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Dossou SSK, Song S, Liu A, Li D, Zhou R, Berhe M, Zhang Y, Sheng C, Wang Z, You J, Wang L. Resequencing of 410 Sesame Accessions Identifies SINST1 as the Major Underlying Gene for Lignans Variation. Int J Mol Sci 2023; 24:1055. [PMID: 36674569 PMCID: PMC9860558 DOI: 10.3390/ijms24021055] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
Sesame is a promising oilseed crop that produces specific lignans of clinical importance. Hence, a molecular description of the regulatory mechanisms of lignan biosynthesis is essential for crop improvement. Here, we resequence 410 sesame accessions and identify 5.38 and 1.16 million SNPs (single nucleotide polymorphisms) and InDels, respectively. Population genomic analyses reveal that sesame has evolved a geographic pattern categorized into northern (NC), middle (MC), and southern (SC) groups, with potential origin in the southern region and subsequent introduction to the other regions. Selective sweeps analysis uncovers 120 and 75 significant selected genomic regions in MC and NC groups, respectively. By screening these genomic regions, we unveiled 184 common genes positively selected in these subpopulations for exploitation in sesame improvement. Genome-wide association study identifies 17 and 72 SNP loci for sesamin and sesamolin variation, respectively, and 11 candidate causative genes. The major pleiotropic SNPC/A locus for lignans variation is located in the exon of the gene SiNST1. Further analyses revealed that this locus was positively selected in higher lignan content sesame accessions, and the "C" allele is favorable for a higher accumulation of lignans. Overexpression of SiNST1C in sesame hairy roots significantly up-regulated the expression of SiMYB58, SiMYB209, SiMYB134, SiMYB276, and most of the monolignol biosynthetic genes. Consequently, the lignans content was significantly increased, and the lignin content was slightly increased. Our findings provide insights into lignans and lignin regulation in sesame and will facilitate molecular breeding of elite varieties and marker-traits association studies.
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Affiliation(s)
- Senouwa Segla Koffi Dossou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Laboratory of Plant Physiology and Biotechnologies, Faculty of Sciences, University of Lomé, Lomé 01BP 1515, Togo
| | - Shengnan Song
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Aili Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Donghua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Muez Berhe
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yanxin Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Chen Sheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Zhijian Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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Rifat MH, Ahmed J, Ahmed M, Ahmed F, Gulshan A, Hasan M. Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach. PLoS Comput Biol 2022; 18:e1009539. [PMID: 35709304 PMCID: PMC9242461 DOI: 10.1371/journal.pcbi.1009539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 06/29/2022] [Accepted: 05/09/2022] [Indexed: 11/18/2022] Open
Abstract
Accelerated cell death 11 (ACD11) is an autoimmune gene that suppresses pathogen infection in plants by preventing plant cells from becoming infected by any pathogen. This gene is widely known for growth inhibition, premature leaf chlorosis, and defense-related programmed cell death (PCD) in seedlings before flowering in Arabidopsis plant. Specific amino acid changes in the ACD11 protein’s highly conserved domains are linked to autoimmune symptoms including constitutive defensive responses and necrosis without pathogen awareness. The molecular aspect of the aberrant activity of the ACD11 protein is difficult to ascertain. The purpose of our study was to find the most deleterious mutation position in the ACD11 protein and correlate them with their abnormal expression pattern. Using several computational methods, we discovered PCD vulnerable single nucleotide polymorphisms (SNPs) in ACD11. We analysed the RNA-Seq data, identified the detrimental nonsynonymous SNPs (nsSNP), built genetically mutated protein structures and used molecular docking to assess the impact of mutation. Our results demonstrated that the A15T and A39D mutations in the GLTP domain were likely to be extremely detrimental mutations that inhibit the expression of the ACD11 protein domain by destabilizing its composition, as well as disrupt its catalytic effectiveness. When compared to the A15T mutant, the A39D mutant was more likely to destabilize the protein structure. In conclusion, these mutants can aid in the better understanding of the vast pool of PCD susceptibilities connected to ACD11 gene GLTP domain activation. Non synonymous single nucleotide polymorphism (nsSNP) is a process in which amino acid sequence of a protein is altered as a result of single nucleotide alteration in the coding region (mRNA) of any living organism. Therefore, the entire protein structure, interactions and stability are altered, which may have a negative impact on living organisms. Hence, to completely comprehend this biological process, we must first solve the unresolved mutational protein structure and mutated protein interactions. The major goal of our research is to identify the most harmful mutation in our target protein structure and how it interacts within cells. However, it was discovered that only a few alterations in residues had the largest negative impact on the protein’s internal structure and also on the protein-ligand interactions. We show that based on the amino acid sequence of a protein computationally, it is feasible to discover mutational positions in the sequence, generate mutation protein structure and interactions with related ligands. Our findings show that the essential mechanisms underlying protein mutations generated by this process are identical. The capacity to correctly detect mutations from sequence allows the annotation and study of protein-ligand interactions throughout a whole organism, which might aid function prediction and gene expression.
