101
|
Schwersensky M, Rooman M, Pucci F. Large-scale in silico mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness. BMC Biol 2020; 18:146. [PMID: 33081759 PMCID: PMC7576759 DOI: 10.1186/s12915-020-00870-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 09/16/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND How, and the extent to which, evolution acts on DNA and protein sequences to ensure mutational robustness and evolvability is a long-standing open question in the field of molecular evolution. We addressed this issue through the first structurome-scale computational investigation, in which we estimated the change in folding free energy upon all possible single-site mutations introduced in more than 20,000 protein structures, as well as through available experimental stability and fitness data. RESULTS At the amino acid level, we found the protein surface to be more robust against random mutations than the core, this difference being stronger for small proteins. The destabilizing and neutral mutations are more numerous in the core and on the surface, respectively, whereas the stabilizing mutations are about 4% in both regions. At the genetic code level, we observed smallest destabilization for mutations that are due to substitutions of base III in the codon, followed by base I, bases I+III, base II, and other multiple base substitutions. This ranking highly anticorrelates with the codon-anticodon mispairing frequency in the translation process. This suggests that the standard genetic code is optimized to limit the impact of random mutations, but even more so to limit translation errors. At the codon level, both the codon usage and the usage bias appear to optimize mutational robustness and translation accuracy, especially for surface residues. CONCLUSION Our results highlight the non-universality of mutational robustness and its multiscale dependence on protein features, the structure of the genetic code, and the codon usage. Our analyses and approach are strongly supported by available experimental mutagenesis data.
Collapse
Affiliation(s)
- Martin Schwersensky
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, CP 165/61, Roosevelt Ave. 50, Brussels, 1050, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, CP 165/61, Roosevelt Ave. 50, Brussels, 1050, Belgium.
- Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe, Brussels, 1050, Belgium.
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, CP 165/61, Roosevelt Ave. 50, Brussels, 1050, Belgium.
- Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe, Brussels, 1050, Belgium.
| |
Collapse
|
102
|
Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design. Sci Rep 2020; 10:15643. [PMID: 32973171 PMCID: PMC7519053 DOI: 10.1038/s41598-020-72533-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/19/2020] [Indexed: 12/28/2022] Open
Abstract
As the SARS-CoV-2 pandemic is rapidly progressing, the need for the development of an effective vaccine is critical. A promising approach for vaccine development is to generate, through codon pair deoptimization, an attenuated virus. This approach carries the advantage that it only requires limited knowledge specific to the virus in question, other than its genome sequence. Therefore, it is well suited for emerging viruses, for which we may not have extensive data. We performed comprehensive in silico analyses of several features of SARS-CoV-2 genomic sequence (e.g., codon usage, codon pair usage, dinucleotide/junction dinucleotide usage, RNA structure around the frameshift region) in comparison with other members of the coronaviridae family of viruses, the overall human genome, and the transcriptome of specific human tissues such as lung, which are primarily targeted by the virus. Our analysis identified the spike (S) and nucleocapsid (N) proteins as promising targets for deoptimization and suggests a roadmap for SARS-CoV-2 vaccine development, which can be generalizable to other viruses.
Collapse
|
103
|
Davidi D, Shamshoum M, Guo Z, Bar‐On YM, Prywes N, Oz A, Jablonska J, Flamholz A, Wernick DG, Antonovsky N, de Pins B, Shachar L, Hochhauser D, Peleg Y, Albeck S, Sharon I, Mueller‐Cajar O, Milo R. Highly active rubiscos discovered by systematic interrogation of natural sequence diversity. EMBO J 2020; 39:e104081. [PMID: 32500941 PMCID: PMC7507306 DOI: 10.15252/embj.2019104081] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 04/30/2020] [Accepted: 05/07/2020] [Indexed: 11/09/2022] Open
Abstract
CO2 is converted into biomass almost solely by the enzyme rubisco. The poor carboxylation properties of plant rubiscos have led to efforts that made it the most kinetically characterized enzyme, yet these studies focused on < 5% of its natural diversity. Here, we searched for fast-carboxylating variants by systematically mining genomic and metagenomic data. Approximately 33,000 unique rubisco sequences were identified and clustered into ≈ 1,000 similarity groups. We then synthesized, purified, and biochemically tested the carboxylation rates of 143 representatives, spanning all clusters of form-II and form-II/III rubiscos. Most variants (> 100) were active in vitro, with the fastest having a turnover number of 22 ± 1 s-1 -sixfold faster than the median plant rubisco and nearly twofold faster than the fastest measured rubisco to date. Unlike rubiscos from plants and cyanobacteria, the fastest variants discovered here are homodimers and exhibit a much simpler folding and activation kinetics. Our pipeline can be utilized to explore the kinetic space of other enzymes of interest, allowing us to get a better view of the biosynthetic potential of the biosphere.
Collapse
Affiliation(s)
- Dan Davidi
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
- Present address:
Department of GeneticsHarvard Medical SchoolBostonMAUSA
| | - Melina Shamshoum
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Zhijun Guo
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Yinon M Bar‐On
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Noam Prywes
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Aia Oz
- Migal Galilee Research InstituteKiryat ShmonaIsrael
- Tel Hai CollegeUpper GalileeIsrael
| | - Jagoda Jablonska
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Avi Flamholz
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - David G Wernick
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
- Present address:
BASF Enzymes LLCSan DiegoCAUSA
| | - Niv Antonovsky
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
- Present address:
Laboratory of Genetically Encoded Small MoleculesThe Rockefeller UniversityNew YorkNYUSA
| | - Benoit de Pins
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Lior Shachar
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Dina Hochhauser
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Yoav Peleg
- Department of Life Sciences Core FacilitiesWeizmann Institute of ScienceRehovotIsrael
| | - Shira Albeck
- Department of Life Sciences Core FacilitiesWeizmann Institute of ScienceRehovotIsrael
| | - Itai Sharon
- Migal Galilee Research InstituteKiryat ShmonaIsrael
- Tel Hai CollegeUpper GalileeIsrael
| | | | - Ron Milo
- Department of Plant and Environmental SciencesWeizmann Institute of ScienceRehovotIsrael
| |
Collapse
|
104
|
Wu H, Bao Z, Mou C, Chen Z, Zhao J. Comprehensive Analysis of Codon Usage on Porcine Astrovirus. Viruses 2020; 12:v12090991. [PMID: 32899965 PMCID: PMC7552017 DOI: 10.3390/v12090991] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 08/26/2020] [Accepted: 09/03/2020] [Indexed: 02/04/2023] Open
Abstract
Porcine astrovirus (PAstV), associated with mild diarrhea and neurological disease, is transmitted in pig farms worldwide. The purpose of this study is to elucidate the main factors affecting codon usage to PAstVs. Phylogenetic analysis showed that the subtype PAstV-5 sat at the bottom of phylogenetic tree, followed by PAstV-3, PAstV-1, PAstV-2, and PAstV-4, indicating that the five existing subtypes (PAstV1-PAstV5) may be formed by multiple differentiations of PAstV ancestors. A codon usage bias was found in the PAstVs-2,3,4,5 from the analyses of effective number of codons (ENC) and relative synonymous codon usage (RSCU). Nucleotides A/U are more frequently used than nucleotides C/G in the genome CDSs of the PAstVs-3,4,5. Codon usage patterns of PAstV-5 are dominated by mutation pressure and natural selection, while natural selection is the main evolutionary force that affects the codon usage pattern of PAstVs-2,3,4. The analyses of codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) showed the codon usage similarities between the PAstV and animals might contribute to the broad host range and the cross-species transmission of astrovirus. Our results provide insight into understanding the PAstV evolution and codon usage patterns.
Collapse
Affiliation(s)
- Huiguang Wu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (H.W.); (Z.B.); (C.M.)
- Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Zhengyu Bao
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (H.W.); (Z.B.); (C.M.)
| | - Chunxiao Mou
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (H.W.); (Z.B.); (C.M.)
- Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Zhenhai Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (H.W.); (Z.B.); (C.M.)
- Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (Z.C.); (J.Z.)
| | - Jingwen Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Correspondence: (Z.C.); (J.Z.)
| |
Collapse
|
105
|
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]
|
106
|
Villafana RT, Rampersad SN. Signatures of TRI5, TRI8 and TRI11 Protein Sequences of Fusarium incarnatum-equiseti Species Complex (FIESC) Indicate Differential Trichothecene Analogue Production. Toxins (Basel) 2020; 12:E386. [PMID: 32545314 PMCID: PMC7354511 DOI: 10.3390/toxins12060386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 11/24/2022] Open
Abstract
The variability and phylogeny among TRI5, TRI8 and TRI11 nucleotide and translated protein sequences of isolates from Trinidad belonging to Fusarium incarnatum-equiseti species complex (FIESC) were compared with FIESC reference sequences. Taxa appeared to be more divergent when DNA sequences were analyzed compared to protein sequences. Neutral and non-neutral mutations in TRI protein sequences that may correspond to variability in the function and structure of the selected TRI proteins were identified. TRI5p had the lowest amino acid diversity with zero predicted non-neutral mutations. TRI5p had potentially three protein disorder regions compared to TRI8p with five protein disorder regions. The deduced TRI11p was more conserved than TRI8p of the same strains. Amino acid substitutions that may be non-neutral to protein function were only detected in diacetoxyscirpenol (DAS) and fusarenon-X (FUS-X) producers of the reference sequence subset for TRI8p and TRI11p. The deduced TRI5 and TRI8 amino acid sequences were mapped to known 3D-structure models and indicated that variations in specific protein order/disorder regions exist in these sequences which affect the overall structural conservation of TRI proteins. Assigning single or combination non-neutral mutations to a particular toxicogenic phenotype may be more representative of potential compared to using genotypic data alone, especially in the absence of wet-lab, experimental validation.
Collapse
Affiliation(s)
| | - Sephra N. Rampersad
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago, West Indies;
| |
Collapse
|
107
|
Tian HF, Hu QM, Xiao HB, Zeng LB, Meng Y, Li Z. Genetic and codon usage bias analyses of major capsid protein gene in Ranavirus. INFECTION GENETICS AND EVOLUTION 2020; 84:104379. [PMID: 32497680 DOI: 10.1016/j.meegid.2020.104379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/07/2020] [Accepted: 05/22/2020] [Indexed: 12/29/2022]
Abstract
The Ranavirus (one genus of Iridovidae family) is an emerging pathogen that infects fish, amphibian, and reptiles, and causes great economical loss and ecological threat to farmed and wild animals globally. The major capsid protein (MCP) has been used as genetic typing marker and as target to design vaccines. Herein, the codon usage pattern of 73 MCP genes of Ranavirus and Lymphocystivirus are studied by calculating effective number of codons (ENC), relative synonymous codon usage (RSCU), codon adaptation index (CAI), and relative codon deoptimization index (RCDI), and similarity index (SiD). The Ranavirus are confirmed to be classified into five groups by using phylogenetic analysis, and varied nucleotide compositions and hierarchical cluster analysis based on RSCU. The results revealed different codon usage patterns among Lymphocystivirus and five groups of Ranavirus. Ranavirus had six over-represented codons ended with G/C nucleotide, while Lymphocystivirus had six over-represented codons ended with A/T nucleotide. A comparative analysis of parameters that define virus and host relatedness in terms of codon usage were analyzed indicated that Amphibian-like ranaviruses (ALRVs) seem to possess lower ENC values and higher CAIs in contrast to other ranaviruses isolated from fishes, and two groups (FV3-like and CMTV-like group) of them had received higher selection pressure from their hosts as having higher relative codon deoptimization index (RCDI) and similarity index (SiD). The correspondence analysis (COA) and Spearman's rank correlation analyses revealed that nucleotide compositions, relative dinucleotide frequency, mutation pressure, and natural translational selection shape the codon usage pattern in MCP genes and the ENC-GC3S and neutrality plots indicated that the natural selection is the predominant factor. These results contribute to understanding the evolution of Ranavirus and their adaptions to their hosts.
