PMC11045102 DOI: 10.1371/journal.pone.0302224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Crimean-Congo haemorrhagic fever orthonairovirus (CCHFV) is a negative-sense, single-stranded RNA virus with a segmented genome and the causative agent of a severe Crimean-Congo haemorrhagic fever (CCHF) disease. The virus is transmitted mainly by tick species in Hyalomma genus but other ticks such as representatives of genera Dermacentor and Rhipicephalus may also be involved in virus life cycle. To improve our understanding of CCHFV adaptation to its tick species, we compared nucleotide composition and codon usage patterns among the all CCHFV strains i) which sequences and other metadata as locality of collection and date of isolation are available in GenBank and ii) which were isolated from in-field collected tick species. These criteria fulfilled 70 sequences (24 coding for S, 23 for M, and 23 for L segment) of virus isolates originating from different representatives of Hyalomma and Rhipicephalus genera. Phylogenetic analyses confirmed that Hyalomma- and Rhipicephalus-originating CCHFV isolates belong to phylogenetically distinct CCHFV clades. Analyses of nucleotide composition among the Hyalomma- and Rhipicephalus-originating CCHFV isolates also showed significant differences, mainly in nucleotides located at the 3rd codon positions indicating changes in codon usage among these lineages. Analyses of codon adaptation index (CAI), effective number of codons (ENC), and other codon usage statistics revealed significant differences between Hyalomma- and Rhipicephalus-isolated CCHFV strains. Despite both sets of strains displayed a higher adaptation to use codons that are preferred by Hyalomma ticks than Rhipicephalus ticks, there were distinct codon usage preferences observed between the two tick species. These findings suggest that over the course of its long co-evolution with tick vectors, CCHFV has optimized its codon usage to efficiently utilize translational resources of Hyalomma species.
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Affiliation(s)
- Seyma S. Celina
- Faculty of Tropical AgriSciences, Center for Infectious Animal Diseases, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Jiří Černý
- Faculty of Tropical AgriSciences, Center for Infectious Animal Diseases, Czech University of Life Sciences Prague, Prague, Czech Republic
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Khandia R, Pandey MK, Khan AA, Baklanov I, Alanazi AM, Nepali P, Gurjar P, Choudhary OP. Synthetic biology approach revealed enhancement in haeme oxygenase-1 gene expression by codon pair optimization while reduction by codon deoptimization. Ann Med Surg (Lond) 2024; 86:1359-1369. [PMID: 38463112 PMCID: PMC10923308 DOI: 10.1097/ms9.0000000000001465] [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: 09/13/2023] [Accepted: 10/23/2023] [Indexed: 03/12/2024] Open
Abstract
Haem oxygenase-1 (HO-1) is a ubiquitously expressed gene involved in cellular homoeostasis, and its imbalance in expression results in various disorders. To alleviate such disorders, HO-1 gene expression needs to be modulated. Codon usage bias results from evolutionary forces acting on any nucleotide sequence and determines the gene expression. Like codon usage bias, codon pair bias also exists, playing a role in gene expression. In the present study, HO-1 gene was recoded by manipulating codon and codon pair bias, and four such constructs were made through codon/codon pair deoptimization and codon/codon pair optimization to reduce and enhance the HO-1 gene expression. Codon usage analysis was done for these constructs for four tissues brain, heart, pancreas and liver. Based on codon usage in different tissues, gene expression of these tissues was determined in terms of the codon adaptation index. Based on the codon adaptation index, minimum free energy, and translation efficiency, constructs were evaluated for enhanced or decreased HO-1 expression. The analysis revealed that for enhancing gene expression, codon pair optimization, while for reducing gene expression, codon deoptimization is efficacious. The recoded constructs developed in the study could be used in gene therapy regimens to cure HO-1 over or underexpression-associated disorders.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, MP, India
| | - Megha Katare Pandey
- Translational Medicine Center, All India Institute of Medical Sciences, Bhopal, MP, India
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Igor Baklanov
- Department of Philosophy, North Caucasus Federal University, Pushkina, Stavropol, Russia
| | - Amer M. Alanazi
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Prakash Nepali
- Bhimad Primary Health Care Center, Government of Nepal, Tanahun, Nepal
| | - Pankaj Gurjar
- Centre for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Om Prakash Choudhary
- Department of Veterinary Anatomy, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Rampura Phul, Bathinda, Punjab, India
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Powers EN, Kuwayama N, Sousa C, Reynaud K, Jovanovic M, Ingolia NT, Brar GA. Dbp1 is a low performance paralog of RNA helicase Ded1 that drives impaired translation and heat stress response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.12.575095. [PMID: 38260653 PMCID: PMC10802583 DOI: 10.1101/2024.01.12.575095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Ded1 and Dbp1 are paralogous conserved RNA helicases that enable translation initiation in yeast. Ded1 has been heavily studied but the role of Dbp1 is poorly understood. We find that the expression of these two helicases is controlled in an inverse and condition-specific manner. In meiosis and other long-term starvation states, Dbp1 expression is upregulated and Ded1 is downregulated, whereas in mitotic cells, Dbp1 expression is extremely low. Inserting the DBP1 ORF in place of the DED1 ORF cannot replace the function of Ded1 in supporting translation, partly due to inefficient mitotic translation of the DBP1 mRNA, dependent on features of its ORF sequence but independent of codon optimality. Global measurements of translation rates and 5' leader translation, activity of mRNA-tethered helicases, ribosome association, and low temperature growth assays show that-even at matched protein levels-Ded1 is more effective than Dbp1 at activating translation, especially for mRNAs with structured 5' leaders. Ded1 supports halting of translation and cell growth in response to heat stress, but Dbp1 lacks this function, as well. These functional differences in the ability to efficiently mediate translation activation and braking can be ascribed to the divergent, disordered N- and C-terminal regions of these two helicases. Altogether, our data show that Dbp1 is a "low performance" version of Ded1 that cells employ in place of Ded1 under long-term conditions of nutrient deficiency.
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Liu Y, Xu W, Yang P, Liu X. Revealing Molecular Patterns of Alzheimer's Disease Risk Gene Expression Signatures in COVID-19 Brains. J Alzheimers Dis 2024; 101:31-48. [PMID: 39058446 DOI: 10.3233/jad-240609] [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: 07/28/2024]
Abstract
Background Various virus infections are known to predispose to Alzheimer's disease (AD), and a linkage between COVID-19 and AD has been established. COVID-19 infection modulates the gene expression of the genes implicated in progression of AD. Objective Determination of molecular patterns and codon usage and context analysis for the genes that are modulated during COVID-19 infection and are implicated in AD was the target of the study. Methods Our study employed a comprehensive array of research methods, including relative synonymous codon usage, Codon adaptation index analysis, Neutrality and parity analysis, Rare codon analyses, and codon context analysis. This meticulous approach was crucial in determining the molecular patterns present in genes up or downregulated during COVID-19 infection. Results G/C ending codons were preferred in upregulated genes while not in downregulated genes, and in both gene sets, longer genes have high expressivity. Similarly, T over A nucleotide was preferred, and selection was the major evolutionary force in shaping codon usage in both gene sets. Apart from stops codons, codons CGU - Arg, AUA - Ile, UUA - Leu, UCG - Ser, GUA - Val, and CGA - Arg in upregulated genes, while CUA - Leu, UCG - Ser, and UUA - Leu in downregulated genes were present below the 0.5%. Glutamine-initiated codon pairs have high residual values in upregulated genes. Identical codon pairs GAG-GAG and GUG-GUG were preferred in both gene sets. Conclusions The shared and unique molecular features in the up- and downregulated gene sets provide insights into the complex interplay between COVID-19 infection and AD. Further studies are required to elucidate the relationship of these molecular patterns with AD pathology.
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Affiliation(s)
- Yan Liu
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Third Hospital of Shanxi Medical University, Tongji Shanxi Hospital, Taiyuan, China
| | - Weiyue Xu
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Third Hospital of Shanxi Medical University, Tongji Shanxi Hospital, Taiyuan, China
| | - Pan Yang
- TEDA institute of Biological Science and Biotechnology, Nankai University, TEDA, Tianjin, China
| | - Xingshun Liu
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, China
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Corzo G, Seeling-Branscomb CE, Seeling JM. Differential Synonymous Codon Selection in the B56 Gene Family of PP2A Regulatory Subunits. Int J Mol Sci 2023; 25:392. [PMID: 38203563 PMCID: PMC10778929 DOI: 10.3390/ijms25010392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/18/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
Protein phosphatase 2A (PP2A) functions as a tumor suppressor and consists of a scaffolding, catalytic, and regulatory subunit. The B56 gene family of regulatory subunits impart distinct functions onto PP2A. Codon usage bias (CUB) involves the selection of synonymous codons, which can affect gene expression by modulating processes such as transcription and translation. CUB can vary along the length of a gene, and differential use of synonymous codons can be important in the divergence of gene families. The N-termini of the gene product encoded by B56α possessed high CUB, high GC content at the third codon position (GC3), and high rare codon content. In addition, differential CUB was found in the sequence encoding two B56γ N-terminal splice forms. The sequence encoding the N-termini of B56γ/γ, relative to B56δ/γ, displayed CUB, utilized more frequent codons, and had higher GC3 content. B56α mRNA had stronger than predicted secondary structure at their 5' end, and the B56δ/γ splice variants had long regions of weaker than predicted secondary structure at their 5' end. The data suggest that B56α is expressed at relatively low levels as compared to the other B56 isoforms and that the B56δ/γ splice variant is expressed more highly than B56γ/γ.
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Affiliation(s)
- Gabriel Corzo
- Department of Biology, Hofstra University, Hempstead, NY 11549, USA;
| | | | - Joni M. Seeling
- Department of Biology, Hofstra University, Hempstead, NY 11549, USA;
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Chan DTC, Baldwin GS, Bernstein HC. Revealing the Host-Dependent Nature of an Engineered Genetic Inverter in Concordance with Physiology. BIODESIGN RESEARCH 2023; 5:0016. [PMID: 37849456 PMCID: PMC10432152 DOI: 10.34133/bdr.0016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/17/2023] [Indexed: 10/19/2023] Open
Abstract
Broad-host-range synthetic biology is an emerging frontier that aims to expand our current engineerable domain of microbial hosts for biodesign applications. As more novel species are brought to "model status," synthetic biologists are discovering that identically engineered genetic circuits can exhibit different performances depending on the organism it operates within, an observation referred to as the "chassis effect." It remains a major challenge to uncover which genome-encoded and biological determinants will underpin chassis effects that govern the performance of engineered genetic devices. In this study, we compared model and novel bacterial hosts to ask whether phylogenomic relatedness or similarity in host physiology is a better predictor of genetic circuit performance. This was accomplished using a comparative framework based on multivariate statistical approaches to systematically demonstrate the chassis effect and characterize the performance dynamics of a genetic inverter circuit operating within 6 Gammaproteobacteria. Our results solidify the notion that genetic devices are strongly impacted by the host context. Furthermore, we formally determined that hosts exhibiting more similar metrics of growth and molecular physiology also exhibit more similar performance of the genetic inverter, indicating that specific bacterial physiology underpins measurable chassis effects. The result of this study contributes to the field of broad-host-range synthetic biology by lending increased predictive power to the implementation of genetic devices in less-established microbial hosts.
