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Majumder A, Kanti Mondal S, Mukhoty S, Bag S, Mondal A, Begum Y, Sharma K, Banik A. Virtual screening and docking analysis of novel ligands for selective enhancement of tea ( Camellia sinensis) flavonoids. Food Chem X 2022; 13:100212. [PMID: 35498963 PMCID: PMC9039891 DOI: 10.1016/j.fochx.2022.100212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/15/2021] [Accepted: 01/13/2022] [Indexed: 12/12/2022] Open
Abstract
Tea-specific flavonoid biosynthetic pathway (FBP) was retrieved from KEGG. Putative ligands were predicted to enhance enzymes-substrate binding affinity. FBP genes showed moderately higher expression & relatively strong codon adaptation. Most of the genes were AT-rich and biased to A/U-ending synonymous codons. Mutational selection was determining the selective constraints on codon bias.
Flavour of tea is mainly contributed by a group of polyphenols – flavonoids. However, the content of flavonoid fluctuates seasonally and is found to be higher in the first flush of tea, when compared to the second flush. This disparity in the flavonoid content, and hence taste, incurs heavy economic losses to the tea plantation industry each harvest season. For our present study, four key product-specific enzymes (PAL, FNS, FLS and ANS) of the tea-specific flavonoid pathway were selected to perform molecular docking studies with specific virtually screened allosteric modulators. Results of docking analyses showed Naringenin, 2-Morpholin-4-ium-4-ylethanesulfonate, 6-C-Glucosylquercetin, 2-Oxoglutaric acid, 3,5,7,3′,4′-pentahydroxyflavone to be capable of improving the spontaneity of the enzyme-substrate reactions in terms of docking score, RMSD values, and non-covalent interactions (H-bond,hydrophobic interaction, Π-stacking, salt bridge, etc.). Further, the evolutionary relationship of tea flavonoid pathway enzymes was constructed and compared with related taxa. The codon usage-based of tea flavonoid biosynthetic genes indicated the non-biasness of their nucleotide composition. Overall this study will provide a direction towards putative ligand-dependent enhancement of flavonoid content, irrespective of seasonal variation.
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Key Words
- 4CL, Tyrosine ammonia lyase
- AMF, Arbuscular Mycorrhizal Fungi
- ANR, anthocyanidin reductase
- ANS, anthocyanidinsynthase
- C4H, trans-cinnamate-4-
- CAI, Codon Adaptation Index
- CHI, chalcone isomerase
- CHS, 4-coumarat
- CoA, ligase chalcone synthase
- Codon usage indices
- DFR, dihydroflavonol 4-reductase
- ENc, Effective number of codons
- F3H, flavanone 3-hydroxylase
- F3′5′H, flavonoid 3′5′-hydroxylase
- F3′H, flavonoid 3′-hydroxylase
- FLS, Flavonol synthase
- FNS, flavone synthase
- Flavonoids
- GC1, GC2, and GC3-GC, content at the first, second, and third codon positions
- GC3s, frequency of either G or C at the third codon position of synonymous codons
- H 0, null hypothesisno selection
- IAA, Indole acetic acid
- LAR, leucoanthocyanidin reductase
- Ligands
- Molecular docking
- PAL, phenylalanine ammonia-lyase
- RMSD, root-mean-square deviation
- RSCU, Relative Synonymous Codon Usage
- TAL, monooxygenase
- Tea flush
- UGT72, UDP-3 glycosyltransferases
- Virtual screening
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Affiliation(s)
- Anusha Majumder
- Laboratory of Microbial Interaction, School of Biotechnology, Presidency University, Kolkata, West Bengal, India
| | - Sunil Kanti Mondal
- Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
| | - Samyabrata Mukhoty
- Department of Biotechnology, The University of Burdwan, Burdwan, West Bengal, India
| | - Sagar Bag
- Laboratory of Microbial Interaction, School of Biotechnology, Presidency University, Kolkata, West Bengal, India
| | - Anupam Mondal
- Laboratory of Microbial Interaction, School of Biotechnology, Presidency University, Kolkata, West Bengal, India
| | - Yasmin Begum
- Department of Biophysics, Molecular Biology, and Bioinformatics, University of Calcutta, 92, APC Road, Kolkata 700009, West Bengal, India.,Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, JD-2, Sector III, Salt Lake, Kolkata 700106, West Bengal, India
| | - Kalpna Sharma
- R&D Centre, Danguajhar Tea Garden, Goodricke Group Ltd., Jalpaiguri, West Bengal, India
| | - Avishek Banik
- Laboratory of Microbial Interaction, School of Biotechnology, Presidency University, Kolkata, West Bengal, India
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Dissimilation of synonymous codon usage bias in virus-host coevolution due to translational selection. Nat Ecol Evol 2020; 4:589-600. [PMID: 32123323 DOI: 10.1038/s41559-020-1124-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/21/2020] [Indexed: 12/13/2022]
Abstract
Eighteen of the 20 amino acids are each encoded by more than one synonymous codon. Due to differential transfer RNA supply within the cell, synonymous codons are not used with equal frequency, a phenomenon termed codon usage bias (CUB). Previous studies have demonstrated that CUB of endogenous genes trans-regulates the translational efficiency of other genes. We hypothesized similar effects for CUB of exogenous genes on host translation, and tested it in the case of viral infection, a common form of naturally occurring exogenous gene translation. We analysed public Ribo-Seq datasets from virus-infected yeast and human cells and showed that virus CUB trans-regulated tRNA availability, and therefore the relative decoding time of codons. Manipulative experiments in yeast using 37 synonymous fluorescent proteins confirmed that an exogenous gene with CUB more similar to that of the host would apply decreased translational load on the host per unit of expression, whereas expression of the exogenous gene was elevated. The combination of these two effects was that exogenous genes with CUB overly similar to that of the host severely impeded host translation. Finally, using a manually curated list of viruses and natural and symptomatic hosts, we found that virus CUB tended to be more similar to that of symptomatic hosts than that of natural hosts, supporting a general deleterious effect of excessive CUB similarity between virus and host. Our work revealed repulsion between virus and host CUBs when they are overly similar, a previously unrecognized complexity in the coevolution of virus and host.