Collapse
Affiliation(s)
- Hai-Feng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Qiao-Mu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Han-Bing Xiao
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Ling-Bing Zeng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China
| | - Yan Meng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
| | - Zhong Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
| |
Collapse
|
108
|
Wu Y, Liu Q, Weiss B, Kaltenpoth M, Kadowaki T. Honey Bee Suppresses the Parasitic Mite Vitellogenin by Antimicrobial Peptide. Front Microbiol 2020; 11:1037. [PMID: 32523577 PMCID: PMC7261897 DOI: 10.3389/fmicb.2020.01037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/27/2020] [Indexed: 01/04/2023] Open
Abstract
The negative effects of honey bee parasitic mites and deformed wing virus (DWV) on honey bee and colony health have been well characterized. However, the relationship between DWV and mites, particularly viral replication inside the mites, remains unclear. Furthermore, the physiological outcomes of honey bee immune responses stimulated by DWV and the mite to the host (honey bee) and perhaps the pathogen/parasite (DWV/mite) are not yet understood. To answer these questions, we studied the tripartite interactions between the honey bee, Tropilaelaps mercedesae, and DWV as the model. T. mercedesae functioned as a vector for DWV without supporting active viral replication. Thus, DWV negligibly affected mite fitness. Mite infestation induced mRNA expression of antimicrobial peptides (AMPs), Defensin-1 and Hymenoptaecin, which correlated with DWV copy number in honey bee pupae and mite feeding, respectively. Feeding T. mercedesae with fruit fly S2 cells heterologously expressing honey bee Hymenoptaecin significantly downregulated mite Vitellogenin expression, indicating that the honey bee AMP manipulates mite reproduction upon feeding on bee. Our results provide insights into the mechanism of DWV transmission by the honey bee parasitic mite to the host, and the novel role of AMP in defending against mite infestation.
Collapse
Affiliation(s)
- Yunfei Wu
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Qiushi Liu
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Benjamin Weiss
- Department for Evolutionary Ecology, Institute for Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Martin Kaltenpoth
- Department for Evolutionary Ecology, Institute for Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Tatsuhiko Kadowaki
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| |
Collapse
|
109
|
Jitobaom K, Phakaratsakul S, Sirihongthong T, Chotewutmontri S, Suriyaphol P, Suptawiwat O, Auewarakul P. Codon usage similarity between viral and some host genes suggests a codon-specific translational regulation. Heliyon 2020; 6:e03915. [PMID: 32395662 PMCID: PMC7205639 DOI: 10.1016/j.heliyon.2020.e03915] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/02/2020] [Accepted: 04/30/2020] [Indexed: 02/03/2023] Open
Abstract
The codon usage pattern is a specific characteristic of each species; however, the codon usage of all of the genes in a genome is not uniform. Intriguingly, most viruses have codon usage patterns that are vastly different from the optimal codon usage of their hosts. How viral genes with different codon usage patterns are efficiently expressed during a viral infection is unclear. An analysis of the similarity between viral codon usage and the codon usage of the individual genes of a host genome has never been performed. In this study, we demonstrated that the codon usage of human RNA viruses is similar to that of some human genes, especially those involved in the cell cycle. This finding was substantiated by its concordance with previous reports of an upregulation at the protein level of some of these biological processes. It therefore suggests that some suboptimal viral codon usage patterns may actually be compatible with cellular translational machineries in infected conditions.
Collapse
Affiliation(s)
- Kunlakanya Jitobaom
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
| | - Supinya Phakaratsakul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
| | | | - Sasithorn Chotewutmontri
- Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Prapat Suriyaphol
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Center of Excellence in Bioinformatics and Clinical Data Management, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Ornpreya Suptawiwat
- Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Prasert Auewarakul
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
| |
Collapse
|
110
|
Wright G, Rodriguez A, Li J, Clark PL, Milenković T, Emrich SJ. Analysis of computational codon usage models and their association with translationally slow codons. PLoS One 2020; 15:e0232003. [PMID: 32352987 PMCID: PMC7192439 DOI: 10.1371/journal.pone.0232003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/05/2020] [Indexed: 11/19/2022] Open
Abstract
Improved computational modeling of protein translation rates, including better prediction of where translational slowdowns along an mRNA sequence may occur, is critical for understanding co-translational folding. Because codons within a synonymous codon group are translated at different rates, many computational translation models rely on analyzing synonymous codons. Some models rely on genome-wide codon usage bias (CUB), believing that globally rare and common codons are the most informative of slow and fast translation, respectively. Others use the CUB observed only in highly expressed genes, which should be under selective pressure to be translated efficiently (and whose CUB may therefore be more indicative of translation rates). No prior work has analyzed these models for their ability to predict translational slowdowns. Here, we evaluate five models for their association with slowly translated positions as denoted by two independent ribosome footprint (RFP) count experiments from S. cerevisiae, because RFP data is often considered as a “ground truth” for translation rates across mRNA sequences. We show that all five considered models strongly associate with the RFP data and therefore have potential for estimating translational slowdowns. However, we also show that there is a weak correlation between RFP counts for the same genes originating from independent experiments, even when their experimental conditions are similar. This raises concerns about the efficacy of using current RFP experimental data for estimating translation rates and highlights a potential advantage of using computational models to understand translation rates instead.
Collapse
Affiliation(s)
- Gabriel Wright
- Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, IN, United States of America
- * E-mail:
| | - Anabel Rodriguez
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN, United States of America
| | - Jun Li
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN, United States of America
| | - Patricia L. Clark
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN, United States of America
| | - Tijana Milenković
- Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, IN, United States of America
| | - Scott J. Emrich
- Department of Electrical Engineering & Computer Science, University of Tennessee, Knoxville, TN, United States of America
| |
Collapse
|
111
|
Computational Resources for Molecular Biology: Special Issue 2020. J Mol Biol 2020; 432:3361-3363. [PMID: 32298696 DOI: 10.1016/j.jmb.2020.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
112
|
Comparative Genomics of Two New HF1-like Haloviruses. Genes (Basel) 2020; 11:genes11040405. [PMID: 32276506 PMCID: PMC7230728 DOI: 10.3390/genes11040405] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 12/14/2022] Open
Abstract
Few genomes of the HF1-group of viruses are currently available, and further examples would enhance the understanding of their evolution, improve their gene annotation, and assist in understanding gene function and regulation. Two novel HF1-group haloviruses, Serpecor1 and Hardycor2, were recovered from widely separated hypersaline lakes in Australia. Both are myoviruses with linear dsDNA genomes and infect the haloarchaeon Halorubrum coriense. Both genomes possess long, terminal direct repeat (TDR) sequences (320 bp for Serpecor1 and 306 bp for Hardycor2). The Serpecor1 genome is 74,196 bp in length, 57.0% G+C, and has 126 annotated coding sequences (CDS). Hardycor2 has a genome of 77,342 bp, 55.6% G+C, and 125 annotated CDS. They show high nucleotide sequence similarity to each other (78%) and with HF1 (>75%), and carry similar intergenic repeat (IR) sequences to those originally described in HF1 and HF2. Hardycor2 carries a DNA methyltransferase gene in the same genomic neighborhood as the methyltransferase genes of HF1, HF2 and HRTV-5, but is in the opposite orientation, and the inferred proteins are only distantly related. Comparative genomics allowed us to identify the candidate genes mediating cell attachment. The genomes of Serpecor1 and Hardycor2 encode numerous small proteins carrying one or more CxxC motifs, a signature feature of zinc-finger domain proteins that are known to participate in diverse biomolecular interactions.
Collapse
|
113
|
Markina NM, Kotlobay AA, Tsarkova AS. Heterologous Metabolic Pathways: Strategies for Optimal Expression in Eukaryotic Hosts. Acta Naturae 2020; 12:28-39. [PMID: 32742725 PMCID: PMC7385092 DOI: 10.32607/actanaturae.10966] [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: 04/15/2020] [Accepted: 04/29/2020] [Indexed: 11/20/2022] Open
Abstract
Heterologous pathways are linked series of biochemical reactions occurring in a host organism after the introduction of foreign genes. Incorporation of metabolic pathways into host organisms is a major strategy used to increase the production of valuable secondary metabolites. Unfortunately, simple introduction of the pathway genes into the heterologous host in most cases does not result in successful heterologous expression. Extensive modification of heterologous genes and the corresponding enzymes on many different levels is required to achieve high target metabolite production rates. This review summarizes the essential techniques used to create heterologous biochemical pathways, with a focus on the key challenges arising in the process and the major strategies for overcoming them.
Collapse
Affiliation(s)
- N. M. Markina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Planta LLC, Moscow, 121205 Russia
| | - A. A. Kotlobay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - A. S. Tsarkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
| |
Collapse
|
114
|
Kames J, Holcomb DD, Kimchi O, DiCuccio M, Hamasaki-Katagiri N, Wang T, Komar AA, Alexaki A, Kimchi-Sarfaty C. Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.03.30.016832. [PMID: 32511300 PMCID: PMC7217226 DOI: 10.1101/2020.03.30.016832] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
As the SARS-CoV-2 pandemic is rapidly progressing, the need for the development of an effective vaccine is critical. A promising approach for vaccine development is to generate, through codon pair deoptimization, an attenuated virus. This approach carries the advantage that it only requires limited knowledge specific to the virus in question, other than its genome sequence. Therefore, it is well suited for emerging viruses for which we may not have extensive data. We performed comprehensive in silico analyses of several features of SARS-CoV-2 genomic sequence (e.g., codon usage, codon pair usage, dinucleotide/junction dinucleotide usage, RNA structure around the frameshift region) in comparison with other members of the coronaviridae family of viruses, the overall human genome, and the transcriptome of specific human tissues such as lung, which are primarily targeted by the virus. Our analysis identified the spike (S) and nucleocapsid (N) proteins as promising targets for deoptimization and suggests a roadmap for SARS-CoV-2 vaccine development, which can be generalizable to other viruses.