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Affiliation(s)
- Dennis Tin Chat Chan
- Faculty of Biosciences, Fisheries and Economics, UiT, The Arctic University of Norway, 9019 Tromsø, Norway
| | - Geoff S. Baldwin
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
- Imperial College Centre for Synthetic Biology, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Hans C. Bernstein
- Faculty of Biosciences, Fisheries and Economics, UiT, The Arctic University of Norway, 9019 Tromsø, Norway
- The Arctic Centre for Sustainable Energy, UiT, The Arctic University of Norway, 9019 Tromsø, Norway
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Guo X, Zhang Y, Pan Y, Yang K, Tong X, Wang Y. Phylogenetic Analysis and Codon Usage Bias Reveal the Base of Feline and Canine Chaphamaparvovirus for Cross-Species Transmission. Animals (Basel) 2023; 13:2617. [PMID: 37627409 PMCID: PMC10451695 DOI: 10.3390/ani13162617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/29/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Chaphamaparvoviruses (ChPVs) are ancient viruses that have been detected in a variety of hosts. In this study, through a phylogenetic analysis and the adaptability of ChPV to multiple hosts, we evaluated the basis for the ability of feline (FeChPV) and canine ChPV (CaChPV) for cross-species transmission. Phylogenetic analysis showed that FeChPV and CaChPV were closely related. Notably, two strains of ChPVs isolated from domestic cats and two from dogs clustered together with CaChPVs and FeChPVs, respectively, suggesting that the stringent boundaries between canine and feline ChPV may be broken. Further analysis revealed that CaChPV and FeChPV were more adapted to dogs than to cats. Mutation analysis identified several shared mutations in cross-species-transmissible strains. Furthermore, the VP structures of FeChPV and CaChPV exhibited a high degree of similarity across both cross-species-transmissible and non-cross-species-transmissible strains. However, it is crucial to note that these results are largely computational, and limitations exist in terms of the number and diversity of samples analyzed; the capacity for cross-species transmission should be approached with caution and elucidated in further studies.
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Affiliation(s)
- Xu Guo
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yingying Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yang Pan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Kankan Yang
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Xinxin Tong
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Yong Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
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Hosseininejad Z, Daryani A, Fasihi-Ramandi M, Asgarian-Omran H, Valadan R, Nayeri T, Dodangeh S, Sarvi S. In Silico Vaccine Design and Expression of the Multi-Component Protein Candidate against the Toxoplasma gondii Parasite from MIC13, GRA1, and SAG1 Antigens. IRANIAN JOURNAL OF PARASITOLOGY 2023; 18:301-312. [PMID: 37886246 PMCID: PMC10597883 DOI: 10.18502/ijpa.v18i3.13753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/20/2022] [Indexed: 10/28/2023]
Abstract
Background We aimed to design a B and T cell recombinant protein vaccine of Toxoplasma gondii with in silico approach. MIC13 plays an important role in spreading the parasite in the host body. GRA1 causes the persistence of the parasite in the parasitophorous vacuole. SAG1 plays a role in host-cell adhesion and cell invasion. Methods Amino acid positions 73-272 from MIC13, 71-190 from GRA1, and 101-300 from SAG1 were selected and joined with linker A(EAAAK)A. The structures, antigenicity, allergenicity, physicochemical properties, as well as codon optimization and mRNA structure of this recombinant protein called MGS1, were predicted using bioinformatics servers. The designed structure was synthesized and then cloned in pET28a (+) plasmid and transformed into Escherichia coli BL21. Results The number of amino acids in this antigen was 555, and its antigenicity was estimated to be 0.6340. SDS-PAGE and Western blotting confirmed gene expression and successful production of the protein with a molecular weight of 59.56kDa. This protein will be used in our future studies as an anti-Toxoplasma vaccine candidate in animal models. Conclusion In silico methods are efficient for understanding information about proteins, selecting immunogenic epitopes, and finally producing recombinant proteins, as well as reducing the time and cost of vaccine design.
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Affiliation(s)
- Zahra Hosseininejad
- Toxoplasmosis Research Center, Communicable Disease Institute, Mazandaran University of Medical Sciences, Sari, Iran
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ahmad Daryani
- Toxoplasmosis Research Center, Communicable Disease Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mahdi Fasihi-Ramandi
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Hossein Asgarian-Omran
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Reza Valadan
- Department of Immunology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Tooran Nayeri
- Toxoplasmosis Research Center, Communicable Disease Institute, Mazandaran University of Medical Sciences, Sari, Iran
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Samira Dodangeh
- Department of Medical Parasitology and Mycology, Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Shahabeddin Sarvi
- Toxoplasmosis Research Center, Communicable Disease Institute, Mazandaran University of Medical Sciences, Sari, Iran
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Firdaus MER, Mustopa AZ, Ekawati N, Chairunnisa S, Arifah RK, Hertati A, Irawan S, Prastyowati A, Kusumawati A, Nurfatwa M. Optimization, characterization, comparison of self-assembly VLP of capsid protein L1 in yeast and reverse vaccinology design against human papillomavirus type 52. J Genet Eng Biotechnol 2023; 21:68. [PMID: 37222880 DOI: 10.1186/s43141-023-00514-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/06/2023] [Indexed: 05/25/2023]
Abstract
BACKGROUND Vaccination is the one of the agendas of many countries to reduce cervical cancer caused by the Human papillomavirus. Currently, VLP-based vaccine is the most potent vaccine against HPV, which could be produced by a variety of expression systems. Our study focuses on a comparison of recombinant protein expression L1 HPV52 using two common yeasts, Pichia pastoris and Hansenula polymorpha that have been used for vaccine production on an industrial scale. We also applied bioinformatics approach using reverse vaccinology to design alternative multi-epitope vaccines in recombinant protein and mRNA types. RESULTS Our study found that P. pastoris relatively provided higher level of L1 protein expression and production efficiency compared to H. polymorpha in a batch system. However, both hosts showed self-assembly VLP formation and stable integration during protein induction. The vaccine we have designed exhibited high immune activation and safe in computational prediction. It is also potentially suitable for production in a variety of expression systems. CONCLUSION By monitoring the overall optimization parameter assessment, this study can be used as the basis reference for large-scale production of the HPV52 vaccine.
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Affiliation(s)
- Moh Egy Rahman Firdaus
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
- Current Address: Laboratory of Structural Virology, The International Institute of Molecular Mechanisms and Machines (IMOL), Polish Academy of Sciences, Warsaw, Poland
| | - Apon Zaenal Mustopa
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia.
| | - Nurlaili Ekawati
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Sheila Chairunnisa
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Rosyida Khusniatul Arifah
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Ai Hertati
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Shasmita Irawan
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Anika Prastyowati
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Arizah Kusumawati
- Directorate of Laboratory Management Research Facilities, Science and Technology Park, National Research and Innovation Agency (BRIN), Bogor, 16911, West Java, Indonesia
| | - Maritsa Nurfatwa
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
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12
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Azizi H, Knapp JP, Li Y, Berger A, Lafrance MA, Pedersen J, de la Vega MA, Racine T, Kang CY, Mann JFS, Dikeakos JD, Kobinger G, Arts EJ. Optimal Expression, Function, and Immunogenicity of an HIV-1 Vaccine Derived from the Approved Ebola Vaccine, rVSV-ZEBOV. Vaccines (Basel) 2023; 11:977. [PMID: 37243081 PMCID: PMC10223473 DOI: 10.3390/vaccines11050977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Vesicular stomatitis virus (VSV) remains an attractive platform for a potential HIV-1 vaccine but hurdles remain, such as selection of a highly immunogenic HIV-1 Envelope (Env) with a maximal surface expression on recombinant rVSV particles. An HIV-1 Env chimera with the transmembrane domain (TM) and cytoplasmic tail (CT) of SIVMac239 results in high expression on the approved Ebola vaccine, rVSV-ZEBOV, also harboring the Ebola Virus (EBOV) glycoprotein (GP). Codon-optimized (CO) Env chimeras derived from a subtype A primary isolate (A74) are capable of entering a CD4+/CCR5+ cell line, inhibited by HIV-1 neutralizing antibodies PGT121, VRC01, and the drug, Maraviroc. The immunization of mice with the rVSV-ZEBOV carrying the CO A74 Env chimeras results in anti-Env antibody levels as well as neutralizing antibodies 200-fold higher than with the NL4-3 Env-based construct. The novel, functional, and immunogenic chimeras of CO A74 Env with the SIV_Env-TMCT within the rVSV-ZEBOV vaccine are now being tested in non-human primates.
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Affiliation(s)
- Hiva Azizi
- Département de Microbiologie-Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; (H.A.); (A.B.); (M.-A.L.); (J.P.); (M.-A.d.l.V.); (T.R.)
- Human Health Therapeutics, National Research Council Canada, Ottawa, ON K1N 5A2, Canada
| | - Jason P. Knapp
- Department of Microbiology and Immunology, Western University, London, ON N6A 3K7, Canada; (J.P.K.); (Y.L.); (C.-Y.K.); (J.D.D.)
| | - Yue Li
- Department of Microbiology and Immunology, Western University, London, ON N6A 3K7, Canada; (J.P.K.); (Y.L.); (C.-Y.K.); (J.D.D.)
| | - Alice Berger
- Département de Microbiologie-Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; (H.A.); (A.B.); (M.-A.L.); (J.P.); (M.-A.d.l.V.); (T.R.)
| | - Marc-Alexandre Lafrance
- Département de Microbiologie-Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; (H.A.); (A.B.); (M.-A.L.); (J.P.); (M.-A.d.l.V.); (T.R.)
| | - Jannie Pedersen
- Département de Microbiologie-Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; (H.A.); (A.B.); (M.-A.L.); (J.P.); (M.-A.d.l.V.); (T.R.)
| | - Marc-Antoine de la Vega
- Département de Microbiologie-Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; (H.A.); (A.B.); (M.-A.L.); (J.P.); (M.-A.d.l.V.); (T.R.)
- Galveston National Laboratory, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Trina Racine
- Département de Microbiologie-Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada; (H.A.); (A.B.); (M.-A.L.); (J.P.); (M.-A.d.l.V.); (T.R.)
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Chil-Yong Kang
- Department of Microbiology and Immunology, Western University, London, ON N6A 3K7, Canada; (J.P.K.); (Y.L.); (C.-Y.K.); (J.D.D.)
| | - Jamie F. S. Mann
- Bristol Veterinary School, University of Bristol, Langford House, Langford, BS40 5DU Bristol, UK;
| | - Jimmy D. Dikeakos
- Department of Microbiology and Immunology, Western University, London, ON N6A 3K7, Canada; (J.P.K.); (Y.L.); (C.-Y.K.); (J.D.D.)
| | - Gary Kobinger
- Galveston National Laboratory, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Eric J. Arts
- Department of Microbiology and Immunology, Western University, London, ON N6A 3K7, Canada; (J.P.K.); (Y.L.); (C.-Y.K.); (J.D.D.)
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13
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Wang H, Liu S, Lv Y, Wei W. Codon usage bias of Venezuelan equine encephalitis virus and its host adaption. Virus Res 2023; 328:199081. [PMID: 36854361 DOI: 10.1016/j.virusres.2023.199081] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 09/14/2022] [Accepted: 02/24/2023] [Indexed: 03/02/2023]
Abstract
Venezuelan equine encephalitis virus (VEEV) is an emerging zoonotic virus in the alphavirus genus. It can be transmitted to humans due to spillover from equid-mosquito cycles. The symptoms caused by VEEV include fever, headache, myalgia, nausea, and vomiting. It can also cause encephalitis in severe cases. The evolutionary features of VEEV are largely unknown. In this study, we comprehensively analyzed the codon usage pattern of VEEV by computing a variety of indicators, such as effective number of codons (ENc), codon adaptation index (CAI), relative synonymous codon usage (RSCU), on 130 VEEV coding sequences retrieved from GenBank. The results showed that the codon usage bias of VEEV is relatively low. ENc-GC3s plot, neutrality plot, and CAI-ENc correlation analyses supported that translational selection plays an important role in shaping the codon usage pattern of VEEV whereas the mutation pressure has a minor influence. Analysis of RSCU values showed that most of the preferred codons in VEEV are C/G-ended. Analysis of dinucleotide composition found that all CG- and UA-containing codons are not preferentially used. Phylogenetic analysis showed that VEEV isolates can be clustered into three genera and evolutionary force affects the codon usage pattern. Furthermore, a correspondence analysis (COA) showed that aromaticity and hydrophobicity as well as geographical distribution also have certain effects on the codon usage variation of VEEV, suggesting the possible involvement of translational selection. Overall, the codon usage of VEEV is comparatively slight and translational selection might be the main factor that shapes the codon usage pattern of VEEV. This study will promote our understanding about the evolution of VEEV and its host adaption, and might provide some clues for preventing the cross-species transmission of VEEV.