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Mazumdar P, Binti Othman R, Mebus K, Ramakrishnan N, Ann Harikrishna J. Codon usage and codon pair patterns in non-grass monocot genomes. ANNALS OF BOTANY 2017; 120:893-909. [PMID: 29155926 PMCID: PMC5710610 DOI: 10.1093/aob/mcx112] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 09/19/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS Studies on codon usage in monocots have focused on grasses, and observed patterns of this taxon were generalized to all monocot species. Here, non-grass monocot species were analysed to investigate the differences between grass and non-grass monocots. METHODS First, studies of codon usage in monocots were reviewed. The current information was then extended regarding codon usage, as well as codon-pair context bias, using four completely sequenced non-grass monocot genomes (Musa acuminata, Musa balbisiana, Phoenix dactylifera and Spirodela polyrhiza) for which comparable transcriptome datasets are available. Measurements were taken regarding relative synonymous codon usage, effective number of codons, derived optimal codon and GC content and then the relationships investigated to infer the underlying evolutionary forces. KEY RESULTS The research identified optimal codons, rare codons and preferred codon-pair context in the non-grass monocot species studied. In contrast to the bimodal distribution of GC3 (GC content in third codon position) in grasses, non-grass monocots showed a unimodal distribution. Disproportionate use of G and C (and of A and T) in two- and four-codon amino acids detected in the analysis rules out the mutational bias hypothesis as an explanation of genomic variation in GC content. There was found to be a positive relationship between CAI (codon adaptation index; predicts the level of expression of a gene) and GC3. In addition, a strong correlation was observed between coding and genomic GC content and negative correlation of GC3 with gene length, indicating a strong impact of GC-biased gene conversion (gBGC) in shaping codon usage and nucleotide composition in non-grass monocots. CONCLUSION Optimal codons in these non-grass monocots show a preference for G/C in the third codon position. These results support the concept that codon usage and nucleotide composition in non-grass monocots are mainly driven by gBGC.
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Affiliation(s)
- Purabi Mazumdar
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
| | - RofinaYasmin Binti Othman
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Katharina Mebus
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
| | - N Ramakrishnan
- Electrical and Computer System Engineering, School of Engineering, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Jennifer Ann Harikrishna
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur, Malaysia
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- For correspondence. E-mail:
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Wen Y, Zou Z, Li H, Xiang Z, He N. Analysis of codon usage patterns in Morus notabilis based on genome and transcriptome data. Genome 2017; 60:473-484. [PMID: 28177830 DOI: 10.1139/gen-2016-0129] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Codons play important roles in regulating gene expression levels and mRNA half-lives. However, codon usage and related studies in multicellular organisms still lag far behind those in unicellular organisms. In this study, we describe for the first time genome-wide patterns of codon bias in Morus notabilis (mulberry tree), and analyze genome-wide codon usage in 12 other species within the order Rosales. The codon usage of M. notabilis was affected by nucleotide composition, mutation pressure, nature selection, and gene expression level. Translational selection optimal codons were identified and highly expressed genes of M. notabilis tended to use the optimal codons. Genes with higher expression levels have shorter coding region and lower amino acid complexity. Housekeeping genes showed stronger translational selection, which, notably, was not caused by the large differences between the expression level of housekeeping genes and other genes.
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Affiliation(s)
- Yan Wen
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, China
| | - Ziliang Zou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, China
| | - Hongshun Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, China
| | - Zhonghuai Xiang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, China
| | - Ningjia He
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, China.,State Key Laboratory of Silkworm Genome Biology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, China
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