Collapse
Affiliation(s)
- Jacob Kames
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA
| | - David D. Holcomb
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA
| | - Ofer Kimchi
- Harvard University School of Engineering and Applied Sciences
| | - Michael DiCuccio
- National Center of Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Nobuko Hamasaki-Katagiri
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA
| | - Tony Wang
- Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Viral Products, Food and Drug Administration, Silver Spring, MD, USA
| | - Anton A. Komar
- Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA
| | - Aikaterini Alexaki
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA
| | - Chava Kimchi-Sarfaty
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, MD, USA
| |
Collapse
|
115
|
Abstract
The posttranscriptional modification of messenger RNA (mRNA) and transfer RNA (tRNA) provides an additional layer of regulatory complexity during gene expression. Here, we show that a tRNA methyltransferase, TRMT10A, interacts with an mRNA demethylase FTO (ALKBH9), both in vitro and inside cells. TRMT10A installs N 1-methylguanosine (m1G) in tRNA, and FTO performs demethylation on N 6-methyladenosine (m6A) and N 6,2'-O-dimethyladenosine (m6Am) in mRNA. We show that TRMT10A ablation not only leads to decreased m1G in tRNA but also significantly increases m6A levels in mRNA. Cross-linking and immunoprecipitation, followed by high-throughput sequencing results show that TRMT10A shares a significant overlap of associated mRNAs with FTO, and these mRNAs have accelerated decay rates potentially through the regulation by a specific m6A reader, YTHDF2. Furthermore, transcripts with increased m6A upon TRMT10A ablation contain an overrepresentation of m1G9-containing tRNAs codons read by tRNAGln(TTG), tRNAArg(CCG), and tRNAThr(CGT) These findings collectively reveal the presence of coordinated mRNA and tRNA methylations and demonstrate a mechanism for regulating gene expression through the interactions between mRNA and tRNA modifying enzymes.
Collapse
|
116
|
Hernandez‐Alias X, Benisty H, Schaefer MH, Serrano L. Translational efficiency across healthy and tumor tissues is proliferation-related. Mol Syst Biol 2020; 16:e9275. [PMID: 32149479 PMCID: PMC7061310 DOI: 10.15252/msb.20199275] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/11/2020] [Accepted: 02/11/2020] [Indexed: 12/20/2022] Open
Abstract
Different tissues express genes with particular codon usage and anticodon tRNA repertoires. However, the codon-anticodon co-adaptation in humans is not completely understood, nor is its effect on tissue-specific protein levels. Here, we first validated the accuracy of small RNA-seq for tRNA quantification across five human cell lines. We then analyzed the tRNA abundance of more than 8,000 tumor samples from TCGA, together with their paired mRNA-seq and proteomics data, to determine the Supply-to-Demand Adaptation. We thereby elucidate that the dynamic adaptation of the tRNA pool is largely related to the proliferative state across tissues. The distribution of such tRNA pools over the whole cellular translatome affects the subsequent translational efficiency, which functionally determines a condition-specific expression program both in healthy and tumor states. Furthermore, the aberrant translational efficiency of some codons in cancer, exemplified by ProCCA and GlyGGT, is associated with poor patient survival. The regulation of these tRNA profiles is partly explained by the tRNA gene copy numbers and their promoter DNA methylation.
Collapse
Affiliation(s)
- Xavier Hernandez‐Alias
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Hannah Benisty
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Martin H Schaefer
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Department of Experimental OncologyIEO, European Institute of Oncology IRCCSMilanItaly
| | - Luis Serrano
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- ICREABarcelonaSpain
| |
Collapse
|
117
|
Dinan AM, Lukhovitskaya NI, Olendraite I, Firth AE. A case for a negative-strand coding sequence in a group of positive-sense RNA viruses. Virus Evol 2020; 6:veaa007. [PMID: 32064120 PMCID: PMC7010960 DOI: 10.1093/ve/veaa007] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Positive-sense single-stranded RNA viruses form the largest and most diverse group of eukaryote-infecting viruses. Their genomes comprise one or more segments of coding-sense RNA that function directly as messenger RNAs upon release into the cytoplasm of infected cells. Positive-sense RNA viruses are generally accepted to encode proteins solely on the positive strand. However, we previously identified a surprisingly long (∼1,000-codon) open reading frame (ORF) on the negative strand of some members of the family Narnaviridae which, together with RNA bacteriophages of the family Leviviridae, form a sister group to all other positive-sense RNA viruses. Here, we completed the genomes of three mosquito-associated narnaviruses, all of which have the long reverse-frame ORF. We systematically identified narnaviral sequences in public data sets from a wide range of sources, including arthropod, fungal, and plant transcriptomic data sets. Long reverse-frame ORFs are widespread in one clade of narnaviruses, where they frequently occupy >95 per cent of the genome. The reverse-frame ORFs correspond to a specific avoidance of CUA, UUA, and UCA codons (i.e. stop codon reverse complements) in the forward-frame RNA-dependent RNA polymerase ORF. However, absence of these codons cannot be explained by other factors such as inability to decode these codons or GC3 bias. Together with other analyses, we provide the strongest evidence yet of coding capacity on the negative strand of a positive-sense RNA virus. As these ORFs comprise some of the longest known overlapping genes, their study may be of broad relevance to understanding overlapping gene evolution and de novo origin of genes.
Collapse
Affiliation(s)
- Adam M Dinan
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Nina I Lukhovitskaya
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Ingrida Olendraite
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| |
Collapse
|
118
|
Bindels DS, Postma M, Haarbosch L, van Weeren L, Gadella TWJ. Multiparameter screening method for developing optimized red-fluorescent proteins. Nat Protoc 2020; 15:450-478. [PMID: 31942080 DOI: 10.1038/s41596-019-0250-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/19/2019] [Indexed: 11/09/2022]
Abstract
Genetically encoded fluorescent proteins (FPs) are highly utilized in cell biology research to study proteins of interest or signal processes using biosensors. To perform well in specific applications, these FPs require a multitude of tailored properties. It is for this reason that they need to be optimized by using mutagenesis. The optimization process through screening is often based solely on bacterial colony brightness, but multiple parameters ultimately determine the performance of an optimal FP. Instead of characterizing other properties after selection, we developed a multiparameter screening method based on four critical parametersscreened simultaneously: fluorescence lifetime, cellular brightness, maturation efficiency, and photostability. First, a high-throughput primary screen (based on fluorescence lifetime and cellular brightness using a mutated FP library) is performed in bacterial colonies. A secondary multiparameter screen based on all four parameters, using a novel bacterial-mammalian dual-expression vector enables expression of the best FP variants in mammalian cell lines. A newly developed automated multiparameter acquisition and cell-based analysis approach for 96-well plates further increased workflow efficiency. We used this protocol to yield the record-bright mScarlet, a fast-maturating mScarlet-I, and a photostable mScarlet-H. This protocol can also be applied to other FP classes or Förster resonance energy transfer (FRET)-based biosensors with minor adaptations. With an available mutant library of a template FP and a complete and tested laboratory setup, a single round of multiparameter screening (including the primary bacterial screen, secondary mammalian cell screen, sequencing, and data processing) can be performed within 2 weeks.
Collapse
Affiliation(s)
- Daphne S Bindels
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Marten Postma
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Lindsay Haarbosch
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Theodorus W J Gadella
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
| |
Collapse
|
119
|
Kames J, Alexaki A, Holcomb DD, Santana-Quintero LV, Athey JC, Hamasaki-Katagiri N, Katneni U, Golikov A, Ibla JC, Bar H, Kimchi-Sarfaty C. TissueCoCoPUTs: Novel Human Tissue-Specific Codon and Codon-Pair Usage Tables Based on Differential Tissue Gene Expression. J Mol Biol 2020; 432:3369-3378. [PMID: 31982380 DOI: 10.1016/j.jmb.2020.01.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/19/2019] [Accepted: 01/08/2020] [Indexed: 02/05/2023]
Abstract
Protein expression in multicellular organisms varies widely across tissues. Codon usage in the transcriptome of each tissue is derived from genomic codon usage and the relative expression level of each gene. We created a comprehensive computational resource that houses tissue-specific codon, codon-pair, and dinucleotide usage data for 51 Homo sapiens tissues (TissueCoCoPUTs: https://hive.biochemistry.gwu.edu/review/tissue_codon), using transcriptome data from the Broad Institute Genotype-Tissue Expression (GTEx) portal. Distances between tissue-specific codon and codon-pair frequencies were used to generate a dendrogram based on the unique patterns of codon and codon-pair usage in each tissue that are clearly distinct from the genomic distribution. This novel resource may be useful in unraveling the relationship between codon usage and tRNA abundance, which could be critical in determining translation kinetics and efficiency across tissues. Areas of investigation such as biotherapeutic development, tissue-specific genetic engineering, and genetic disease prediction will greatly benefit from this resource.
Collapse
Affiliation(s)
- Jacob Kames
- Division of Plasma Protein Therapeutics, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Aikaterini Alexaki
- Division of Plasma Protein Therapeutics, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - David D Holcomb
- Division of Plasma Protein Therapeutics, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Luis V Santana-Quintero
- High Performance Integrated Environment, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - John C Athey
- Division of Plasma Protein Therapeutics, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Nobuko Hamasaki-Katagiri
- Division of Plasma Protein Therapeutics, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Upendra Katneni
- Division of Plasma Protein Therapeutics, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Anton Golikov
- High Performance Integrated Environment, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Juan C Ibla
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Haim Bar
- Department of Statistics, University of Connecticut, Storrs, CT, 06268, USA
| | - Chava Kimchi-Sarfaty
- Division of Plasma Protein Therapeutics, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, 20993, USA.
| |
Collapse
|
120
|
Sharma P, Sonawane P, Herpai D, D’Agostino R, Rossmeisl J, Tatter S, Debinski W. Multireceptor targeting of glioblastoma. Neurooncol Adv 2020; 2:vdaa107. [PMID: 33150335 PMCID: PMC7596893 DOI: 10.1093/noajnl/vdaa107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Treatment for glioblastoma (GBM) remains an unmet need in medicine. Novel therapies that address GBM complexity and heterogeneity in particular are warranted. To this end, we target 4 tumor-associated receptors at a time that span virtually all of the GBM microenvironment including bulk tumor cells, infiltrating tumor cells, neovasculature, and tumor-infiltrating cells with one pharmaceutical agent delivering a cytotoxic load. METHODS We engineered multivalent ligand-based vector proteins termed QUAD with an ability to bind to 4 of the following GBM-associated receptors: IL-13RA2, EphA2, EphA3, and EphB2. We conjugated QUAD with a modified bacterial toxin PE38QQR and tested it in vitro and in vivo. RESULTS The QUAD variants preserved functional characteristics of the respective ligands for the 4 receptors. The QUAD 3.0 variant conjugate was highly cytotoxic to GBM cells, but it was nontoxic in mice, and the conjugate exhibited strong antitumor effect in a dog with spontaneous GBM. CONCLUSION The QUAD addresses, to a large extent, the issues of intra- and intertumoral heterogeneity and, at the same time, it targets several pathophysiologically important tumor compartments in GBM through multiple receptors overexpressed in tumors allowing for what we call "molecular resection." QUAD-based targeted agents warrant further pre- and clinical development.