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Affiliation(s)
- Hongju Wang
- Kaifeng Key Laboratory of Infection and Biological Safety, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Shijie Liu
- School of Clinical Medicine, Henan University, Kaifeng, China
| | - Yao Lv
- School of Clinical Medicine, Henan University, Kaifeng, China
| | - Wenqiang Wei
- Kaifeng Key Laboratory of Infection and Biological Safety, School of Basic Medical Sciences, Henan University, Kaifeng, China.
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14
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Bhakta S, Bhattacharya A. In silico evolutionary and structural analysis of cAMP response proteins (CARPs) from Leishmania major. Arch Microbiol 2023; 205:125. [PMID: 36941487 DOI: 10.1007/s00203-023-03463-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/23/2023]
Abstract
With unidentified chemical triggers and novel-effectors, cAMP signaling is broadly noncanonical in kinetoplastida parasites. Though novel protein kinase A regulatory subunits (PKAR) have been identified earlier, cAMP Response Proteins (CARPs) have been identified as a unique and definite cAMP effector of trypanosomatids. CARP1-CARP4 emerged as critical regulatory components of cAMP signaling pathway in Trypanosoma with evidences that CARP3 can directly interact with a flagellar adenylate cyclase (AC). CARP-mediated regulations, identified so far, reflects the mechanistic diversity of cAMP signaling. Albeit the function of the orthologous is not yet delineated, in kinetoplastids like Leishmania, presence of CARP1, 2 and 4 orthologues suggests existence of conserved effector mechanisms. Targeting CARP orthologues in Leishmania, a comprehensive evolutionary analysis of CARPs have been aimed in this study which revealed phylogenetic relationship, codon adaptation and structural heterogeneity among the orthologues, warranting functional analysis in future to explore their involvement in infectivity.
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Affiliation(s)
- Swarnav Bhakta
- Department of Biotechnology, Adamas University, Barasat-Barrackpore Rd., Kolkata, 700126, India
| | - Arijit Bhattacharya
- Department of Microbiology, Adamas University, Barasat-Barrackpore Rd., Kolkata, 700126, India.
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15
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Davoodi P, Ghaderi-Zefrehei M, Dolatabady MM, Razmkabir M, Kianpour S, Esfahani EN, Smith J. In silico investigation of uncoupling protein function in avian genomes. Front Vet Sci 2023; 9:1085112. [PMID: 36744229 PMCID: PMC9893418 DOI: 10.3389/fvets.2022.1085112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/28/2022] [Indexed: 01/20/2023] Open
Abstract
Introduction The uncoupling proteins (UCPs) are involved in lipid metabolism and belong to a family of mitochondrial anionic transporters. In poultry, only one UCP homologue has been identified and experimentally shown to be associated with growth, feed conversion ratio, and abdominal fat according to its predominant expression in bird muscles. In endotherm birds, cell metabolic efficiency can be tuned by the rate of mitochondrial coupling. Thus, avUCP may be a key contributor to controlling metabolic rate during particular environmental changes. Methods This study aimed to perform a set of in-silico investigations primarily focused on the structural, biological, and biomimetic functions of avUCP. Thereby, using in silico genome analyses among 8 avian species (chicken, turkey, swallow, manakin, sparrow, wagtail, pigeon, and mallard) and a series of bioinformatic approaches, we provide phylogenetic inference and comparative genomics of avUCPs and investigate whether sequence variation can alter coding sequence characteristics, the protein structure, and its biological features. Complementarily, a combination of literature mining and prediction approaches was also applied to predict the gene networks of avUCP to identify genes, pathways, and biological crosstalk associated with avUCP function. Results The results showed the evolutionary alteration of UCP proteins in different avian species. Uncoupling proteins in avian species are highly conserved trans membrane proteins as seen by sequence alignment, physio-chemical parameters, and predicted protein structures. Taken together, avUCP has the potential to be considered a functional marker for the identification of cell metabolic state, thermogenesis, and oxidative stress caused by cold, heat, fasting, transfer, and other chemical stimuli stresses in birds. It can also be deduced that avUCP, in migrant or domestic birds, may increase heat stress resistance by reducing fatty acid transport/b-oxidation and thermoregulation alongside antioxidant defense mechanisms. The predicted gene network for avUCP highlighted a cluster of 21 genes involved in response to stress and 28 genes related to lipid metabolism and the proton buffering system. Finally, among 11 enriched pathways, crosstalk of 5 signaling pathways including MAPK, adipocytokine, mTOR, insulin, ErbB, and GnRH was predicted, indicating a possible combination of positive or negative feedback among pathways to regulate avUCP functions. Discussion Genetic selection for fast-growing commercial poultry has unintentionally increased susceptibility to many kinds of oxidative stress, and so avUCP could be considered as a potential candidate gene for balancing energy expenditure and reactive oxygen species production, especially in breeding programs. In conclusion, avUCP can be introduced as a pleiotropic gene that requires the contribution of regulatory genes, hormones, pathways, and genetic crosstalk to allow its finely-tuned function.
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Affiliation(s)
- Peymaneh Davoodi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Mostafa Ghaderi-Zefrehei
- Department of Animal Science, Faculty of Agriculture, Yasouj University, Yasouj, Iran,*Correspondence: Mostafa Ghaderi-Zefrehei ✉ ; ✉
| | | | - Mohammad Razmkabir
- Department of Animal Science, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Somayeh Kianpour
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | | | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom,Jacqueline Smith ✉
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16
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Desingu PA, Rubeni TP, Sundaresan NR. Evolution of monkeypox virus from 2017 to 2022: In the light of point mutations. Front Microbiol 2022; 13:1037598. [PMID: 36590408 PMCID: PMC9795006 DOI: 10.3389/fmicb.2022.1037598] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
Monkeypox virus (MPXV) causing multi-country outbreak-2022 is related to viruses caused outbreak-2017-2018 in West Africa. Still not fully understood which proteins of the MPXV discovered in Nigeria in 2017 have mutated through different lineages to the extent that it could cause a multi-country outbreak in 2022; similarly, codon usage bias, host adaptation indices, and the role of selection or mutation pressure in the mutated genes are also not fully studied. Here we report that according to the available sequence data this monkeypox virus acquires point mutations in multiple proteins in each period, and these point mutations accumulate and become a virus that can root outbreak-2022. Viruses exported from Nigeria to Singapore, Israel, and the United Kingdom in 2018-2019 were developed as evolutionary ancestors to B.1 viruses (MPXVs causing multi-country outbreak-2022) through MPXV/United States/2021/MD virus. Although these exported viruses have different amino acid mutations in different proteins, amino acid mutations in 10 proteins are common among them. The MPXV-United Kingdom-P2 virus evolved with only mutations in these 10 proteins and further evolved into MPXV/United States/2021/MD with amino acid mutations in 26 (including amino acid mutations in 10 proteins of the MPXV-United States-P2) proteins. It is noteworthy that specific amino acid mutations in these 22/26 (presence in MPXV/United States/2021/MD) proteins are present in B.1 viruses. Further, analysis of Relative Synonymous Codon Usage (RSCU), Synonymous Codon Usage Fraction (SCUF), and Effective Number of Codons (ENc) revealed codon usage bias in genes that exhibited nucleotide mutations in lineage B.1. Also, host adaptation indices analyzes such as Codon Adaptation Index (CAI), Expected-CAI (eCAI), Relative Codon Deoptimization Index (RCDI) and Expected value for the RCDI (eRCDI) analyzes reveal that the genes that demonstrated nucleotide mutations in lineage B.1 are favorable for human adaptation. Similarly, ENc-GC3s plot, Neutrality plot, and Parity Rule 2 (PR2)-bias plot analyzes suggest a major role of selection pressure than mutation pressure in the evolution of genes displaying nucleotide mutations in lineage B.1. Overall, from 2017 to 2022, MPXV's mutation and spread suggests that this virus continues to evolve through point mutation in the genes according to the available sequence data.
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17
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Tyagi A, Nagar V. Genome dynamics, codon usage patterns and influencing factors in Aeromonas hydrophila phages. Virus Res 2022; 320:198900. [PMID: 36029927 DOI: 10.1016/j.virusres.2022.198900] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/29/2022]
Abstract
In the present study, genome characteristics and codon usage patterns of 44 Aeromonas hydrophila phages were studied. Phage genomes varied from 30.8 to 262.0 kb with mean±SD and median values of 111.3 ± 81.4 kb and 79.4 kb, respectively. Though the great variation in phage GC contents (35.1-62.2%) was observed, GC contents of all phages (except two phages) were significantly less than the GC content (62.4 ± 5.6%) of the host. The effective number of codons (ENC) values of phage genes ranged from 27.7 to 61 with a mean±SD value of 47.4 ± 6.8. Out of a total 5773 phage genes, 207 (3.6%), 3,528 (61.1%) and 2,012 (34.9%) genes had strong (ENC < 35), moderate (35 < ENC < 50) and low (ENC ≥ 50) codon usage bias, respectively. During relative synonymous codon usage (RSCU) analysis, shared usage of preferred codons was also observed between the phages and host. During codon adaptation index (CAI) analysis, 1028 (17.8%) phage genes showed significant adaptation towards the host. Among these genes, 797 (78.0%) genes encoded hypothetical proteins or proteins of unknown function; whereas 118 (12%) genes encoded the phage structural and packaging proteins. Segregation of ENC, RSCU and CAI analysis results based on genome size also indicated that codon usage bias was more prominent in phages with small genomes. Correlation, neutrality and GC3 versus ENC analyzes indicated a more dominant role of natural selection in shaping the codon usage patterns of A. hydrophila phages. The findings of the current study could be useful from evolutionary and host-pathogen interaction perspectives leading to efficient utilization of phages for therapeutic and other applications.
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Affiliation(s)
- Anuj Tyagi
- Department of Aquatic Environment, College of Fisheries, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab 141004, India.
| | - Vandan Nagar
- Food Microbiology Group, Food Technology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400085, India
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18
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Alqahtani T, Khandia R, Puranik N, Alqahtani AM, Chidambaram K, Kamal MA. Codon Usage is Influenced by Compositional Constraints in Genes Associated with Dementia. Front Genet 2022; 13:884348. [PMID: 36017501 PMCID: PMC9395603 DOI: 10.3389/fgene.2022.884348] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/18/2022] [Indexed: 11/28/2022] Open
Abstract
Dementia is a clinical syndrome characterized by progressive cognitive decline, and the symptoms could be gradual, persistent, and progressive. In the present study, we investigated 47 genes that have been linked to dementia. Compositional, selectional, and mutational forces were seen to be involved. Nucleotide components that influenced A- and GC-affected codon usages bias at all three codon positions. The influence of these two compositional constraints on codon usage bias (CUB) was positive for nucleotide A and negative for GC. Nucleotide A also experienced the highest mutational force, and GC-ending codons were preferred over AT-ending codons. A high bias toward GC-ending codons enhances the gene expression level, evidenced by the positive association between CAI- and GC-ending codons. Unusual behavior of the TTG codon showing an inverse relationship with the GC-ending codon and negative influence of gene expression, behavior contrary to all other GC-ending codons, shows an operative selectional force. Furthermore, parity analysis, higher translational selection value, preference of GC-ending codons over AT-ending codons, and association of gene length with gene expression refer to the dominant role of selection pressure with compositional constraint and mutational force-shaping codon usage.
