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Anwar AM, Aljabri M, El-Soda M. Patterns of genome-wide codon usage bias in tobacco, tomato and potato. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1911684] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Ali Mostafa Anwar
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Maha Aljabri
- Department of Biology, Faculty of Applied Sciences, Umm Al‐Qura University, Makkah, Saudi Arabia
- Research Laboratories Centre, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mohamed El-Soda
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt
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Sablok G, Chen TW, Lee CC, Yang C, Gan RC, Wegrzyn JL, Porta NL, Nayak KC, Huang PJ, Varotto C, Tang P. ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications. DNA Res 2017; 24:327-332. [PMID: 28419256 PMCID: PMC5499650 DOI: 10.1093/dnares/dsw044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 09/14/2016] [Indexed: 01/01/2023] Open
Abstract
Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes. In light of the importance of codon usage patterns in the development of hyper-expression organelle transgenics, we present ChloroMitoCU, the first-ever curated, web-based reference catalog of the codon usage patterns in organelle genomes. ChloroMitoCU contains the pre-compiled codon usage patterns of 328 chloroplast genomes (29,960 CDS) and 3,502 mitochondrial genomes (49,066 CDS), enabling genome-wide exploration and comparative analysis of codon usage patterns across species. ChloroMitoCU allows the phylogenetic comparison of codon usage patterns across organelle genomes, the prediction of codon usage patterns based on user-submitted transcripts or assembled organelle genes, and comparative analysis with the pre-compiled patterns across species of interest. ChloroMitoCU can increase our understanding of the biased patterns of codon usage in organelle genomes across multiple clades. ChloroMitoCU can be accessed at: http://chloromitocu.cgu.edu.tw/
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Affiliation(s)
- Gaurav Sablok
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige (TN), Italy
| | - Ting-Wen Chen
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
| | - Chi-Ching Lee
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
| | - Chi Yang
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
| | - Ruei-Chi Gan
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University 10 of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3043 USA
| | - Nicola L Porta
- Department of Sustainable Agrobiosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige (TN), Italy.,MOUNTFOR Project Centre, European Forest Institute, Via E. Mach 1, 38010 San Michele all'Adige, Trento, Italy
| | - Kinshuk C Nayak
- Bioinformatics Centre, Institute of Life Sciences, Department of Biotechnology, Govt. India, Nalco Square, Bhubaneswar - 751 023, India
| | - Po-Jung Huang
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan 333, Taiwan
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige (TN), Italy
| | - Petrus Tang
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan 333, Taiwan.,Molecular Infectious Diseases Research Center, Chang Gung Memorial Hospital, Kweishan, Taoyuan 333, Taiwan
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Cohen O, Oberhardt M, Yizhak K, Ruppin E. Essential Genes Embody Increased Mutational Robustness to Compensate for the Lack of Backup Genetic Redundancy. PLoS One 2016; 11:e0168444. [PMID: 27997585 PMCID: PMC5173180 DOI: 10.1371/journal.pone.0168444] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 12/01/2016] [Indexed: 11/23/2022] Open
Abstract
Genetic robustness is a hallmark of cells, occurring through many mechanisms and at many levels. Essential genes lack the common robustness mechanism of genetic redundancy (i.e., existing alongside other genes with the same function), and thus appear at first glance to leave cells highly vulnerable to genetic or environmental perturbations. Here we explore a hypothesis that cells might protect against essential gene loss through mechanisms that occur at various cellular levels aside from the level of the gene. Using Escherichia coli and Saccharomyces cerevisiae as models, we find that essential genes are enriched over non-essential genes for properties we call "coding efficiency" and "coding robustness", denoting respectively a gene's efficiency of translation and robustness to non-synonymous mutations. The coding efficiency levels of essential genes are highly positively correlated with their evolutionary conservation levels, suggesting that this feature plays a key role in protecting conserved, evolutionarily important genes. We then extend our hypothesis into the realm of metabolic networks, showing that essential metabolic reactions are encoded by more "robust" genes than non-essential reactions, and that essential metabolites are produced by more reactions than non-essential metabolites. Taken together, these results testify that robustness at the gene-loss level and at the mutation level (and more generally, at two cellular levels that are usually treated separately) are not decoupled, but rather, that cellular vulnerability exposed due to complete gene loss is compensated by increased mutational robustness. Why some genes are backed up primarily against loss and others against mutations still remains an open question.
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Affiliation(s)
- Osher Cohen
- School of Computer Sciences and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Matthew Oberhardt
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, United States of America
| | - Keren Yizhak
- School of Computer Sciences and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eytan Ruppin
- School of Computer Sciences and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, United States of America
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Aklilu BB, Culligan KM. Molecular Evolution and Functional Diversification of Replication Protein A1 in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:33. [PMID: 26858742 PMCID: PMC4731521 DOI: 10.3389/fpls.2016.00033] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 01/10/2016] [Indexed: 05/23/2023]
Abstract
Replication protein A (RPA) is a heterotrimeric, single-stranded DNA binding complex required for eukaryotic DNA replication, repair, and recombination. RPA is composed of three subunits, RPA1, RPA2, and RPA3. In contrast to single RPA subunit genes generally found in animals and yeast, plants encode multiple paralogs of RPA subunits, suggesting subfunctionalization. Genetic analysis demonstrates that five Arabidopsis thaliana RPA1 paralogs (RPA1A to RPA1E) have unique and overlapping functions in DNA replication, repair, and meiosis. We hypothesize here that RPA1 subfunctionalities will be reflected in major structural and sequence differences among the paralogs. To address this, we analyzed amino acid and nucleotide sequences of RPA1 paralogs from 25 complete genomes representing a wide spectrum of plants and unicellular green algae. We find here that the plant RPA1 gene family is divided into three general groups termed RPA1A, RPA1B, and RPA1C, which likely arose from two progenitor groups in unicellular green algae. In the family Brassicaceae the RPA1B and RPA1C groups have further expanded to include two unique sub-functional paralogs RPA1D and RPA1E, respectively. In addition, RPA1 groups have unique domains, motifs, cis-elements, gene expression profiles, and pattern of conservation that are consistent with proposed functions in monocot and dicot species, including a novel C-terminal zinc-finger domain found only in plant RPA1C-like sequences. These results allow for improved prediction of RPA1 subunit functions in newly sequenced plant genomes, and potentially provide a unique molecular tool to improve classification of Brassicaceae species.
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Affiliation(s)
- Behailu B. Aklilu
- Department of Molecular, Cellular and Biomedical Sciences, University of New HampshireDurham, NH, USA
- Program in Genetics, University of New HampshireDurham, NH, USA
| | - Kevin M. Culligan
- Department of Molecular, Cellular and Biomedical Sciences, University of New HampshireDurham, NH, USA
- Program in Genetics, University of New HampshireDurham, NH, USA
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