Collapse
Affiliation(s)
- Puja Sharma
- Brain Tumor Center of Excellence, Wake Forest Baptist Medical Center Comprehensive Cancer Center, Winston-Salem, North Carolina, USA
| | - Poonam Sonawane
- Brain Tumor Center of Excellence, Wake Forest Baptist Medical Center Comprehensive Cancer Center, Winston-Salem, North Carolina, USA
- Children’s Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Denise Herpai
- Brain Tumor Center of Excellence, Wake Forest Baptist Medical Center Comprehensive Cancer Center, Winston-Salem, North Carolina, USA
| | - Ralph D’Agostino
- Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - John Rossmeisl
- Neurology and Neurosurgery, Department of Small Animal Clinical Sciences, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia, USA
| | - Stephen Tatter
- Brain Tumor Center of Excellence, Wake Forest Baptist Medical Center Comprehensive Cancer Center, Winston-Salem, North Carolina, USA
- Department of Neurosurgery, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina, USA
| | - Waldemar Debinski
- Brain Tumor Center of Excellence, Wake Forest Baptist Medical Center Comprehensive Cancer Center, Winston-Salem, North Carolina, USA
| |
Collapse
|
121
|
Latham AP, Zhang B. Maximum Entropy Optimized Force Field for Intrinsically Disordered Proteins. J Chem Theory Comput 2019; 16:773-781. [PMID: 31756104 DOI: 10.1021/acs.jctc.9b00932] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Intrinsically disordered proteins (IDPs) constitute a significant fraction of eukaryotic proteomes. High-resolution characterization of IDP conformational ensembles can help elucidate their roles in a wide range of biological processes but remains challenging both experimentally and computationally. Here, we present a generic algorithm to improve the accuracy of coarse-grained IDP models using a diverse set of experimental measurements. It combines maximum entropy optimization and least-squares regression to systematically adjust model parameters and improve the agreement between simulation and experiment. We successfully applied the algorithm to derive a transferable force field, which we term the maximum entropy optimized force field (MOFF), for de novo prediction of IDP structures. Statistical analysis of force field parameters reveals features of amino acid interactions not captured by potentials designed to work well for folded proteins. We anticipate its combination of efficiency and accuracy will make MOFF useful for studying the phase separation of IDPs, which drives the formation of various biological compartments.
Collapse
Affiliation(s)
- Andrew P Latham
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Bin Zhang
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| |
Collapse
|
122
|
Galano-Frutos JJ, García-Cebollada H, Sancho J. Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when. Brief Bioinform 2019; 22:3-19. [PMID: 31813950 DOI: 10.1093/bib/bbz146] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/22/2019] [Accepted: 10/25/2019] [Indexed: 12/18/2022] Open
Abstract
The increasing ease with which massive genetic information can be obtained from patients or healthy individuals has stimulated the development of interpretive bioinformatics tools as aids in clinical practice. Most such tools analyze evolutionary information and simple physical-chemical properties to predict whether replacement of one amino acid residue with another will be tolerated or cause disease. Those approaches achieve up to 80-85% accuracy as binary classifiers (neutral/pathogenic). As such accuracy is insufficient for medical decision to be based on, and it does not appear to be increasing, more precise methods, such as full-atom molecular dynamics (MD) simulations in explicit solvent, are also discussed. Then, to describe the goal of interpreting human genetic variations at large scale through MD simulations, we restrictively refer to all possible protein variants carrying single-amino-acid substitutions arising from single-nucleotide variations as the human variome. We calculate its size and develop a simple model that allows calculating the simulation time needed to have a 0.99 probability of observing unfolding events of any unstable variant. The knowledge of that time enables performing a binary classification of the variants (stable-potentially neutral/unstable-pathogenic). Our model indicates that the human variome cannot be simulated with present computing capabilities. However, if they continue to increase as per Moore's law, it could be simulated (at 65°C) spending only 3 years in the task if we started in 2031. The simulation of individual protein variomes is achievable in short times starting at present. International coordination seems appropriate to embark upon massive MD simulations of protein variants.
Collapse
Affiliation(s)
- Juan J Galano-Frutos
- Protein Folding and Molecular Design (ProtMol)' group at BIFI, University of Zaragoza
| | | | - Javier Sancho
- Protein Folding and Molecular Design (ProtMol)' group at BIFI, University of Zaragoza
| |
Collapse
|
123
|
Leith EM, O'Dell WB, Ke N, McClung C, Berkmen M, Bergonzo C, Brinson RG, Kelman Z. Characterization of the internal translation initiation region in monoclonal antibodies expressed in Escherichia coli. J Biol Chem 2019; 294:18046-18056. [PMID: 31604819 DOI: 10.1074/jbc.ra119.011008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/07/2019] [Indexed: 01/16/2023] Open
Abstract
Monoclonal antibodies (mAbs) represent an important platform for the development of biotherapeutic products. Most mAbs are produced in mammalian cells, but several mAbs are made in Escherichia coli, including therapeutic fragments. The NISTmAb is a well-characterized reference material made widely available to facilitate the development of both originator biologics and biosimilars. Here, when expressing NISTmAb from codon-optimized constructs in E. coli (eNISTmAb), a truncated variant of its heavy chain was observed. N-terminal protein sequencing and mutagenesis analyses indicated that the truncation resulted from an internal translation initiation from a GTG codon (encoding Val) within eNISTmAb. Using computational and biochemical approaches, we demonstrate that this translation initiates from a weak Shine-Dalgarno sequence and is facilitated by a putative ribosomal protein S1-binding site. We also observed similar internal initiation in the mAb adalimumab (the amino acid sequence of the drug Humira) when expressed in E. coli Of note, these internal initiation regions were likely an unintended result of the codon optimization for E. coli expression, and the amino acid pattern from which it is derived was identified as a Pro-Ser-X-X-X-Val motif. We discuss the implications of our findings for E. coli protein expression and codon optimization and outline possible strategies for reducing the likelihood of internal translation initiation and truncated product formation.
Collapse
Affiliation(s)
- Erik M Leith
- Biomolecular Labeling Laboratory, National Institute of Standards and Technology and Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850
| | - William B O'Dell
- Biomolecular Labeling Laboratory, National Institute of Standards and Technology and Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850; National Institute of Standards and Technology, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850
| | - Na Ke
- New England Biolabs, Ipswich, Massachusetts 01938
| | | | | | - Christina Bergonzo
- National Institute of Standards and Technology, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850
| | - Robert G Brinson
- National Institute of Standards and Technology, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850
| | - Zvi Kelman
- Biomolecular Labeling Laboratory, National Institute of Standards and Technology and Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850; National Institute of Standards and Technology, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850.
| |
Collapse
|
124
|
Hunt R, Hettiarachchi G, Katneni U, Hernandez N, Holcomb D, Kames J, Alnifaidy R, Lin B, Hamasaki-Katagiri N, Wesley A, Kafri T, Morris C, Bouché L, Panico M, Schiller T, Ibla J, Bar H, Ismail A, Morris H, Komar A, Kimchi-Sarfaty C. A Single Synonymous Variant (c.354G>A [p.P118P]) in ADAMTS13 Confers Enhanced Specific Activity. Int J Mol Sci 2019; 20:ijms20225734. [PMID: 31731663 PMCID: PMC6888508 DOI: 10.3390/ijms20225734] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/09/2019] [Accepted: 11/13/2019] [Indexed: 12/18/2022] Open
Abstract
Synonymous variants within coding regions may influence protein expression and function. We have previously reported increased protein expression levels ex vivo (~120% in comparison to wild-type) from a synonymous polymorphism variant, c.354G>A [p.P118P], of the ADAMTS13 gene, encoding a plasma protease responsible for von Willebrand Factor (VWF) degradation. In the current study, we investigated the potential mechanism(s) behind the increased protein expression levels from this variant and its effect on ADAMTS13 physico-chemical properties. Cell-free assays showed enhanced translation of the c.354G>A variant and the analysis of codon usage characteristics suggested that introduction of the frequently used codon/codon pair(s) may have been potentially responsible for this effect. Limited proteolysis, however, showed no substantial influence of altered translation on protein conformation. Analysis of post-translational modifications also showed no notable differences but identified three previously unreported glycosylation markers. Despite these similarities, p.P118P variant unexpectedly showed higher specific activity. Structural analysis using modeled interactions indicated that subtle conformational changes arising from altered translation kinetics could affect interactions between an exosite of ADAMTS13 and VWF resulting in altered specific activity. This report highlights how a single synonymous nucleotide variation can impact cellular expression and specific activity in the absence of measurable impact on protein structure.
Collapse
Affiliation(s)
- Ryan Hunt
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - Gaya Hettiarachchi
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - Upendra Katneni
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - Nancy Hernandez
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - David Holcomb
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - Jacob Kames
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - Redab Alnifaidy
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - Brian Lin
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - Nobuko Hamasaki-Katagiri
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - Aaron Wesley
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Present Address: Department of Emergency Medicine, Banner University Medical Center, The University of Arizona, Tucson, AZ 85724, USA
| | - Tal Kafri
- Gene Therapy Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Laura Bouché
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
- Present Address: Antikor Biopharma Ltd., Stevenage Bioscience Catalyst, Gunnels Wood Road, Stevenage SG1 2FX, UK
| | - Maria Panico
- BioPharmaSpec Ltd., St. Saviour JE2 7LA, UK or or
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Tal Schiller
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
| | - Juan Ibla
- Departments of Cardiac Surgery and Anesthesiology, Perioperative and Pain Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Haim Bar
- Department of Statistics, University of Connecticut, Storrs, CT 06269, USA
| | - Amra Ismail
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological & Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | - Howard Morris
- BioPharmaSpec Ltd., St. Saviour JE2 7LA, UK or or
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Anton Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological & Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | - Chava Kimchi-Sarfaty
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & Research, US FDA, Silver Spring, MD 20993, USA
- Correspondence: ; Tel.: +1-(240)-402-8203
| |
Collapse
|
125
|
Alexaki A, Hettiarachchi GK, Athey JC, Katneni UK, Simhadri V, Hamasaki-Katagiri N, Nanavaty P, Lin B, Takeda K, Freedberg D, Monroe D, McGill JR, Peters R, Kames JM, Holcomb DD, Hunt RC, Sauna ZE, Gelinas A, Janjic N, DiCuccio M, Bar H, Komar AA, Kimchi-Sarfaty C. Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies. Sci Rep 2019; 9:15449. [PMID: 31664102 PMCID: PMC6820528 DOI: 10.1038/s41598-019-51984-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/09/2019] [Indexed: 11/16/2022] Open
Abstract
Synonymous codons occur with different frequencies in different organisms, a phenomenon termed codon usage bias. Codon optimization, a common term for a variety of approaches used widely by the biopharmaceutical industry, involves synonymous substitutions to increase protein expression. It had long been presumed that synonymous variants, which, by definition, do not alter the primary amino acid sequence, have no effect on protein structure and function. However, a critical mass of reports suggests that synonymous codon variations may impact protein conformation. To investigate the impact of synonymous codons usage on protein expression and function, we designed an optimized coagulation factor IX (FIX) variant and used multiple methods to compare its properties to the wild-type FIX upon expression in HEK293T cells. We found that the two variants differ in their conformation, even when controlling for the difference in expression levels. Using ribosome profiling, we identified robust changes in the translational kinetics of the two variants and were able to identify a region in the gene that may have a role in altering the conformation of the protein. Our data have direct implications for codon optimization strategies, for production of recombinant proteins and gene therapies.