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Affiliation(s)
- Taha Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Nidhi Puranik
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, India
| | - Ali M Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Kumarappan Chidambaram
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Amjad Kamal
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh.,Enzymoics, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
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19
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Duarte-Velázquez I, de la Mora J, Ramírez-Prado JH, Aguillón-Bárcenas A, Tornero-Gutiérrez F, Cordero-Loreto E, Anaya-Velázquez F, Páramo-Pérez I, Rangel-Serrano Á, Muñoz-Carranza SR, Romero-González OE, Cardoso-Reyes LR, Rodríguez-Ojeda RA, Mora-Montes HM, Vargas-Maya NI, Padilla-Vaca F, Franco B. Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships. PeerJ 2022; 10:e13772. [PMID: 35880217 PMCID: PMC9308461 DOI: 10.7717/peerj.13772] [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: 03/29/2022] [Accepted: 07/01/2022] [Indexed: 01/17/2023] Open
Abstract
Organisms need mechanisms to perceive the environment and respond accordingly to environmental changes or the presence of hazards. Transcription factors (TFs) are required for cells to respond to the environment by controlling the expression of genes needed. Escherichia coli has been the model bacterium for many decades, and still, there are features embedded in its genome that remain unstudied. To date, 58 TFs remain poorly characterized, although their binding sites have been experimentally determined. This study showed that these TFs have sequence variation at the third codon position G+C content but maintain the same Codon Adaptation Index (CAI) trend as annotated functional transcription factors. Most of these transcription factors are in areas of the genome where abundant repetitive and mobile elements are present. Sequence divergence points to groups with distinctive sequence signatures but maintaining the same type of DNA binding domain. Finally, the analysis of the promoter sequences of the 58 TFs showed A+T rich regions that agree with the features of horizontally transferred genes. The findings reported here pave the way for future research of these TFs that may uncover their role as spare factors in case of lose-of-function mutations in core TFs and trace back their evolutionary history.
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Affiliation(s)
- Isabel Duarte-Velázquez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Javier de la Mora
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autonoma de Mexico, Mexico City, México
| | | | - Alondra Aguillón-Bárcenas
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Fátima Tornero-Gutiérrez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Eugenia Cordero-Loreto
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Fernando Anaya-Velázquez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Itzel Páramo-Pérez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Ángeles Rangel-Serrano
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | | | | | - Luis Rafael Cardoso-Reyes
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | | | - Héctor Manuel Mora-Montes
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Naurú Idalia Vargas-Maya
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Felipe Padilla-Vaca
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Bernardo Franco
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
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20
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Mitra A, Acharya K, Bhattacharya A. Evolutionary analysis of globin domains from kinetoplastids. Arch Microbiol 2022; 204:493. [PMID: 35841431 DOI: 10.1007/s00203-022-03107-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/14/2022] [Accepted: 06/24/2022] [Indexed: 11/25/2022]
Abstract
Globin (Gb) domains function in sensing gaseous ligands like oxygen and nitric oxide. In recent years, Gb domain containing heme binding adenylate cyclases (OsAC or GbAC) emerged as significant modulator of Leishmania response to hypoxia and oxidative stress. During progression of life cycle stages, kinetoplastids experience altered condition in insect vectors or other hosts. Moreover, marked diversity in life style has been accounted among kinetoplastids. Distribution and abundance of Gb-domains vary between different groups of kinetoplastids. While in bodonoids, Gbs are not combined with any other functional domains, in trypanosomatids it is either fused with adenylate cyclase (AC) or oxidoreductase (OxR) domains. In salivarian trypanosomatids and Leishmania (Viannia) subtypes, no gene product featuring Gbs can be identified. In this context, evolution of Gb-domains in kinetoplastids was explored. GbOxR derived Gbs clustered with bacterial flavohemoglobins (fHb) including one fHb from Advenella, an endosymbiont of monoxeneous trypanosomatids. Codon adaptation and other evolutionary analysis suggested that OsAC (LmjF.28.0090), the solitary Gb-domain featuring gene product in Leishmania, was acquired via possible horizontal gene transfer. Substantial functional divergence was estimated between orthologues of genes encoding GbAC or GbOxR; an observation also reflected in structural alignment and heme-binding residue predictions. Orthologue-paralogue and synteny analysis indicated genomic reduction in GbOxR and GbAC loci for dixeneous trypanosomatids.
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Affiliation(s)
- Akash Mitra
- Department of Microbiology, Adamas University, Barasat-Barrackpore Rd, Kolkata, 700126, India.,Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Mangalore, 575018, India
| | - Kusumita Acharya
- Department of Microbiology, Adamas University, Barasat-Barrackpore Rd, Kolkata, 700126, India
| | - Arijit Bhattacharya
- Department of Microbiology, Adamas University, Barasat-Barrackpore Rd, Kolkata, 700126, India.
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21
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Cho M, Min X, Son HS. Analysis of evolutionary and genetic patterns in structural genes of primate lentiviruses. Genes Genomics 2022; 44:773-791. [PMID: 35511321 PMCID: PMC9068864 DOI: 10.1007/s13258-022-01257-6] [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: 02/02/2022] [Accepted: 04/09/2022] [Indexed: 12/01/2022]
Abstract
Background Primate lentiviruses (HIV1, HIV2, and Simian immunodeficiency virus [SIV]) cause immune deficiency, encephalitis, and infectious anemia in mammals such as cattle, cat, goat, sheep, horse, and puma. Objective This study was designed and conducted with the main purpose of confirming the overall codon usage pattern of primate lentiviruses and exploring the evolutionary and genetic characteristics commonly or specifically expressed in HIV1, HIV2, and SIV. Methods The gag, pol, and env gene sequences of HIV1, HIV2, and SIV were analyzed to determine their evolutionary relationships, nucleotide compositions, codon usage patterns, neutrality, selection pressure (influence of mutational pressure and natural selection), and viral adaptation to human codon usage. Results A strong ‘A’ bias was confirmed in all three structural genes, consistent with previous findings regarding HIV. Notably, the ENC-GC3s plot and neutral evolution analysis showed that all primate lentiviruses were more affected by selection pressure than by mutation caused by the GC composition of the gene, consistent with prior reports regarding HIV1. The overall codon usage bias of pol was highest among the structural genes, while the codon usage bias of env was lowest. The virus groups showing high codon bias in all three genes were HIV1 and SIVcolobus. The codon adaptation index (CAI) and similarity D(A, B) values indicated that although there was a high degree of similarity to human codon usage in all three structural genes of HIV, this similarity was not caused by translation pressure. In addition, compared with HIV1, the codon usage of HIV2 is more similar to the human codon usage, but the overall codon usage bias is lower. Conclusion The origin viruses of HIV (SIVcpz_gor and SIVsmm) exhibit greater similarity to human codon usage in the gag gene, confirming their robust adaptability to human codon usage. Therefore, HIV1 and HIV2 may have evolved to avoid human codon usage by selection pressure in the gag gene after interspecies transmission from SIV hosts to humans. By overcoming safety and stability issues, information from codon usage analysis will be useful for attenuated HIV1 vaccine development. A recoded HIV1 variant can be used as a vaccine vector or in immunotherapy to induce specific innate immune responses. Further research regarding HIV1 dinucleotide usage and codon pair usage will facilitate new approaches to the treatment of AIDS.
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Affiliation(s)
- Myeongji Cho
- Laboratory of Computational Virology & Viroinformatics, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.,Institute of Health and Environment, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Xianglan Min
- Laboratory of Computational Virology & Viroinformatics, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Hyeon S Son
- Laboratory of Computational Virology & Viroinformatics, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea. .,Institute of Health and Environment, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea. .,Interdisciplinary Graduate Program in Bioinformatics, College of Natural Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
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22
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Guo HX, Zhu SB, Deng Z, Guo FB. EcoliGD: An Online Tool for Designing Escherichia coli Genome. ACS Synth Biol 2022; 11:2267-2274. [PMID: 35770895 DOI: 10.1021/acssynbio.2c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Synthetic biology is an important interdisciplinary field that has emerged in this century, focusing on the rewriting and reprogramming of DNA through the cycles of "design-edit", and so, the cell's own operating system, its genome, is naturally coming into focus. Here, we propose EcoliGD, an online genome design tool with a visual interactive interface and the function of browsing information, as well as the ability to perform insertion, exchange, deletion, and codon replacement operations on the E. coli genome and display the results in real-time. Users can utilize EcoliGD to check various functional characteristic about E. coli genes, to help them build their genomes. Furthermore, we also collected experimentally verified large genomic segments that have been successfully deleted from the genome for users to choose from and simplify the genome. EcoliGD can help recode the entire E. coli genome, providing a novel way to explore the diversity and function of this microorganism. The EcoliGD web tool is available at http://guolab.whu.edu.cn/EcoliGD/.
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Affiliation(s)
- Hai-Xia Guo
- School of Life Science and Technology, University of Electronic Science and Technology of China, 611731, Chengdu, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
| | - Sen-Bin Zhu
- School of Life Science and Technology, University of Electronic Science and Technology of China, 611731, Chengdu, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
| | - Feng-Biao Guo
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, China
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23
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DNA Markers for Detection and Genotyping of Xanthomonas euroxanthea. Microorganisms 2022; 10:microorganisms10061078. [PMID: 35744598 PMCID: PMC9227330 DOI: 10.3390/microorganisms10061078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 12/04/2022] Open
Abstract
Xanthomonas euroxanthea is a bacterial species encompassing both pathogenic and non-pathogenic strains and is frequently found colonizing the same host plants as X. arboricola. This presents the need to develop a detection and genotyping assay able to track these bacteria in microbial consortia with other xanthomonads. Eight X. euroxanthea-specific DNA markers (XEA1-XEA8) were selected by comparative genomics and validated in silico regarding their specificity and consistency using BLASTn, synteny analysis, CG content, codon usage (CAI/eCAI values) and genomic proximity to plasticity determinants. In silico, the selected eight DNA markers were found to be specific and conserved across the genomes of 11 X. euroxanthea strains, and in particular, five DNA markers (XEA4, XEA5, XEA6, XEA7 and XEA8) were unfailingly found in these genomes. A multiplex of PCR targeting markers XEA1 (819 bp), XEA8 (648 bp) and XEA5 (295 bp) was shown to successfully detect X. euroxanthea down to 1 ng of DNA (per PCR reaction). The topology of trees generated with the concatenated sequences of three markers (XEA5, XEA6 and XEA8) and four housekeeping genes (gyrB, rpoD, fyuA and acnB) underlined the equal discriminatory power of these features and thus the suitability of the DNA markers to discriminate X. euroxanthea lineages. Overall, this study displays a DNA-marker-based method for the detection and genotyping of X. euroxanthea strains, contributing to monitoring for its presence in X. arboricola-colonizing habitats. The present study proposes a workflow for the selection of species-specific detection markers. Prospectively, this assay could contribute to unveil alternative host species of Xanthomonas euroxanthea; and improve the control of phytopathogenic strains.