Collapse
Affiliation(s)
- Aikaterini Alexaki
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Gaya K Hettiarachchi
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - John C Athey
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Upendra K Katneni
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Vijaya Simhadri
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Nobuko Hamasaki-Katagiri
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Puja Nanavaty
- Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA
| | - Brian Lin
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Kazuyo Takeda
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Darón Freedberg
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Dougald Monroe
- University of North Carolina at Chapel hill, Chapel hill, NC, USA
| | - Joseph R McGill
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | | | - Jacob M Kames
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - David D Holcomb
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Ryan C Hunt
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Zuben E Sauna
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | | | | | - Michael DiCuccio
- National Center of Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Haim Bar
- Department of Statistics, University of Connecticut, Storrs, CT, USA
| | - Anton A Komar
- Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA
| | - Chava Kimchi-Sarfaty
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
| |
Collapse
|
126
|
Dershem R, Metpally RPR, Jeffreys K, Krishnamurthy S, Smelser DT, Hershfinkel M, Carey DJ, Robishaw JD, Breitwieser GE. Rare-variant pathogenicity triage and inclusion of synonymous variants improves analysis of disease associations of orphan G protein-coupled receptors. J Biol Chem 2019; 294:18109-18121. [PMID: 31628190 DOI: 10.1074/jbc.ra119.009253] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 10/08/2019] [Indexed: 02/02/2023] Open
Abstract
The pace of deorphanization of G protein-coupled receptors (GPCRs) has slowed, and new approaches are required. Small molecule targeting of orphan GPCRs can potentially be of clinical benefit even if the endogenous receptor ligand has not been identified. Many GPCRs lack common variants that lead to reproducible genome-wide disease associations, and rare-variant approaches have emerged as a viable alternative to identify disease associations for such genes. Therefore, our goal was to prioritize orphan GPCRs by determining their associations with human diseases in a large clinical population. We used sequence kernel association tests to assess the disease associations of 85 orphan or understudied GPCRs in an unselected cohort of 51,289 individuals. Using rare loss-of-function variants, missense variants predicted to be pathogenic or likely pathogenic, and a subset of rare synonymous variants that cause large changes in local codon bias as independent data sets, we found strong, phenome-wide disease associations shared by two or more variant categories for 39% of the GPCRs. To validate the bioinformatics and sequence kernel association test analyses, we functionally characterized rare missense and synonymous variants of GPR39, a family A GPCR, revealing altered expression or Zn2+-mediated signaling for members of both variant classes. These results support the utility of rare variant analyses for identifying disease associations for GPCRs that lack impactful common variants. We highlight the importance of rare synonymous variants in human physiology and argue for their routine inclusion in any comprehensive analysis of genomic variants as potential causes of disease.
Collapse
Affiliation(s)
- Ridge Dershem
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Raghu P R Metpally
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Kirk Jeffreys
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Sarathbabu Krishnamurthy
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Diane T Smelser
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Michal Hershfinkel
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 8410501 Israel
| | -
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York 10591
| | - David J Carey
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822
| | - Janet D Robishaw
- Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida 33431
| | - Gerda E Breitwieser
- Department of Molecular and Functional Genomics, Geisinger, Weis Center for Research, Danville, Pennsylvania 17822.
| |
Collapse
|
127
|
Mazumder TH, Uddin A, Chakraborty S. Insights into the nucleotide composition and codon usage pattern of human tumor suppressor genes. Mol Carcinog 2019; 59:15-23. [PMID: 31583785 DOI: 10.1002/mc.23124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 09/05/2019] [Accepted: 09/21/2019] [Indexed: 01/21/2023]
Abstract
Tumor suppressor genes encode different proteins that inhibit the uncontrolled proliferation of cell growth and tumor development. To acquire clues for predicting gene expression level, it is essential to understand the codon usage bias (CUB) of genes to characterize genome which possesses its own compositional characteristics and unique coding sequences. We used bioinformatic tools to analyze the codon usage patterns of 637 human tumor suppressor genes as no work was reported earlier. The mean effective number of codons of these genes was 48, indicating low CUB. Our results exhibited a significant positive correlation among different nucleotide compositions and the codons ending with C base was most frequently used along with the most over-represented codon CTG and GTG codifying leucine and valine amino acid, respectively, in human tumor suppressor genes. The neutrality plot showed a significant positive correlation (Pearson, r = 0. 646; P < .01) suggesting that mutation on GC bias might affect the CUB. However, the linear regression coefficient of GC12 on GC3 in human tumor suppressor genes suggested that natural selection played a major role while mutation pressure played a minor role in the codon usage patterns of tumor suppressor genes in human. Our study would throw light into the factors that affect CUB and the codon usage patterns in the human tumor suppressor genes.
Collapse
Affiliation(s)
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Hailakandi, Assam, India
| | | |
Collapse
|
128
|
Gonzalez-Sanchez B, Vega-Rodríguez MA, Santander-Jiménez S. Multi-objective protein encoding: Redefinition of the problem, new problem-aware operators, and approach based on Variable Neighborhood Search. Inf Sci (N Y) 2019. [DOI: 10.1016/j.ins.2019.05.088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
129
|
Raghavan SS, Chee S, Li J, Poschmann J, Nagarajan N, Jia Wei S, Verma CS, Ghadessy FJ. Development and application of a transcriptional sensor for detection of heterologous acrylic acid production in E. coli. Microb Cell Fact 2019; 18:139. [PMID: 31426802 PMCID: PMC6699081 DOI: 10.1186/s12934-019-1185-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/03/2019] [Indexed: 12/20/2022] Open
Abstract
Background Acrylic acid (AA) is a widely used commodity chemical derived from non-renewable fossil fuel sources. Alternative microbial-based production methodologies are being developed with the aim of providing “green” acrylic acid. These initiatives will benefit from component sensing tools that facilitate rapid and easy detection of in vivo AA production. Results We developed a novel transcriptional sensor facilitating in vivo detection of acrylic acid (AA). RNAseq analysis of Escherichia coli exposed to sub-lethal doses of acrylic acid identified a selectively responsive promoter (PyhcN) that was cloned upstream of the eGFP gene. In the presence of AA, eGFP expression in E. coli cells harbouring the sensing construct was readily observable by fluorescence read-out. Low concentrations of AA (500 μM) could be detected whilst the closely related lactic and 3-hydroxy propionic acids failed to activate the sensor. We further used the developed AA-biosensor for in vivo FACS-based screening and identification of amidase mutants with improved catalytic properties for deamination of acrylamide to acrylic acid. Conclusions The transcriptional AA sensor developed in this study will benefit strain, enzyme and pathway engineering initiatives targeting the efficient formation of bio-acrylic acid. Electronic supplementary material The online version of this article (10.1186/s12934-019-1185-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sarada S Raghavan
- p53 Laboratory Technology Development Group, A*STAR, 8A Biomedical Grove #06-06 Immunos, Singapore, 138648, Singapore
| | - Sharon Chee
- p53 Laboratory Technology Development Group, A*STAR, 8A Biomedical Grove #06-06 Immunos, Singapore, 138648, Singapore
| | - Juntao Li
- Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672, Singapore
| | - Jeremie Poschmann
- Centre de Recherche en Transplantation et Immunologie, Inserm, CHU-Nantes, Nantes, France
| | - Niranjan Nagarajan
- Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore, 138672, Singapore
| | - Siau Jia Wei
- p53 Laboratory Technology Development Group, A*STAR, 8A Biomedical Grove #06-06 Immunos, Singapore, 138648, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Singapore, 138671, Singapore.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Farid J Ghadessy
- p53 Laboratory Technology Development Group, A*STAR, 8A Biomedical Grove #06-06 Immunos, Singapore, 138648, Singapore.
| |
Collapse
|
130
|
Katneni UK, Liss A, Holcomb D, Katagiri NH, Hunt R, Bar H, Ismail A, Komar AA, Kimchi‐Sarfaty C. Splicing dysregulation contributes to the pathogenicity of several F9 exonic point variants. Mol Genet Genomic Med 2019; 7:e840. [PMID: 31257730 PMCID: PMC6687662 DOI: 10.1002/mgg3.840] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 06/10/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Pre-mRNA splicing is a complex process requiring the identification of donor site, acceptor site, and branch point site with an adjacent polypyrimidine tract sequence. Splicing is regulated by splicing regulatory elements (SREs) with both enhancer and suppressor functions. Variants located in exonic regions can impact splicing through dysregulation of native splice sites, SREs, and cryptic splice site activation. While splicing dysregulation is considered primary disease-inducing mechanism of synonymous variants, its contribution toward disease phenotype of non-synonymous variants is underappreciated. METHODS In this study, we analyzed 415 disease-causing and 120 neutral F9 exonic point variants including both synonymous and non-synonymous for their effect on splicing using a series of in silico splice site prediction tools, SRE prediction tools, and in vitro minigene assays. RESULTS The use of splice site and SRE prediction tools in tandem provided better prediction but were not always in agreement with the minigene assays. The net effect of splicing dysregulation caused by variants was context dependent. Minigene assays revealed that perturbed splicing can be found. CONCLUSION Synonymous variants primarily cause disease phenotype via splicing dysregulation while additional mechanisms such as translation rate also play an important role. Splicing dysregulation is likely to contribute to the disease phenotype of several non-synonymous variants.
Collapse
Affiliation(s)
- Upendra K. Katneni
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & ResearchUS FDASilver SpringMaryland
| | - Aaron Liss
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & ResearchUS FDASilver SpringMaryland
| | - David Holcomb
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & ResearchUS FDASilver SpringMaryland
| | - Nobuko H. Katagiri
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & ResearchUS FDASilver SpringMaryland
| | - Ryan Hunt
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & ResearchUS FDASilver SpringMaryland
| | - Haim Bar
- Department of StatisticsUniversity of ConnecticutStorrsConnecticut
| | - Amra Ismail
- Department of Biological, Geological and Environmental Sciences, Center for Gene Regulation in Health and DiseaseCleveland State UniversityClevelandOhio
| | - Anton A. Komar
- Department of Biological, Geological and Environmental Sciences, Center for Gene Regulation in Health and DiseaseCleveland State UniversityClevelandOhio
| | - Chava Kimchi‐Sarfaty
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation & ResearchUS FDASilver SpringMaryland
| |
Collapse
|
131
|
Sorek M, Cohen LRZ, Meshorer E. Open chromatin structure in PolyQ disease-related genes: a potential mechanism for CAG repeat expansion in the normal human population. NAR Genom Bioinform 2019; 1:e3. [PMID: 33575550 PMCID: PMC7671342 DOI: 10.1093/nargab/lqz003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/07/2019] [Accepted: 07/16/2019] [Indexed: 02/05/2023] Open
Abstract
The human genome contains dozens of genes that encode for proteins containing long poly-glutamine repeats (polyQ, usually encoded by CAG codons) of 10Qs or more. However, only nine of these genes have been reported to expand beyond the healthy variation and cause diseases. To address whether these nine disease-associated genes are unique in any way, we compared genetic and epigenetic features relative to other types of genes, especially repeat containing genes that do not cause diseases. Our analyses show that in pluripotent cells, the nine polyQ disease-related genes are characterized by an open chromatin profile, enriched for active chromatin marks and depleted for suppressive chromatin marks. By contrast, genes that encode for polyQ-containing proteins that are not associated with diseases, and other repeat containing genes, possess a suppressive chromatin environment. We propose that the active epigenetic landscape support decreased genomic stability and higher susceptibility for expansion mutations.