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24
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Dewi KS, Chairunnisa S, Swasthikawati S, Yuliawati, Agustiyanti DF, Mustopa AZ, Kusharyoto W, Ningrum RA. Production of codon-optimized Human papillomavirus type 52 L1 virus-like particles in Pichia pastoris BG10 expression system. Prep Biochem Biotechnol 2022; 53:148-156. [PMID: 35302435 DOI: 10.1080/10826068.2022.2048262] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Cervical cancer caused by Human papillomavirus (HPV) is one of the most common causes of cancer death in women worldwide. Even though the disease can be avoided by immunization, the expensive price of HPV vaccines makes it hard to be accessed by women in middle-low-income countries. Thus, the development of generic HPV vaccines is needed to address inequalities in life-saving access. This study aimed to develop the HPV52 L1 VLP-based recombinant vaccine using Pichia pastoris expression system. The l1 gene was codon-optimized based on P. pastoris codon usage resulting CAI value of 0.804. The gene was inserted into the pD902 plasmid under the regulation of the AOX1 promoter. The linear plasmid was transformed into P. pastoris BG10 genome and screened in YPD medium containing zeocin antibiotic. Colony of transformant that grown on highest zeocin concentration was characterized by genomic PCR and sequencing. The positive clone was selected and expressed using BMGY/BMMY medium induced with various methanol concentrations. The SDS-PAGE and Western blot analyses showed that 55 kDa L1 protein was successfully expressed using an optimum concentration of 1% methanol. The self-assembly of HPV52 L1 protein was also proven using TEM analysis. Moreover, we also analyzed the B-cell epitope of HPV52 L1 protein based on several criteria, including antigenicity, surface accessibility, flexibility, and hydrophilicity. We assumed that epitope 476GLQARPKLKRPASSAPRTSTKKKKV500 could be developed as an epitope-based vaccine with a neutralizing antibody response toward HPV52 infection. Finally, our study provided the alternative for developing low-cost HPV vaccines, either VLP or epitope-based.
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Affiliation(s)
- Kartika Sari Dewi
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Sheila Chairunnisa
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Sri Swasthikawati
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Yuliawati
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Dian Fitria Agustiyanti
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Apon Zainal Mustopa
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Wien Kusharyoto
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
| | - Ratih Asmana Ningrum
- Research Center for Biotechnology, Research Organization of Life Sciences, National Research and Innovation Agency of The Republic of Indonesia (BRIN), Cibinong Sciences Center, Cibinong, Bogor, Indonesia
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25
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Coetzee G, Smith JJ, Görgens JF. Influence of codon optimization, promoter, and strain selection on the heterologous production of a β-fructofuranosidase from Aspergillus fijiensis ATCC 20611 in Pichia pastoris. Folia Microbiol (Praha) 2022; 67:339-350. [PMID: 35133569 DOI: 10.1007/s12223-022-00947-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 01/01/2022] [Indexed: 12/21/2022]
Abstract
Fructooligosaccharides (FOS) are compounds possessing various health properties and are added to functional foods as prebiotics. The commercial production of FOS is done through the enzymatic transfructolysation of sucrose by β-fructofuranosidases which is found in various organisms of which Aureobasidium pullulans and Aspergillus niger are the most well known. This study overexpressed two differently codon-optimized variations of the Aspergillus fijiensis β-fructofuranosidase-encoding gene (fopA) under the transcriptional control of either the alcohol oxidase (AOX1) or glyceraldehyde-3-phosphate dehydrogenase (GAP) promoters. When cultivated in shake flasks, the two codon-optimized variants displayed similar volumetric enzyme activities when expressed under control of the same promoter with the GAP strains producing 11.7 U/ml and 12.7 U/ml, respectively, and the AOX1 strains 95.8 U/ml and 98.6 U/ml, respectively. However, the highest production levels were achieved for both codon-optimized genes when expressed under control of the AOX1 promoter. The AOX1 promoter was superior to the GAP promoter in bioreactor cultivations for both codon-optimized genes with 13,702 U/ml and 2718 U/ml for the AOX1 promoter for ATUM and GeneArt®, respectively, and 6057 U/ml and 1790 U/ml for the GAP promoter for ATUM and GeneArt®, respectively. The ATUM-optimized gene produced higher enzyme activities when compared to the one from GeneArt®, under the control of both promoters.
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Affiliation(s)
- Gerhardt Coetzee
- Department of Process Engineering, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
| | - Jacques J Smith
- Department of Process Engineering, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Johann F Görgens
- Department of Process Engineering, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
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26
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Rahman SU, Abdullah M, Khan AW, Haq MIU, Haq NU, Aziz A, Tao S. A detailed comparative analysis of codon usage bias in Alongshan virus. Virus Res 2022; 308:198646. [PMID: 34822954 DOI: 10.1016/j.virusres.2021.198646] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/05/2021] [Accepted: 11/19/2021] [Indexed: 11/25/2022]
Abstract
Alongshan virus (ALSV) is an emerging tick-borne pathogen that infects humans, causing febrile disease. ALSV uses Ixodes Persulcatus ticks to infect humans with a wide range of signs, from asymptomatic to encephalitis-like syndrome. There is an increasing public health concern about the ALSV infection. To get insight into the impacts of viral relations with their hosts on viral ability, survival, and evasion from hosts immune systems remain unknown. The codon usage is a driving force in viral genome evolution; therefore, we enrolled 41 ALSV strains in codon usage analysis to elucidate the molecular evolutionary dynamics of ALSV. The results indicate that the overall codon usage among ALSV isolates is relatively similar and slightly biased. Base compositions for the cds were in order of G >A >C >U and in the third position of codons G3 >A3 >C3 >T3. The RSCU values revealed that the more frequently used codons were mostly GC ended. Different codon preferences in ALSV genes in relation to codon usage of H. sapiens and Ixodes Persulcatus genes were found. Neutrality plot was determined to reveal the superiority of natural selection over directional mutation pressure in causing CUB based on GC12 versus GC3 contents. The results of these studies suggest that the emergence of ALSV in China, Russia and Finland may also be reflected in ALSV codon usage. Altogether, the presence of both mutation pressure and natural selection effect in shaping the codon usage patterns of ALSV.
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Affiliation(s)
- Siddiq Ur Rahman
- Department of Computer Science & Bioinformatics, Khushal Khan Khattak University, Karak, Khyber Pakhtunkhwa 27200, Pakistan; College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, China.
| | - Muhammad Abdullah
- Department of Computer Science & Bioinformatics, Khushal Khan Khattak University, Karak, Khyber Pakhtunkhwa 27200, Pakistan
| | - Abdul Wajid Khan
- Department of Computer Science & Bioinformatics, Khushal Khan Khattak University, Karak, Khyber Pakhtunkhwa 27200, Pakistan
| | - Muhammad Inam Ul Haq
- Department of Computer Science & Bioinformatics, Khushal Khan Khattak University, Karak, Khyber Pakhtunkhwa 27200, Pakistan
| | - Noor Ul Haq
- Department of Computer Science & Bioinformatics, Khushal Khan Khattak University, Karak, Khyber Pakhtunkhwa 27200, Pakistan
| | - Abdul Aziz
- Department of Computer Science & Bioinformatics, Khushal Khan Khattak University, Karak, Khyber Pakhtunkhwa 27200, Pakistan
| | - Shiheng Tao
- College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, China.
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27
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Coupled protein synthesis and ribosome-guided piRNA processing on mRNAs. Nat Commun 2021; 12:5970. [PMID: 34645830 PMCID: PMC8514520 DOI: 10.1038/s41467-021-26233-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022] Open
Abstract
PIWI-interacting small RNAs (piRNAs) protect the germline genome and are essential for fertility. piRNAs originate from transposable element (TE) RNAs, long non-coding RNAs, or 3´ untranslated regions (3´UTRs) of protein-coding messenger genes, with the last being the least characterized of the three piRNA classes. Here, we demonstrate that the precursors of 3´UTR piRNAs are full-length mRNAs and that post-termination 80S ribosomes guide piRNA production on 3´UTRs in mice and chickens. At the pachytene stage, when other co-translational RNA surveillance pathways are sequestered, piRNA biogenesis degrades mRNAs right after pioneer rounds of translation and fine-tunes protein production from mRNAs. Although 3´UTR piRNA precursor mRNAs code for distinct proteins in mice and chickens, they all harbor embedded TEs and produce piRNAs that cleave TEs. Altogether, we discover a function of the piRNA pathway in fine-tuning protein production and reveal a conserved piRNA biogenesis mechanism that recognizes translating RNAs in amniotes.
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28
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Wysocka A, Jagielska E, Łężniak Ł, Sabała I. Two New M23 Peptidoglycan Hydrolases With Distinct Net Charge. Front Microbiol 2021; 12:719689. [PMID: 34630350 PMCID: PMC8498115 DOI: 10.3389/fmicb.2021.719689] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/16/2021] [Indexed: 11/13/2022] Open
Abstract
Bacterial peptidoglycan hydrolases play an essential role in cell wall metabolism during bacterial growth, division, and elongation (autolysins) or in the elimination of closely related species from the same ecological niche (bacteriocins). Most studies concerning the peptidoglycan hydrolases present in Gram-positive bacteria have focused on clinically relevant Staphylococcus aureus or the model organism Bacillus subtilis, while knowledge relating to other species remains limited. Here, we report two new peptidoglycan hydrolases from the M23 family of metallopeptidases derived from the same staphylococcal species, Staphylococcus pettenkoferi. They share modular architecture, significant sequence identity (60%), catalytic and binding residue conservation, and similar modes of activation, but differ in gene distribution, putative biological role, and, strikingly, in their isoelectric points (pIs). One of the peptides has a high pI, similar to that reported for all M23 peptidases evaluated to date, whereas the other displays a low pI, a unique feature among M23 peptidases. Consequently, we named them SpM23_B (Staphylococcus pettenkoferi M23 "Basic") and SpM23_A (Staphylococcus pettenkoferi M23 "Acidic"). Using genetic and biochemical approaches, we have characterized these two novel lytic enzymes, both in vitro and in their physiological context. Our study presents a detailed characterization of two novel and clearly distinct peptidoglycan hydrolases to understand their role in bacterial physiology.
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Affiliation(s)
- Alicja Wysocka
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Elżbieta Jagielska
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Łukasz Łężniak
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Izabela Sabała
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
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29
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Hoxie I, Dennehy JJ. Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns. Viruses 2021; 13:v13081460. [PMID: 34452326 PMCID: PMC8402926 DOI: 10.3390/v13081460] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/29/2022] Open
Abstract
Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortment-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments’ geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different tree spaces from each other and from the rest of the genome. By contrast, segments 10 and 11 (NSP4 and NSP5/6) occupied nearly indistinguishable tree spaces, suggesting strong co-segregation. Host-species barriers appeared to vary by segment, with segment 9 (VP7) presenting the weakest association with host species. Bayesian Skyride plots were generated for each segment to compare relative genetic diversity among segments over time. All segments showed a dramatic decrease in diversity around 2007 coinciding with the introduction of RVA vaccines. To assess selection pressures, codon adaptation indices and relative codon deoptimization indices were calculated with respect to different host genomes. Codon usage varied by segment with segment 11 (NSP5) exhibiting significantly higher adaptation to host genomes. Furthermore, RVA codon usage patterns appeared optimized for expression in humans and birds relative to the other hosts examined, suggesting that translational efficiency is not a barrier in RVA zoonosis.
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Affiliation(s)
- Irene Hoxie
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
- Correspondence:
| | - John J. Dennehy
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
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30
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Han P, Shichino Y, Schneider-Poetsch T, Mito M, Hashimoto S, Udagawa T, Kohno K, Yoshida M, Mishima Y, Inada T, Iwasaki S. Genome-wide Survey of Ribosome Collision. Cell Rep 2021; 31:107610. [PMID: 32375038 DOI: 10.1016/j.celrep.2020.107610] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 03/18/2020] [Accepted: 04/13/2020] [Indexed: 12/31/2022] Open
Abstract
Ribosome movement is not always smooth and is rather often impeded. For ribosome pauses, fundamental issues remain to be addressed, including where ribosomes pause on mRNAs, what kind of RNA/amino acid sequence causes this pause, and the physiological significance of this attenuation of protein synthesis. Here, we survey the positions of ribosome collisions caused by ribosome pauses in humans and zebrafish using modified ribosome profiling. Collided ribosomes, i.e., disomes, emerge at various sites: Pro-Pro/Gly/Asp motifs; Arg-X-Lys motifs; stop codons; and 3' untranslated regions. The electrostatic interaction between the charged nascent chain and the ribosome exit tunnel determines the eIF5A-mediated disome rescue at the Pro-Pro sites. In particular, XBP1u, a precursor of endoplasmic reticulum (ER)-stress-responsive transcription factor, shows striking queues of collided ribosomes and thus acts as a degradation substrate by ribosome-associated quality control. Our results provide insight into the causes and consequences of ribosome pause by dissecting collided ribosomes.
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Affiliation(s)
- Peixun Han
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan; RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Tilman Schneider-Poetsch
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Satoshi Hashimoto
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Tsuyoshi Udagawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Kenji Kohno
- Institute for Research Initiatives, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yuichiro Mishima
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Shintaro Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan; RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan.
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31
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Pinaud S, Tetreau G, Poteaux P, Galinier R, Chaparro C, Lassalle D, Portet A, Simphor E, Gourbal B, Duval D. New Insights Into Biomphalysin Gene Family Diversification in the Vector Snail Biomphalaria glabrata. Front Immunol 2021; 12:635131. [PMID: 33868258 PMCID: PMC8047071 DOI: 10.3389/fimmu.2021.635131] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 03/08/2021] [Indexed: 11/30/2022] Open
Abstract
Aerolysins initially characterized as virulence factors in bacteria are increasingly found in massive genome and transcriptome sequencing data from metazoans. Horizontal gene transfer has been demonstrated as the main way of aerolysin-related toxins acquisition in metazoans. However, only few studies have focused on their potential biological functions in such organisms. Herein, we present an extensive characterization of a multigene family encoding aerolysins - named biomphalysin - in Biomphalaria glabrata snail, the intermediate host of the trematode Schistosoma mansoni. Our results highlight that duplication and domestication of an acquired bacterial toxin gene in the snail genome result in the acquisition of a novel and diversified toxin family. Twenty-three biomphalysin genes were identified. All are expressed and exhibited a tissue-specific expression pattern. An in silico structural analysis was performed to highlight the central role played by two distinct domains i) a large lobe involved in the lytic function of these snail toxins which constrained their evolution and ii) a small lobe which is structurally variable between biomphalysin toxins and that matched to various functional domains involved in moiety recognition of targets cells. A functional approach suggests that the repertoire of biomphalysins that bind to pathogens, depends on the type of pathogen encountered. These results underline a neo-and sub-functionalization of the biomphalysin toxins, which have the potential to increase the range of effectors in the snail’s immune arsenal.
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Affiliation(s)
- Silvain Pinaud
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Guillaume Tetreau
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Pierre Poteaux
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Richard Galinier
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Cristian Chaparro
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Damien Lassalle
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Anaïs Portet
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Elodie Simphor
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Benjamin Gourbal
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - David Duval
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
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32
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de Oliveira Ribeiro G, da Costa AC, Gill DE, Ribeiro ESD, Rego MODS, Monteiro FJC, Villanova F, Nogueira JS, Maeda AY, de Souza RP, Tahmasebi R, Morais VS, Pandey RP, Raj VS, Scandar SAS, da Silva Vasami FG, D'Agostino LG, Maiorka PC, Deng X, Nogueira ML, Sabino EC, Delwart E, Leal É, Cunha MS. Guapiaçu virus, a new insect-specific flavivirus isolated from two species of Aedes mosquitoes from Brazil. Sci Rep 2021; 11:4674. [PMID: 33633167 PMCID: PMC7907106 DOI: 10.1038/s41598-021-83879-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 02/03/2021] [Indexed: 12/18/2022] Open
Abstract
Classical insect-flaviviruses (cISFVs) and dual host-related insect-specific flavivirus (dISFV) are within the major group of insect-specific flavivirus. Remarkably dISFV are evolutionarily related to some of the pathogenic flavivirus, such as Zika and dengue viruses. The Evolutionary relatedness of dISFV to flavivirus allowed us to investigate the evolutionary principle of host adaptation. Additionally, dISFV can be used for the development of flavivirus vaccines and to explore underlying principles of mammalian pathogenicity. Here we describe the genetic characterization of a novel putative dISFV, termed Guapiaçu virus (GUAPV). Distinct strains of GUAPV were isolated from pools of Aedes terrens and Aedes scapularis mosquitoes. Additionally, we also detected viral GUAPV RNA in a plasma sample of an individual febrile from the Amazon region (North of Brazil). Although GUAPV did not replicate in tested mammalian cells, 3′UTR secondary structures duplication and codon usage index were similar to pathogenic flavivirus.
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Affiliation(s)
| | | | - Danielle Elise Gill
- Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil
| | - Edcelha Soares D'Athaide Ribeiro
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Rua Tancredo Neves, 1.118, Macapá, AP, CEP 68905-230, Brazil
| | - Marlisson Octavio da S Rego
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Rua Tancredo Neves, 1.118, Macapá, AP, CEP 68905-230, Brazil
| | - Fred Julio Costa Monteiro
- Public Health Laboratory of Amapa-LACEN/AP, Health Surveillance Superintendence of Amapa, Rua Tancredo Neves, 1.118, Macapá, AP, CEP 68905-230, Brazil
| | - Fabiola Villanova
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, 66075-000, Brazil
| | - Juliana Silva Nogueira
- Vector-Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, SP, 01246-000, Brazil
| | - Adriana Yurika Maeda
- Vector-Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, SP, 01246-000, Brazil
| | - Renato Pereira de Souza
- Vector-Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, SP, 01246-000, Brazil
| | - Roozbeh Tahmasebi
- Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil
| | - Vanessa S Morais
- Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat, Haryana, India
| | - V Samuel Raj
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat, Haryana, India
| | | | | | | | - Paulo César Maiorka
- Department of Pathology, Faculty of Veterinary Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Xutao Deng
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118-4417, USA.,Department Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | | | - Ester Cerdeira Sabino
- Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil
| | - Eric Delwart
- Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA, 94118-4417, USA. .,Department Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94143, USA.
| | - Élcio Leal
- Institute of Biological Sciences, Federal University of Pará, Belém, Pará, 66075-000, Brazil.
| | - Mariana Sequetin Cunha
- Institute of Tropical Medicine, University of São Paulo, São Paulo, SP, 05403-000, Brazil. .,Vector-Borne Diseases Laboratory, Virology Center, Adolfo Lutz Institute, São Paulo, SP, 01246-000, Brazil.
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Ranaghan MJ, Li JJ, Laprise DM, Garvie CW. Assessing optimal: inequalities in codon optimization algorithms. BMC Biol 2021; 19:36. [PMID: 33607980 PMCID: PMC7893858 DOI: 10.1186/s12915-021-00968-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 01/26/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Custom genes have become a common resource in recombinant biology over the last 20 years due to the plummeting cost of DNA synthesis. These genes are often "optimized" to non-native sequences for overexpression in a non-native host by substituting synonymous codons within the coding DNA sequence (CDS). A handful of studies have compared native and optimized CDSs, reporting different levels of soluble product due to the accumulation of misfolded aggregates, variable activity of enzymes, and (at least one report of) a change in substrate specificity. No study, to the best of our knowledge, has performed a practical comparison of CDSs generated from different codon optimization algorithms or reported the corresponding protein yields. RESULTS In our efforts to understand what factors constitute an optimized CDS, we identified that there is little consensus among codon-optimization algorithms, a roughly equivalent chance that an algorithm-optimized CDS will increase or diminish recombinant yields as compared to the native DNA, a near ubiquitous use of a codon database that was last updated in 2007, and a high variability of output CDSs by some algorithms. We present a case study, using KRas4B, to demonstrate that a median codon frequency may be a better predictor of soluble yields than the more commonly utilized CAI metric. CONCLUSIONS We present a method for visualizing, analyzing, and comparing algorithm-optimized DNA sequences for recombinant protein expression. We encourage researchers to consider if DNA optimization is right for their experiments, and work towards improving the reproducibility of published recombinant work by publishing non-native CDSs.
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Affiliation(s)
- Matthew J Ranaghan
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.
| | - Jeffrey J Li
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Dylan M Laprise
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Colin W Garvie
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
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34
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The nearly complete mitogenome of the Southeast Asian firefly Pteroptyx tener (Coleoptera: Lampyridae). Mol Biol Rep 2021; 48:1281-1290. [PMID: 33582950 DOI: 10.1007/s11033-021-06189-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/28/2021] [Indexed: 10/22/2022]
Abstract
The estuarine firefly, Pteroptyx tener, aggregates in the thousands in mangrove trees lining tidal rivers in Southeast Asia where they engage one another in a nocturnal, pre-mating ritual of synchronised courtship flashes. Unfortunately, populations of the species by virtue of being restricted to isolated estuarine rivers systems in the region, are at risk of genetic isolation. Because of this concern we undertook the task of sequencing and characterising the mitochondrial DNA genome of P. tener, as the first step towards helping us to characterise and better understand their genetic diversity. We sequenced and assembled the mitochondrial DNA genome of P. tener from two male and female specimens from the district of Kuala Selangor in Peninsular Malaysia and announce the molecules in this publication. We also reconstructed the phylogenetic trees of all available lampyrids mitogenomes and suggest the need to re-examine our current understanding of their classification which have largely been based on morphological data and the cox1 gene. Separately, our analysis of codon usage patterns among lampyrid mitogenomes showed that the codon usage in a majority of the protein-coding genes were non-neutral. Codon usage patterns between mitogenome sequences of P. tener were, however, largely neutral. Our findings demonstrate the usefulness of mitochondrial genes/mitogenomes for analysing both inter- and intra- specific variation in the Lampyridae to aid in species discovery in this highly variable genus; and elucidate the phylogenetic relationships of Pteroptyx spp. from the region.
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35
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Expression of transgenes enriched in rare codons is enhanced by the MAPK pathway. Sci Rep 2020; 10:22166. [PMID: 33335127 PMCID: PMC7746698 DOI: 10.1038/s41598-020-78453-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/23/2020] [Indexed: 11/10/2022] Open
Abstract
The ability to translate three nucleotide sequences, or codons, into amino acids to form proteins is conserved across all organisms. All but two amino acids have multiple codons, and the frequency that such synonymous codons occur in genomes ranges from rare to common. Transcripts enriched in rare codons are typically associated with poor translation, but in certain settings can be robustly expressed, suggestive of codon-dependent regulation. Given this, we screened a gain-of-function library for human genes that increase the expression of a GFPrare reporter encoded by rare codons. This screen identified multiple components of the mitogen activated protein kinase (MAPK) pathway enhancing GFPrare expression. This effect was reversed with inhibitors of this pathway and confirmed to be both codon-dependent and occur with ectopic transcripts naturally coded with rare codons. Finally, this effect was associated, at least in part, with enhanced translation. We thus identify a potential regulatory module that takes advantage of the redundancy in the genetic code to modulate protein expression.
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36
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Biological Characteristics and Patterns of Codon Usage Evolution for the African Genotype Zika Virus. Viruses 2020; 12:v12111306. [PMID: 33202554 PMCID: PMC7696518 DOI: 10.3390/v12111306] [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: 09/08/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 11/17/2022] Open
Abstract
We investigated temporal trends of codon usage changes for different host species to determine their importance in Zika virus (ZIKV) evolution. Viral spillover resulting from the potential of codon adaptation to host genome was also assessed for the African genotype ZIKV in comparison to the Asian genotype. To improve our understanding on its zoonotic maintenance, we evaluated in vitro the biological properties of the African genotype ZIKV in vertebrate and mosquito cell lines. Analyses were performed in comparison to Yellow fever virus (YFV). Despite significantly lower codon adaptation index trends than YFV, ZIKV showed evident codon adaptation to vertebrate hosts, particularly for the green African monkey Chlorocebus aethiops. PCA and CAI analyses at the individual ZIKV gene level for both human and Aedes aegypti indicated a clear distinction between the two genotypes. African ZIKV isolates showed higher virulence in mosquito cells than in vertebrate cells. Their higher replication in mosquito cells than African YFV confirmed the role of mosquitoes in the natural maintenance of the African genotype ZIKV. An analysis of individual strain growth characteristics indicated that the widely used reference strain MR766 replicates poorly in comparison to African ZIKV isolates. The recombinant African Zika virus strain ArD128000*E/NS5 may be a good model to include in studies on the mechanism of host tropism, as it cannot replicate in the tested vertebrate cell line.