Collapse
Affiliation(s)
- Matan Sorek
- Edmond and Lily Safra Center for Brain Sciences, Edmond J. Safra Campus, Jerusalem, Hebrew University of Jerusalem, 9190401, Israel.,Department of Genetics, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Jerusalem, Hebrew University of Jerusalem, 9190401, Israel
| | - Lea R Z Cohen
- Edmond and Lily Safra Center for Brain Sciences, Edmond J. Safra Campus, Jerusalem, Hebrew University of Jerusalem, 9190401, Israel.,Department of Genetics, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Jerusalem, Hebrew University of Jerusalem, 9190401, Israel
| | - Eran Meshorer
- Edmond and Lily Safra Center for Brain Sciences, Edmond J. Safra Campus, Jerusalem, Hebrew University of Jerusalem, 9190401, Israel.,Department of Genetics, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Jerusalem, Hebrew University of Jerusalem, 9190401, Israel
| |
Collapse
|
132
|
Abstract
The universal triple-nucleotide genetic code is often viewed as a given, randomly selected through evolution. However, as summarized in this article, many observations and deductions within structural and thermodynamic frameworks help to explain the forces that must have shaped the code during the early evolution of life on Earth.
Collapse
|
133
|
Hettiarachchi GK, Katneni UK, Hunt RC, Kames JM, Athey JC, Bar H, Sauna ZE, McGill JR, Ibla JC, Kimchi-Sarfaty C. Translational and transcriptional responses in human primary hepatocytes under hypoxia. Am J Physiol Gastrointest Liver Physiol 2019; 316:G720-G734. [PMID: 30920299 PMCID: PMC6620582 DOI: 10.1152/ajpgi.00331.2018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The liver is the primary source of a large number of plasma proteins and plays a critical role in multiple biological processes. Inadequate oxygen supply characterizing various clinical settings such as liver transplantation exposes the liver to hypoxic conditions. Studies assessing hypoxia-induced global translational changes in liver are lacking. Here, we employed a recently developed ribosome-profiling technique to assess global translational responses of human primary hepatocytes exposed to acute hypoxic stress (1% O2) for the short term. In parallel, transcriptome profiling was performed to assess mRNA expression changes. We found that translational responses appeared earlier and were predominant over transcriptional responses. A significant decrease in translational efficiency of several ribosome genes indicated translational inhibition of new ribosome protein synthesis in hypoxia. Pathway enrichment analysis highlighted altered translational regulation of MAPK signaling, drug metabolism, oxidative phosphorylation, and nonalcoholic fatty liver disease pathways. Gene Ontology enrichment analysis revealed terms related to translation, metabolism, angiogenesis, apoptosis, and response to stress. Transcriptional induction of genes encoding heat shock proteins was observed within 30 min of hypoxia. Induction of genes encoding stress response mediators, metabolism regulators, and proangiogenic proteins was observed at 240 min. Despite the liver being the primary source of coagulation proteins and the implicated role of hypoxia in thrombosis, limited differences were observed in genes encoding coagulation-associated proteins. Overall, our study demonstrates the predominance of translational regulation over transcription and highlights differentially regulated pathways or biological processes in short-term hypoxic stress responses of human primary hepatocytes. NEW & NOTEWORTHY The novelty of this study lies in applying parallel ribosome- and transcriptome-profiling analyses to human primary hepatocytes in hypoxia. To our knowledge, this is the first study to assess global translational responses using ribosome profiling in hypoxic hepatocytes. Our results demonstrate the predominance of translational responses over transcriptional responses in early hepatic hypoxic stress responses. Furthermore, our study reveals multiple pathways and specific genes showing altered regulation in hypoxic hepatocytes.
Collapse
Affiliation(s)
- Gaya K. Hettiarachchi
- 1Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland
| | - Upendra K. Katneni
- 1Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland
| | - Ryan C. Hunt
- 1Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland
| | - Jacob M. Kames
- 1Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland
| | - John C. Athey
- 1Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland
| | - Haim Bar
- 2Department of Statistics, University of Connecticut, Storrs, Connecticut
| | - Zuben E. Sauna
- 1Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland
| | - Joseph R. McGill
- 1Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland
| | - Juan C. Ibla
- 3Department of Anesthesiology, Perioperative and Pain Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Chava Kimchi-Sarfaty
- 1Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland
| |
Collapse
|
134
|
Zhao W, Liu S, Du G, Zhou J. An efficient expression tag library based on self-assembling amphipathic peptides. Microb Cell Fact 2019; 18:91. [PMID: 31133014 PMCID: PMC6535861 DOI: 10.1186/s12934-019-1142-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 05/17/2019] [Indexed: 11/10/2022] Open
Abstract
Background Self-assembling amphipathic peptides (SAPs) may improve protein production or induce the formation of inclusion bodies by fusing them to the N-terminus of proteins. However, they do not function uniformly well with all target enzymes and systematic research on how the composition of SAPs influence the production of fusion protein is still limited. Results To improve the efficiency of SAPs, we studied factors that might be involved in SAP-mediated protein production using S1 (AEAEAKAK)2 as the original SAP and green fluorescent protein (GFP) as the reporter. The results indicate that hydrophobicity and net charges of SAPs play a key role in protein expression. As hydrophobicity regulation tend to cause the formation of insoluble inclusion bodies of protein, an expression tag library composed of SAPs, which varied in net charge (from + 1 to + 20), was constructed based on the random amplification of S1nv1 (ANANARAR)10. The efficiency of the library was validated by polygalacturonate lyase (PGL), lipoxygenase (LOX), l-asparaginase (ASN) and transglutaminase (MTG). To accelerate preliminary screening, each enzyme was fused at the C-terminus with GFP. Among the four enzyme fusions, the SAPs with + 2 – + 6 net charges were optimal for protein expression. Finally, application of the library improved the expression of PGL, LOX, ASN, and MTG by 8.3, 3.5, 2.64, and 3.68-fold relative to that of the corresponding wild-type enzyme, respectively. Conclusions This is the first report to study key factors of SAPs as an expression tag to enhance recombinant enzyme production. The SAP library could be used as a novel plug-and-play protein-engineering method to screen for enzymes or proteins with enhanced production. Electronic supplementary material The online version of this article (10.1186/s12934-019-1142-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Weixin Zhao
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China.,School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Song Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China. .,School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Guocheng Du
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China.,School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| |
Collapse
|
135
|
Pedro AQ, Queiroz JA, Passarinha LA. Smoothing membrane protein structure determination by initial upstream stage improvements. Appl Microbiol Biotechnol 2019; 103:5483-5500. [PMID: 31127356 PMCID: PMC7079970 DOI: 10.1007/s00253-019-09873-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 12/14/2022]
Abstract
Membrane proteins (MP) constitute 20–30% of all proteins encoded by the genome of various organisms and perform a wide range of essential biological functions. However, despite they represent the largest class of protein drug targets, a relatively small number high-resolution 3D structures have been obtained yet. Membrane protein biogenesis is more complex than that of the soluble proteins and its recombinant biosynthesis has been a major drawback, thus delaying their further structural characterization. Indeed, the major limitation in structure determination of MP is the low yield achieved in recombinant expression, usually coupled to low functionality, pinpointing the optimization target in recombinant MP research. Recently, the growing attention that have been dedicated to the upstream stage of MP bioprocesses allowed great advances, permitting the evolution of the number of MP solved structures. In this review, we analyse and discuss effective solutions and technical advances at the level of the upstream stage using prokaryotic and eukaryotic organisms foreseeing an increase in expression yields of correctly folded MP and that may facilitate the determination of their three-dimensional structure. A section on techniques used to protein quality control and further structure determination of MP is also included. Lastly, a critical assessment of major factors contributing for a good decision-making process related to the upstream stage of MP is presented.
Collapse
Affiliation(s)
- Augusto Quaresma Pedro
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-001, Covilhã, Portugal
- CICECO - Aveiro Institute of Materials, Department of Chemistry, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - João António Queiroz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-001, Covilhã, Portugal
| | - Luís António Passarinha
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-001, Covilhã, Portugal.
- UCIBIO@REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
| |
Collapse
|
136
|
Holcomb DD, Alexaki A, Katneni U, Kimchi-Sarfaty C. The Kazusa codon usage database, CoCoPUTs, and the value of up-to-date codon usage statistics. INFECTION GENETICS AND EVOLUTION 2019; 73:266-268. [PMID: 31100358 DOI: 10.1016/j.meegid.2019.05.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 10/26/2022]
Affiliation(s)
- David D Holcomb
- Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, USA
| | - Aikaterini Alexaki
- Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, USA
| | - Upendra Katneni
- Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, USA
| | - Chava Kimchi-Sarfaty
- Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, USA.
| |
Collapse
|
137
|
Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design. J Mol Biol 2019; 431:2434-2441. [PMID: 31029701 DOI: 10.1016/j.jmb.2019.04.021] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 02/08/2023]
Abstract
Usage of sequential codon-pairs is non-random and unique to each species. Codon-pair bias is related to but clearly distinct from individual codon usage bias. Codon-pair bias is thought to affect translational fidelity and efficiency and is presumed to be under the selective pressure. It was suggested that changes in codon-pair utilization may affect human disease more significantly than changes in single codons. Although recombinant gene technologies often take codon-pair usage bias into account, codon-pair usage data/tables are not readily available, thus potentially impeding research efforts. The present computational resource (https://hive.biochemistry.gwu.edu/review/codon2) systematically addresses this issue. Building on our recent HIVE-Codon Usage Tables, we constructed a new database to include genomic codon-pair and dinucleotide statistics of all organisms with sequenced genome, available in the GenBank. We believe that the growing understanding of the importance of codon-pair usage will make this resource an invaluable tool to many researchers in academia and pharmaceutical industry.
Collapse
|
138
|
Biswas KK, Palchoudhury S, Chakraborty P, Bhattacharyya UK, Ghosh DK, Debnath P, Ramadugu C, Keremane ML, Khetarpal RK, Lee RF. Codon Usage Bias Analysis of Citrus tristeza Virus: Higher Codon Adaptation to Citrus reticulata Host. Viruses 2019; 11:v11040331. [PMID: 30965565 PMCID: PMC6521185 DOI: 10.3390/v11040331] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/25/2019] [Accepted: 04/03/2019] [Indexed: 12/16/2022] Open
Abstract
Citrus tristeza virus (CTV), a member of the aphid-transmitted closterovirus group, is the causal agent of the notorious tristeza disease in several citrus species worldwide. The codon usage patterns of viruses reflect the evolutionary changes for optimization of their survival and adaptation in their fitness to the external environment and the hosts. The codon usage adaptation of CTV to specific citrus hosts remains to be studied; thus, its role in CTV evolution is not clearly comprehended. Therefore, to better explain the host–virus interaction and evolutionary history of CTV, the codon usage patterns of the coat protein (CP) genes of 122 CTV isolates originating from three economically important citrus hosts (55 isolate from Citrus sinensis, 38 from C. reticulata, and 29 from C. aurantifolia) were studied using several codon usage indices and multivariate statistical methods. The present study shows that CTV displays low codon usage bias (CUB) and higher genomic stability. Neutrality plot and relative synonymous codon usage analyses revealed that the overall influence of natural selection was more profound than that of mutation pressure in shaping the CUB of CTV. The contribution of high-frequency codon analysis and codon adaptation index value show that CTV has host-specific codon usage patterns, resulting in higheradaptability of CTV isolates originating from C. reticulata (Cr-CTV), and low adaptability in the isolates originating from C. aurantifolia (Ca-CTV) and C. sinensis (Cs-CTV). The combination of codon analysis of CTV with citrus genealogy suggests that CTV evolved in C. reticulata or other Citrus progenitors. The outcome of the study enhances the understanding of the factors involved in viral adaptation, evolution, and fitness toward their hosts. This information will definitely help devise better management strategies of CTV.
Collapse
Affiliation(s)
- Kajal Kumar Biswas
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 11012, India.
| | - Supratik Palchoudhury
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 11012, India.
| | - Prosenjit Chakraborty
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 11012, India.
| | - Utpal K Bhattacharyya
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 11012, India.
| | - Dilip K Ghosh
- ICAR-Central Citrus Research Institute, Nagpur 440033, India.
| | - Palash Debnath
- Department of Plant Pathology, Assam Agricultural University, Jorhat 785013, India.
| | - Chandrika Ramadugu
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92507, USA.
| | - Manjunath L Keremane
- National Clonal Germplasm Repository for Citrus & Dates, United States Department of Agriculture-Agricultural Research Service, Riverside, CA 92507, USA.
| | - Ravi K Khetarpal
- Asia-Pacific Association of Agricultural Research Institutions, Bangkok 10100, Thailand.
| | - Richard F Lee
- National Clonal Germplasm Repository for Citrus & Dates, United States Department of Agriculture-Agricultural Research Service, Riverside, CA 92507, USA.
| |
Collapse
|
139
|
"CodonWizard" - An intuitive software tool with graphical user interface for customizable codon optimization in protein expression efforts. Protein Expr Purif 2019; 160:84-93. [PMID: 30953700 DOI: 10.1016/j.pep.2019.03.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/25/2019] [Accepted: 03/31/2019] [Indexed: 11/22/2022]
Abstract
Optimization of coding sequences to maximize protein expression yield is often outsourced to external service providers during commercial gene synthesis and thus unfortunately remains a black box for many researchers. The presented software program "CodonWizard" offers scientists a powerful but easy-to-use tool for customizable codon optimization: The intuitive graphical user interface empowers even scientists inexperienced in the art to straightforward design, modify, test and save complex codon optimization strategies and to publicly share successful otimization strategies among the scientific community. "Codon Wizard" provides highly flexible features for sequence analysis and completely customizable modification/optimization of codon usage of any given input sequence data (DNA/RNA/peptide) using freely combinable algorithms, allowing for implementation of contemporary, well-established optimization strategies as well as novel, proprietary ones alike. Contrary to comparable tools, "Codon Wizard" thus finally opens up ways for an empirical approach to codon optimization and may also >be used completely offline to protect resulting intellectual property. As a benchmark, the reliability, intuitiveness and utility of the application could be demonstrated by increasing the yield of recombinant TEV-protease expressed in E. coli by several orders of magnitude after codon optimization using "CodonWizard" - Permanently available for download on the web at http://schwalbe.org.chemie.uni-frankfurt.de/node/3324.
Collapse
|
140
|
Wright G, Rodriguez A, Clark PL, Emrich S. A New Look at Codon Usage and Protein Expression. EPIC SERIES IN COMPUTING 2019; 60:104-112. [PMID: 35342824 PMCID: PMC8953497 DOI: 10.29007/d4tz] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
%MinMax, a model of intra-gene translational elongation rate, relies on codon usage frequencies. Historically, %MinMax has used tables that measure codon usage bias for all genes in an organism, such as those found at HIVE-CUT. In this paper, we provide evidence that codon usage bias based on all genes is insufficient to accurately measure absolute translation rate. We show that alternative "High-ϕ" codon usage tables, generated by another model (ROC-SEMPPR), are a promising alternative. By creating a hybrid model, future codon usage analyses and their applications (e.g., codon harmonization) are likely to more accurately measure the "tempo" of translation elongation. We also suggest a High-ϕ alternative to the Codon Adaptation Index (CAI), a classic metric of codon usage bias based on highly expressed genes. Significantly, our new alternative is equally well correlated with empirical data as traditional CAI without using experimentally determined expression counts as input.
Collapse
Affiliation(s)
- Gabriel Wright
- Department of Computer Science, University of Notre Dame
| | - Anabel Rodriguez
- Department of Chemistry & Biochemistry, University of Notre Dame
| | - Patricia L Clark
- Department of Chemistry & Biochemistry, University of Notre Dame
| | - Scott Emrich
- Department of Electrical Engineering & Computer Science, University of Tennessee, Knoxville
| |
Collapse
|
141
|
Lischik CQ, Adelmann L, Wittbrodt J. Enhanced in vivo-imaging in medaka by optimized anaesthesia, fluorescent protein selection and removal of pigmentation. PLoS One 2019; 14:e0212956. [PMID: 30845151 PMCID: PMC6405165 DOI: 10.1371/journal.pone.0212956] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/12/2019] [Indexed: 02/07/2023] Open
Abstract
Fish are ideally suited for in vivo-imaging due to their transparency at early stages combined with a large genetic toolbox. Key challenges to further advance imaging are fluorophore selection, immobilization of the specimen and approaches to eliminate pigmentation. We addressed all three and identified the fluorophores and anaesthesia of choice by high throughput time-lapse imaging. Our results indicate that eGFP and mCherry are the best conservative choices for in vivo-fluorescence experiments, when availability of well-established antibodies and nanobodies matters. Still, mVenusNB and mGFPmut2 delivered highest absolute fluorescence intensities in vivo. Immobilization is of key importance during extended in vivo imaging. Here, traditional approaches are outperformed by mRNA injection of α-Bungarotoxin which allows a complete and reversible, transient immobilization. In combination with fully transparent juvenile and adult fish established by the targeted inactivation of both, oca2 and pnp4a via CRISPR/Cas9-mediated gene editing in medaka we could dramatically improve the state-of-the art imaging conditions in post-embryonic fish, now enabling light-sheet microscopy of the growing retina, brain, gills and inner organs in the absence of side effects caused by anaesthetic drugs or pigmentation.
Collapse
Affiliation(s)
- Colin Q Lischik
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany.,Heidelberg Biosciences International Graduate School, Heidelberg University, Heidelberg, Germany
| | - Leonie Adelmann
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| |
Collapse
|
142
|
Engqvist MKM, Rabe KS. Applications of Protein Engineering and Directed Evolution in Plant Research. PLANT PHYSIOLOGY 2019; 179:907-917. [PMID: 30626612 PMCID: PMC6393796 DOI: 10.1104/pp.18.01534] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 12/25/2018] [Indexed: 05/06/2023]
Abstract
Engineered proteins can be used to optimize desired traits in plants; even though recent advances have resulted in new application areas, certain methodological challenges remain.
Collapse
Affiliation(s)
- Martin K M Engqvist
- Department of Biology and Biological Engineering, Chalmers University of Technology, Division of Systems and Synthetic Biology, Gothenburg, Sweden
| | - Kersten S Rabe
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT), Group for Molecular Evolution, Karlsruhe, Germany
| |
Collapse
|
143
|
Multi-Objective Artificial Bee Colony for designing multiple genes encoding the same protein. Appl Soft Comput 2019. [DOI: 10.1016/j.asoc.2018.10.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
144
|
Regensdorff M, Deckena M, Stein M, Borchers A, Scherer G, Lammers M, Hänsch R, Zachgo S, Buschmann H. Transient genetic transformation of Mougeotia scalaris (Zygnematophyceae) mediated by the endogenous α-tubulin1 promoter. JOURNAL OF PHYCOLOGY 2018; 54:840-849. [PMID: 30171607 DOI: 10.1111/jpy.12781] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 08/14/2018] [Indexed: 05/27/2023]
Abstract
Mougeotia scalaris is a filamentous streptophyte alga renowned for light-inducible plastid rotation and microtubule-dependent polarity establishment. As a first step toward transgenic approaches we determined the 5,825 base pair genomic sequence encoding the α-tubulin1 gene (MsTUA1) of M. scalaris (strain SAG 164.80). The subcloned MsTUA1 promoter facilitated strong transgene expression in M. scalaris and tobacco leaf cells, as shown by particle bombardment and the subsequent visualization of expressed fluorescent protein markers. Our results provide a route for the genetic transformation of the filamentous streptophyte alga M. scalaris based on the endogenous TUA1 promoter.
Collapse
Affiliation(s)
- Merle Regensdorff
- Botany Department, School of Biology and Chemistry, Osnabrück University, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Marek Deckena
- Botany Department, School of Biology and Chemistry, Osnabrück University, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Maike Stein
- Botany Department, School of Biology and Chemistry, Osnabrück University, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Agnes Borchers
- Botany Department, School of Biology and Chemistry, Osnabrück University, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Gwydion Scherer
- Botany Department, School of Biology and Chemistry, Osnabrück University, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Maike Lammers
- Botany Department, School of Biology and Chemistry, Osnabrück University, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Robert Hänsch
- Department of Plant Biology, Technische Universität Braunschweig, Humboldtstraße 1, 38106, Braunschweig, Germany
| | - Sabine Zachgo
- Botany Department, School of Biology and Chemistry, Osnabrück University, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Henrik Buschmann
- Botany Department, School of Biology and Chemistry, Osnabrück University, Barbarastraße 11, 49076, Osnabrück, Germany
| |
Collapse
|
145
|
Voogdt CGP, Merchant ME, Wagenaar JA, van Putten JPM. Evolutionary Regression and Species-Specific Codon Usage of TLR15. Front Immunol 2018; 9:2626. [PMID: 30483270 PMCID: PMC6244663 DOI: 10.3389/fimmu.2018.02626] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/25/2018] [Indexed: 01/01/2023] Open
Abstract
Toll-like receptors (TLRs) form an ancient family of innate immune receptors that detect microbial structures and activate the host immune response. Most subfamilies of TLRs (including TLR3, TLR5, and TLR7) are highly conserved among vertebrate species. In contrast, TLR15, a member of the TLR1 subfamily, appears to be unique to birds and reptiles. We investigated the functional evolution of TLR15. Phylogenetic and synteny analyses revealed putative TLR15 orthologs in bird species, several reptilian species and also in a shark species, pointing to an unprecedented date of origin of TLR15 as well as large scale reciprocal loss of this TLR in most other vertebrates. Cloning and functional analysis of TLR15 of the green anole lizard (Anolis carolinensis), salt water crocodile (Crocodylus porosus), American alligator (Alligator mississippiensis), and chicken (Gallus gallus) showed for all species TLR15 specific protease-induced activation of NF-κB, despite highly variable TLR15 protein expression levels. The variable TLR15 expression was consistent in both human and reptilian cells and could be attributed to species-specific differences in TLR15 codon usage. The species-specific codon bias was not or barely noted for more evolutionarily conserved TLRs (e.g., TLR3). Overall, our results indicate that TLR15 originates before the divergence of chondrichthyes fish and tetrapods and that TLR15 of both avian and reptilian species has a conserved function as protease activated receptor. The species-specific codon usage and large scale loss of TLR15 in most vertebrates suggest evolutionary regression of this ancient TLR.