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37
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Dewi KS, Fuad AM. Improving the Expression of Human Granulocyte Colony Stimulating Factor in Escherichia coli by Reducing the GC-content and Increasing mRNA Folding Free Energy at 5'-Terminal End. Adv Pharm Bull 2020; 10:610-616. [PMID: 33072539 PMCID: PMC7539321 DOI: 10.34172/apb.2020.073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 12/24/2019] [Accepted: 01/27/2020] [Indexed: 01/16/2023] Open
Abstract
Purpose: Strategy for improving the production of biopharmaceutical protein continues to develop due to increasing market demand. Human granulocyte colony stimulating factor (hG-CSF) is one of biopharmaceutical proteins that has many applications, and easily produced in Escherichia coli expression system. Previous studies reported that codon usage, rare codon, mRNA folding and GC-content at 5’-terminal end were crucial for protein production in E. coli. In the present study, the effect of reducing the GC-content and increasing the mRNA folding free energy at the 5’-terminal end on the expression level of hG-CSF proteins was investigated. Methods: Synonymous codon substitutions were performed to generate mutant variants of open reading frame (ORF) with lower GC-content at 5’-terminal ends. Oligoanalyzer tool was used to calculate the GC content of eight codons sequence after ATG. Whereas, mRNA folding free energy was predicted using KineFold and RNAfold tools. The template DNA was amplified using three variant forward primers and one same reverse primer. Those DNA fragments were individually cloned into pJexpress414 expression vector and were confirmed using restriction and DNA sequencing analyses. The confirmed constructs were transformed into E. coli NiCo21(DE3) host cells and the recombinant protein was expressed using IPTG-induction. Total protein obtained were characterized using SDS-PAGE, Western blot and ImageJ software analyses. Results: The result showed that the mutant variant with lower GC-content and higher mRNA folding free energy near the translation initiation region (TIR) could produce a higher amount of hG-CSF proteins compared to the original gene sequence. Conclusion: This study emphasized the important role of the nucleotide composition immediately downstream the start codon to achieve high-yield protein product on heterologous expression in E. coli.
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Affiliation(s)
- Kartika Sari Dewi
- Research Center for Biotechnology, Indonesian Institute of Sciences, Cibinong, Bogor, Indonesia, 16911
| | - Asrul Muhamad Fuad
- Research Center for Biotechnology, Indonesian Institute of Sciences, Cibinong, Bogor, Indonesia, 16911
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38
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Silverj A, Rota-Stabelli O. On the correct interpretation of similarity index in codon usage studies: Comparison with four other metrics and implications for Zika and West Nile virus. Virus Res 2020; 286:198097. [DOI: 10.1016/j.virusres.2020.198097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/15/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022]
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39
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Gómez MM, de Mello Volotão E, Assandri IR, Peyrou M, Cristina J. Analysis of codon usage bias in potato virus Y non-recombinant strains. Virus Res 2020; 286:198077. [PMID: 32619560 DOI: 10.1016/j.virusres.2020.198077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 11/30/2022]
Abstract
Potato virus Y (PVY) is a member of the genus Potyvirus, family Potyviridae, is considered one of the most devastating pest affecting economically important crops, such as potato, tobacco, tomato and pepper, representing a serious threat due to high incidence and worldwide distribution. Its economic significance as well as it biological and molecular complexities have aroused great attention, thus several studies have explore it genetic characteristics. However, little is known about PVY codon usage. To shed light on the relation of codon usage among viruses and their hosts is extremely important to understand virus survival, fitness and evolution. In this study, we performed a comprehensive analysis of codon usage and composition of PVY non-recombinant strains (PVYN-NA, PVYEu-N, PVYO, PVYO5, PVYC) based on 130 complete open reading frame sequences extracted from public databases. Furthermore, similarities between the synonymous codon usage of PVY and its main hosts were investigated. The results obtained in the current study suggest that the overall codon usage among PVY genotypes is similar and slightly biased. PVY codon usage is strongly influenced by mutational bias, but also by G + C compositional constraint and dinucleotide composition. Furthermore, similarities among codon usage preferences between PVY strains and analyzed hosts were observed.
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Affiliation(s)
- Mariela Martínez Gómez
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, 11600, Montevideo, Uruguay.
| | - Eduardo de Mello Volotão
- Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, 11600, Montevideo, Uruguay
| | - Isabel Rodríguez Assandri
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, 11600, Montevideo, Uruguay
| | - Mercedes Peyrou
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, 11600, Montevideo, Uruguay
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Igua 4225, 11400, Montevideo, Uruguay
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40
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Tort FL, Castells M, Cristina J. A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses. Virus Res 2020; 283:197976. [PMID: 32294518 PMCID: PMC7152894 DOI: 10.1016/j.virusres.2020.197976] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/08/2020] [Accepted: 04/08/2020] [Indexed: 02/07/2023]
Abstract
An outbreak of atypical pneumonia caused by a novel Betacoronavirus (βCoV), named SARS-CoV-2 has been declared a public health emergency of international concern by the World Health Organization. In order to gain insight into the emergence, evolution and adaptation of SARS-CoV-2 viruses, a comprehensive analysis of genome composition and codon usage of βCoV circulating in China was performed. A biased nucleotide composition was found for SARS-CoV-2 genome. This bias in genomic composition is reflected in its codon and amino acid usage patterns. The overall codon usage in SARS-CoV-2 is similar among themselves and slightly biased. Most of the highly frequent codons are A- and U-ending, which strongly suggests that mutational bias is the main force shaping codon usage in this virus. Significant differences in relative synonymous codon usage frequencies among SARS-CoV-2 and human cells were found. These differences are due to codon usage preferences.
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Affiliation(s)
- Fernando L Tort
- Laboratorio de Virología Molecular, Sede Salto, Centro Universitario Regional, Litoral Norte, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay
| | - Matías Castells
- Laboratorio de Virología Molecular, Sede Salto, Centro Universitario Regional, Litoral Norte, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, 11400, Uruguay.
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41
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Diament A, Weiner I, Shahar N, Landman S, Feldman Y, Atar S, Avitan M, Schweitzer S, Yacoby I, Tuller T. ChimeraUGEM: unsupervised gene expression modeling in any given organism. Bioinformatics 2020; 35:3365-3371. [PMID: 30715207 DOI: 10.1093/bioinformatics/btz080] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/07/2019] [Accepted: 01/30/2019] [Indexed: 01/06/2023] Open
Abstract
MOTIVATION Regulation of the amount of protein that is synthesized from genes has proved to be a serious challenge in terms of analysis and prediction, and in terms of engineering and optimization, due to the large diversity in expression machinery across species. RESULTS To address this challenge, we developed a methodology and a software tool (ChimeraUGEM) for predicting gene expression as well as adapting the coding sequence of a target gene to any host organism. We demonstrate these methods by predicting protein levels in seven organisms, in seven human tissues, and by increasing in vivo the expression of a synthetic gene up to 26-fold in the single-cell green alga Chlamydomonas reinhardtii. The underlying model is designed to capture sequence patterns and regulatory signals with minimal prior knowledge on the host organism and can be applied to a multitude of species and applications. AVAILABILITY AND IMPLEMENTATION Source code (MATLAB, C) and binaries are freely available for download for non-commercial use at http://www.cs.tau.ac.il/~tamirtul/ChimeraUGEM/, and supported on macOS, Linux and Windows. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Alon Diament
- Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv, Israel
| | - Iddo Weiner
- Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv, Israel.,School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv, Israel
| | - Noam Shahar
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv, Israel
| | - Shira Landman
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv, Israel
| | - Yael Feldman
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv, Israel
| | - Shimshi Atar
- Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv, Israel
| | - Meital Avitan
- Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv, Israel.,School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv, Israel
| | - Shira Schweitzer
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv, Israel
| | - Iftach Yacoby
- School of Plant Sciences and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv, Israel.,The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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42
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Mycobacterium lepromatosis genome exhibits unusually high CpG dinucleotide content and selection is key force in shaping codon usage. INFECTION GENETICS AND EVOLUTION 2020; 84:104399. [PMID: 32512206 DOI: 10.1016/j.meegid.2020.104399] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 05/30/2020] [Accepted: 06/03/2020] [Indexed: 01/06/2023]
Abstract
Mycobacterium lepromatosis was identified as a causative agent for leprosy in the year 2008 in the United States and later more cases were identified in Canada, Singapore, Brazil, and Myanmar. It is known to cause diffuse lepromatosis leprosy among humans. Since it is invasive, the mortality rates are higher in comparison to the M. leprae. At genomic level, there exists 90.9% similarity between M. lepromatosis and M. leprae. Codon usage analysis based on analyses of 228 coding sequences (CDSs) of M. lepromatosis, revealed that the genome is GC rich. Among the total 16 dinucleotides, CpG dinucleotide possesses the highest dinucleotide frequency in M. lepromatosis, that is strikingly an unobvious observation since higher CpG is associated with higher proinflammatory cytokine production and NF-κB activation that eventually leads to high pathogenicity. To evade immune response, CpG content is generally less in pathogens. The unusually high CpG content can be explained by the fact that the nucleotide composition of M. lepromatosis is CG rich. Various forces interplay to shape codon usage pattern of any organism including selection; mutation, nucleotide composition as well as GC biased gene conversion. To understand the interplay between various forces; neutrality, parity, Nc-GC3 (Effective number of codons-GC content at 3rd position of the codon), aromaticity (AROMO) and the general average hydropathicity score (GRAVY) analyses have been carried out. The analyses revealed that selection force is the major contributory force. Along with the selection; mutation, nucleotide composition as well as GC biased gene conversion also play role in shaping codon usage bias in M. lepromatosis. This is the first report on the codon usage in M. lepromatosis.
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43
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Fan X, Qiu H, Han W, Wang Y, Xu D, Zhang X, Bhattacharya D, Ye N. Phytoplankton pangenome reveals extensive prokaryotic horizontal gene transfer of diverse functions. SCIENCE ADVANCES 2020; 6:eaba0111. [PMID: 32494685 PMCID: PMC7190310 DOI: 10.1126/sciadv.aba0111] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/03/2020] [Indexed: 05/17/2023]
Abstract
The extent and role of horizontal gene transfer (HGT) in phytoplankton and, more broadly, eukaryotic evolution remain controversial topics. Recent studies substantiate the importance of HGT in modifying or expanding functions such as metal or reactive species detoxification and buttressing halotolerance. Yet, the potential of HGT to significantly alter the fate of species in a major eukaryotic assemblage remains to be established. We provide such an example for the ecologically important lineages encompassed by cryptophytes, rhizarians, alveolates, stramenopiles, and haptophytes ("CRASH" taxa). We describe robust evidence of prokaryotic HGTs in these taxa affecting functions such as polysaccharide biosynthesis. Numbers of HGTs range from 0.16 to 1.44% of CRASH species gene inventories, comparable to the ca. 1% prokaryote-derived HGTs found in the genomes of extremophilic red algae. Our results substantially expand the impact of HGT in eukaryotes and define a set of general principles for prokaryotic gene fixation in phytoplankton genomes.
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Affiliation(s)
- Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Huan Qiu
- Independent scholar, 121 Goucher Terrace, Gaithersburg, MD 20877, USA
| | - Wentao Han
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yitao Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, 59 Dudley Road, Foran Hall 102, New Brunswick, NJ 08901, USA
| | - Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Andolfo G, Di Donato A, Chiaiese P, De Natale A, Pollio A, Jones JDG, Frusciante L, Ercolano MR. Alien Domains Shaped the Modular Structure of Plant NLR Proteins. Genome Biol Evol 2020; 11:3466-3477. [PMID: 31730154 PMCID: PMC7145615 DOI: 10.1093/gbe/evz248] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2019] [Indexed: 12/20/2022] Open
Abstract
Plant innate immunity mostly relies on nucleotide-binding (NB) and leucine-rich repeat (LRR) intracellular receptors to detect pathogen-derived molecules and to induce defense responses. A multitaxa reconstruction of NB-domain associations allowed us to identify the first NB–LRR arrangement in the Chlorophyta division of the Viridiplantae. Our analysis points out that the basic NOD-like receptor (NLR) unit emerged in Chlorophytes by horizontal transfer and its diversification started from Toll/interleukin receptor–NB–LRR members. The operon-based genomic structure of Chromochloris zofingiensis NLR copies suggests a functional origin of NLR clusters. Moreover, the transmembrane signatures of NLR proteins in the unicellular alga C. zofingiensis support the hypothesis that the NLR-based immunity system of plants derives from a cell-surface surveillance system. Taken together, our findings suggest that NLRs originated in unicellular algae and may have a common origin with cell-surface LRR receptors.
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Affiliation(s)
- Giuseppe Andolfo
- Department of Agricultural Sciences, University of Naples "Federico II", Portici (Naples), Italy
| | - Antimo Di Donato
- Department of Agricultural Sciences, University of Naples "Federico II", Portici (Naples), Italy
| | - Pasquale Chiaiese
- Department of Agricultural Sciences, University of Naples "Federico II", Portici (Naples), Italy
| | | | - Antonino Pollio
- Department of Biology, University of Naples "Federico II", Italy
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH Norwich, United Kingdom
| | - Luigi Frusciante
- Department of Agricultural Sciences, University of Naples "Federico II", Portici (Naples), Italy
| | - Maria Raffaella Ercolano
- Department of Agricultural Sciences, University of Naples "Federico II", Portici (Naples), Italy
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45
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Ruggiero RP, Boissinot S. Variation in base composition underlies functional and evolutionary divergence in non-LTR retrotransposons. Mob DNA 2020; 11:14. [PMID: 32280379 PMCID: PMC7140322 DOI: 10.1186/s13100-020-00209-9] [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: 09/26/2019] [Accepted: 03/24/2020] [Indexed: 12/03/2022] Open
Abstract
Background Non-LTR retrotransposons often exhibit base composition that is markedly different from the nucleotide content of their host’s gene. For instance, the mammalian L1 element is AT-rich with a strong A bias on the positive strand, which results in a reduced transcription. It is plausible that the A-richness of mammalian L1 is a self-regulatory mechanism reflecting a trade-off between transposition efficiency and the deleterious effect of L1 on its host. We examined if the A-richness of L1 is a general feature of non-LTR retrotransposons or if different clades of elements have evolved different nucleotide content. We also investigated if elements belonging to the same clade evolved towards different base composition in different genomes or if elements from different clades evolved towards similar base composition in the same genome. Results We found that non-LTR retrotransposons differ in base composition among clades within the same host but also that elements belonging to the same clade differ in base composition among hosts. We showed that nucleotide content remains constant within the same host over extended period of evolutionary time, despite mutational patterns that should drive nucleotide content away from the observed base composition. Conclusions Our results suggest that base composition is evolving under selection and may be reflective of the long-term co-evolution between non-LTR retrotransposons and their host. Finally, the coexistence of elements with drastically different base composition suggests that these elements may be using different strategies to persist and multiply in the genome of their host.
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Affiliation(s)
- Robert P Ruggiero
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates PO 129188
| | - Stéphane Boissinot
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates PO 129188
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46
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Trus I, Udenze D, Berube N, Wheler C, Martel MJ, Gerdts V, Karniychuk U. CpG-Recoding in Zika Virus Genome Causes Host-Age-Dependent Attenuation of Infection With Protection Against Lethal Heterologous Challenge in Mice. Front Immunol 2020; 10:3077. [PMID: 32038625 PMCID: PMC6993062 DOI: 10.3389/fimmu.2019.03077] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022] Open
Abstract
Experimental increase of CpG dinucleotides in an RNA virus genome impairs infection providing a promising approach for vaccine development. While CpG recoding is an emerging and promising vaccine approach, little is known about infection phenotypes caused by recoded viruses in vivo. For example, infection phenotypes, immunogenicity, and protective efficacy induced by CpG-recoded viruses in different age groups were not studied yet. This is important, because attenuation of infection phenotypes caused by recoded viruses may depend on the population-based expression of cellular components targeting viral CpG dinucleotides. In the present study, we generated several Zika virus (ZIKV) variants with the increasing CpG content and compared infection in neonatal and adult mice. Increasing the CpG content caused host-age-dependent attenuation of infection with considerable attenuation in neonates and high attenuation in adults. Expression of the zinc-finger antiviral protein (ZAP)—the host protein targeting viral CpG dinucleotides—was also age-dependent. Similar to the wild-type virus, ZIKV variants with the increased CpG content evoked robust cellular and humoral immune responses and protection against lethal challenge. Collectively, the host age should be accounted for in future studies on mechanisms targeting viral CpG dinucleotides, development of safe dinucleotide recoding strategies, and applications of CpG-recoded vaccines.
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Affiliation(s)
- Ivan Trus
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
| | - Daniel Udenze
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada.,School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada
| | - Nathalie Berube
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
| | - Colette Wheler
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
| | - Marie-Jocelyne Martel
- Department of Obstetrics and Gynecology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Volker Gerdts
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada.,Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Uladzimir Karniychuk
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada.,School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
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Ismail SNFB, Baharum SN, Fazry S, Low CF. Comparative genome analysis reveals a distinct influence of nucleotide composition on virus-host species-specific interaction of prawn-infecting nodavirus. JOURNAL OF FISH DISEASES 2019; 42:1761-1772. [PMID: 31637743 DOI: 10.1111/jfd.13093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/21/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
Abstract
Discovery of species-specific interaction between the host and virus has drawn the interest of many researchers to study the evolution of the newly emerged virus. Comparative genome analysis provides insights of the virus functional genome evolution and the underlying mechanisms of virus-host interactions. The analysis of nucleotide composition signified the evolution of nodavirus towards host specialization in a host-specific mutation manner. GC-rich genome of betanodavirus was significantly deficient in UpA and UpU dinucleotides composition, whilst the AU-rich genome of gammanodavirus was deficient in CpG dinucleotide. The capsid of MrNV and PvNV of gammanodavirus retains the highest abundance of adenine and uracil at the second codon position, respectively, which were found to be very distinctive from the other genera. ENC-GC3 plot inferred the influence of natural selection and mutational pressure in shaping the evolution of MrNV RdRp and capsid, respectively. Furthermore, CAI/eCAI analysis predicts a comparable adaptability of MrNV in squid, Sepia officinalis than its natural host, Macrobrachium rosenbergii. Thus, further study is warranted to investigate the capacity of MrNV replication in S. officinalis owing to its high codon adaptation index.
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Affiliation(s)
| | | | - Shazrul Fazry
- Tasik Chini Research Center, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Selangor, Bangi, Malaysia
| | - Chen Fei Low
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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48
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Wan ZY, Lin G, Yue G. Genes for sexual body size dimorphism in hybrid tilapia (Oreochromis sp. x Oreochromis mossambicus). AQUACULTURE AND FISHERIES 2019. [DOI: 10.1016/j.aaf.2019.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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49
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Comprehensive analysis of genetic and evolutionary features of the hepatitis E virus. BMC Genomics 2019; 20:790. [PMID: 31664890 PMCID: PMC6820953 DOI: 10.1186/s12864-019-6100-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 09/12/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The hepatitis E virus (HEV) is the causative pathogen of hepatitis E, a global public health concern. HEV comprises 8 genotypes with a wide host range and geographic distribution. This study aims to determine the genetic factors influencing the molecular adaptive changes of HEV open reading frames (ORFs) and estimate the HEV origin and evolutionary history. RESULTS Sequences of HEV strains isolated between 1982 and 2017 were retrieved and multiple analyses were performed to determine overall codon usage patterns, effects of natural selection and/or mutation pressure and host influence on the evolution of HEV ORFs. Besides, Bayesian Coalescent Markov Chain Monte Carlo (MCMC) Analysis was performed to estimate the spatial-temporal evolution of HEV. The results indicated an A/C nucleotide bias and ORF-dependent codon usage bias affected mainly by natural selection. The adaptation of HEV ORFs to their hosts was also ORF-dependent, with ORF1 and ORF2 sharing an almost similar adaptation profile to the different hosts. The discriminant analysis based on the adaptation index suggested that ORF1 and ORF3 could play a pivotal role in viral host tropism. CONCLUSION In this study, we estimate that the common ancestor of the modern HEV strains emerged ~ 6000 years ago, in the period following the domestication of pigs. Then, natural selection played the major role in the evolution of the codon usage of HEV ORFs. The significant adaptation of ORF1 of genotype 1 to humans, makes ORF1 an evolutionary indicator of HEV host speciation, and could explain the epidemic character of genotype 1 strains in humans.
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Urquiza-García U, Millar AJ. Expanding the bioluminescent reporter toolkit for plant science with NanoLUC. PLANT METHODS 2019; 15:68. [PMID: 31316580 PMCID: PMC6613265 DOI: 10.1186/s13007-019-0454-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/28/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND Protein data over circadian time scale is scarce for clock transcription factors. Further work in this direction is required for refining quantitative clock models. However, gathering highly resolved dynamics of low-abundance transcription factors has been a major challenge in the field. In this work we provide a new tool that could help this major issue. Bioluminescence is an important tool for gathering data on circadian gene expression. It allows data collection over extended time periods for low signal levels, thanks to a large signal-to-noise ratio. However, the main reporter so far used, firefly luciferase (FLUC), presents some disadvantages for reporting total protein levels. For example, the rapid, post-translational inactivation of this luciferase will result in underestimation of protein numbers. A more stable reporter protein could in principle tackle this issue. We noticed that NanoLUC might fill this gap, given its reported brightness and the stability of both enzyme and substrate. However, no data in plant systems on the circadian time scale had been reported. RESULTS We tested NanoLUC activity under different scenarios that will be important for generating highly quantitative data. These include enzyme purification for calibration curves, expression in transient plant systems, stable transgenic plants and in planta time series over circadian time scales. Furthermore, we show that the difference in substrate use between firefly luciferase and NanoLUC allows tracking of two different reporters from the same samples. We show this by exploring the impact of a BOAp:BOA-NanoLUC construct transformed into a Col-0 CCA1p:FLUC background. CONCLUSIONS We concluded that NanoLUC reporters are compatible with established instrumentation and protocols for firefly luciferase. Overall, our results provide guidelines for researchers gathering dynamic protein data over different time scales and experimental setups.
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Affiliation(s)
- Uriel Urquiza-García
- SynthSys and School of Biological Sciences, University of Edinburgh, C. H. Waddington Building, King’s Buildings, Max Born Crescent, Edinburgh, EH9 3BF Scotland, UK
- Institute for Molecular Plant Sciences, University of Edinburgh, D. Rutherford Building, King’s Buildings, Edinburgh, EH9 3BF UK
| | - Andrew J. Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, C. H. Waddington Building, King’s Buildings, Max Born Crescent, Edinburgh, EH9 3BF Scotland, UK
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