Collapse
Affiliation(s)
- Carlos G P Voogdt
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, Netherlands
| | - Mark E Merchant
- Department of Chemistry, McNeese State University, Lake Charles, LA, United States
| | - Jaap A Wagenaar
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, Netherlands.,Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Jos P M van Putten
- Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
146
|
Pipe SW. Bioengineered molecules for the management of haemophilia: Promise and remaining challenges. Haemophilia 2018; 24 Suppl 6:68-75. [PMID: 29878662 DOI: 10.1111/hae.13507] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2018] [Indexed: 12/14/2022]
Abstract
Recombinant DNA technology has led to accelerating introduction of novel therapeutics for the treatment of haemophilia. This technology has driven the development of recombinant clotting factors, extended half-life clotting factors, alternative biologics to promote haemostasis and enabled the launch of the gene therapy era for haemophilia. At the core of this technology is the ability to study the structure and function of the native molecules and to apply rational bioengineering to overcome limitations to the existing therapies. Through the study of haemophilia-causing mutations, site-directed mutagenesis, detailed structural models and a wide repertoire of animal models, new bioengineering strategies are helping overcome some of the remaining limitations and challenges of traditional clotting factor concentrates. Some of these bioengineering strategies are now being partnered with improvements in vectorology leading to the first wave of successful gene therapy approaches. This study will review past and present bioengineered molecules that are advancing care for haemophilia as well as novel approaches that promise to continue to improve care and outcomes for patients with haemophilia.
Collapse
Affiliation(s)
- S W Pipe
- University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
147
|
Machine Learning for detection of viral sequences in human metagenomic datasets. BMC Bioinformatics 2018; 19:336. [PMID: 30249176 PMCID: PMC6154907 DOI: 10.1186/s12859-018-2340-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 08/28/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Detection of highly divergent or yet unknown viruses from metagenomics sequencing datasets is a major bioinformatics challenge. When human samples are sequenced, a large proportion of assembled contigs are classified as "unknown", as conventional methods find no similarity to known sequences. We wished to explore whether machine learning algorithms using Relative Synonymous Codon Usage frequency (RSCU) could improve the detection of viral sequences in metagenomic sequencing data. RESULTS We trained Random Forest and Artificial Neural Network using metagenomic sequences taxonomically classified into virus and non-virus classes. The algorithms achieved accuracies well beyond chance level, with area under ROC curve 0.79. Two codons (TCG and CGC) were found to have a particularly strong discriminative capacity. CONCLUSION RSCU-based machine learning techniques applied to metagenomic sequencing data can help identify a large number of putative viral sequences and provide an addition to conventional methods for taxonomic classification.
Collapse
|
148
|
Medina-Carmona E, Betancor-Fernández I, Santos J, Mesa-Torres N, Grottelli S, Batlle C, Naganathan AN, Oppici E, Cellini B, Ventura S, Salido E, Pey AL. Insight into the specificity and severity of pathogenic mechanisms associated with missense mutations through experimental and structural perturbation analyses. Hum Mol Genet 2018; 28:1-15. [DOI: 10.1093/hmg/ddy323] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/09/2018] [Indexed: 12/21/2022] Open
Abstract
Abstract
Most pathogenic missense mutations cause specific molecular phenotypes through protein destabilization. However, how protein destabilization is manifested as a given molecular phenotype is not well understood. We develop here a structural and energetic approach to describe mutational effects on specific traits such as function, regulation, stability, subcellular targeting or aggregation propensity. This approach is tested using large-scale experimental and structural perturbation analyses in over thirty mutations in three different proteins (cancer-associated NQO1, transthyretin related with amyloidosis and AGT linked to primary hyperoxaluria type I) and comprising five very common pathogenic mechanisms (loss-of-function and gain-of-toxic function aggregation, enzyme inactivation, protein mistargeting and accelerated degradation). Our results revealed that the magnitude of destabilizing effects and, particularly, their propagation through the structure to promote disease-associated conformational states largely determine the severity and molecular mechanisms of disease-associated missense mutations. Modulation of the structural perturbation at a mutated site is also shown to cause switches between different molecular phenotypes. When very common disease-associated missense mutations were investigated, we also found that they were not among the most deleterious possible missense mutations at those sites, and required additional contributions from codon bias and effects of CpG sites to explain their high frequency in patients. Our work sheds light on the molecular basis of pathogenic mechanisms and genotype–phenotype relationships, with implications for discriminating between pathogenic and neutral changes within human genome variability from whole genome sequencing studies.
Collapse
Affiliation(s)
- Encarnación Medina-Carmona
- Department of Physical Chemistry, University of Granada, Granada, Spain
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, Perugia
| | - Isabel Betancor-Fernández
- Centre for Biomedical Research on Rare Diseases, Hospital Universitario de Canarias, Tenerife, Spain
| | - Jaime Santos
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Noel Mesa-Torres
- Department of Physical Chemistry, University of Granada, Granada, Spain
| | - Silvia Grottelli
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, Perugia
| | - Cristina Batlle
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai, India
| | - Elisa Oppici
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada Le Grazie, Verona, Italy
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, Perugia
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases, Hospital Universitario de Canarias, Tenerife, Spain
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, Granada, Spain
| |
Collapse
|
149
|
Mauro VP. Codon Optimization in the Production of Recombinant Biotherapeutics: Potential Risks and Considerations. BioDrugs 2018; 32:69-81. [PMID: 29392566 DOI: 10.1007/s40259-018-0261-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biotherapeutics are increasingly becoming the mainstay in the treatment of a variety of human conditions, particularly in oncology and hematology. The production of therapeutic antibodies, cytokines, and fusion proteins have markedly accelerated these fields over the past decade and are probably the major contributor to improved patient outcomes. Today, most protein therapeutics are expressed as recombinant proteins in mammalian cell lines. An expression technology commonly used to increase protein levels involves codon optimization. This approach is possible because degeneracy of the genetic code enables most amino acids to be encoded by more than one synonymous codon and because codon usage can have a pronounced influence on levels of protein expression. Indeed, codon optimization has been reported to increase protein expression by > 1000-fold. The primary tactic of codon optimization is to increase the rate of translation elongation by overcoming limitations associated with species-specific differences in codon usage and transfer RNA (tRNA) abundance. However, in mammalian cells, assumptions underlying codon optimization appear to be poorly supported or unfounded. Moreover, because not all synonymous codon mutations are neutral, codon optimization can lead to alterations in protein conformation and function. This review discusses codon optimization for therapeutic protein production in mammalian cells.
Collapse
|
150
|
A Novel Marsupial Hepatitis A Virus Corroborates Complex Evolutionary Patterns Shaping the Genus Hepatovirus. J Virol 2018; 92:JVI.00082-18. [PMID: 29695421 PMCID: PMC6002732 DOI: 10.1128/jvi.00082-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/12/2018] [Indexed: 11/30/2022] Open
Abstract
The discovery of highly diverse nonprimate hepatoviruses illuminated the evolutionary origins of hepatitis A virus (HAV) ancestors in mammals other than primates. Marsupials are ancient mammals that diverged from other Eutheria during the Jurassic. Viruses from marsupials may thus provide important insight into virus evolution. To investigate Hepatovirus macroevolutionary patterns, we sampled 112 opossums in northeastern Brazil. A novel marsupial HAV (MHAV) in the Brazilian common opossum (Didelphis aurita) was detected by nested reverse transcription-PCR (RT-PCR). MHAV concentration in the liver was high, at 2.5 × 109 RNA copies/g, and at least 300-fold higher than those in other solid organs, suggesting hepatotropism. Hepatovirus seroprevalence in D. aurita was 26.6% as determined using an enzyme-linked immunosorbent assay (ELISA). Endpoint titers in confirmatory immunofluorescence assays were high, and marsupial antibodies colocalized with anti-HAV control sera, suggesting specificity of serological detection and considerable antigenic relatedness between HAV and MHAV. MHAV showed all genomic hallmarks defining hepatoviruses, including late-domain motifs likely involved in quasi-envelope acquisition, a predicted C-terminal pX extension of VP1, strong avoidance of CpG dinucleotides, and a type 3 internal ribosomal entry site. Translated polyprotein gene sequence distances of at least 23.7% from other hepatoviruses suggested that MHAV represents a novel Hepatovirus species. Conserved predicted cleavage sites suggested similarities in polyprotein processing between HAV and MHAV. MHAV was nested within rodent hepatoviruses in phylogenetic reconstructions, suggesting an ancestral hepatovirus host switch from rodents into marsupials. Cophylogenetic reconciliations of host and hepatovirus phylogenies confirmed that host-independent macroevolutionary patterns shaped the phylogenetic relationships of extant hepatoviruses. Although marsupials are synanthropic and consumed as wild game in Brazil, HAV community protective immunity may limit the zoonotic potential of MHAV. IMPORTANCE Hepatitis A virus (HAV) is a ubiquitous cause of acute hepatitis in humans. Recent findings revealed the evolutionary origins of HAV and the genus Hepatovirus defined by HAV in mammals other than primates in general and in small mammals in particular. The factors shaping the genealogy of extant hepatoviruses are unclear. We sampled marsupials, one of the most ancient mammalian lineages, and identified a novel marsupial HAV (MHAV). The novel MHAV shared specific features with HAV, including hepatotropism, antigenicity, genome structure, and a common ancestor in phylogenetic reconstructions. Coevolutionary analyses revealed that host-independent evolutionary patterns contributed most to the current phylogeny of hepatoviruses and that MHAV was the most drastic example of a cross-order host switch of any hepatovirus observed so far. The divergence of marsupials from other mammals offers unique opportunities to investigate HAV species barriers and whether mechanisms of HAV immune control are evolutionarily conserved.
Collapse
|