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Affiliation(s)
| | - Jamil Ahmed
- Department of Biochemistry and Chemistry, Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
- * E-mail:
| | - Milad Ahmed
- Department of Animal and Fish Biotechnology, Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Foeaz Ahmed
- Department of Molecular Biology and Genetic Engineering, Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Airin Gulshan
- Department of Pharmaceuticals and Industrial Biotechnology, Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
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Tambe V, Patel S, Shard A, Behera SK, Polaka S, Anup N, Gadeval A, Kalia K, Tekade RK. Dendronized Polymeric Biomaterial for Loading, Stabilization, and Targeted Cytosolic Delivery of microRNA in Cancer Cells. ACS APPLIED BIO MATERIALS 2022. [DOI: 10.1021/acsabm.2c00179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vishakha Tambe
- Department of Pharmaceutics, Department of Pharmaceuticals, Ministry of Chem-icals and Fertilizers, National Institute of Pharmaceutical Education and Research (NIPER)─Ahmedabad, An Institute of National Importance, Government of India, Palaj, Opp. Air Force Station, Gandhinagar 382355, Gujarat, India
| | - Sagarkumar Patel
- Department of Medicinal Chemistry, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, National Institute of Pharmaceutical Education and Research (NIPER)─Ahmedabad, An Institute of National Importance, Government of India, Palaj, Opp. Air Force Station, Gandhinagar 382355, Gujarat, India
| | - Amit Shard
- Department of Medicinal Chemistry, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, National Institute of Pharmaceutical Education and Research (NIPER)─Ahmedabad, An Institute of National Importance, Government of India, Palaj, Opp. Air Force Station, Gandhinagar 382355, Gujarat, India
| | - Santosh Kumar Behera
- Central Instrumentation Facility, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, National Institute of Pharmaceutical Education and Research (NIPER)─Ahmedabad, An Institute of National Importance, Government of India, Palaj, Opp. Air Force Station, Gandhinagar 382355, Gujarat, India
| | - Suryanarayana Polaka
- Department of Pharmaceutics, Department of Pharmaceuticals, Ministry of Chem-icals and Fertilizers, National Institute of Pharmaceutical Education and Research (NIPER)─Ahmedabad, An Institute of National Importance, Government of India, Palaj, Opp. Air Force Station, Gandhinagar 382355, Gujarat, India
| | - Neelima Anup
- Department of Pharmaceutics, Department of Pharmaceuticals, Ministry of Chem-icals and Fertilizers, National Institute of Pharmaceutical Education and Research (NIPER)─Ahmedabad, An Institute of National Importance, Government of India, Palaj, Opp. Air Force Station, Gandhinagar 382355, Gujarat, India
| | - Anuradha Gadeval
- Department of Pharmaceutics, Department of Pharmaceuticals, Ministry of Chem-icals and Fertilizers, National Institute of Pharmaceutical Education and Research (NIPER)─Ahmedabad, An Institute of National Importance, Government of India, Palaj, Opp. Air Force Station, Gandhinagar 382355, Gujarat, India
| | - Kiran Kalia
- Department of Biotechnology, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, National Institute of Pharmaceutical Education and Research (NIPER)─Ahmedabad, An Institute of National Importance, Government of India, Palaj, Opp. Air Force Station, Gandhinagar 382355, Gujarat, India
| | - Rakesh Kumar Tekade
- Department of Pharmaceutics, Department of Pharmaceuticals, Ministry of Chem-icals and Fertilizers, National Institute of Pharmaceutical Education and Research (NIPER)─Ahmedabad, An Institute of National Importance, Government of India, Palaj, Opp. Air Force Station, Gandhinagar 382355, Gujarat, India
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4
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Amiteye S. Basic concepts and methodologies of DNA marker systems in plant molecular breeding. Heliyon 2021; 7:e08093. [PMID: 34765757 PMCID: PMC8569399 DOI: 10.1016/j.heliyon.2021.e08093] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/25/2021] [Accepted: 09/27/2021] [Indexed: 12/27/2022] Open
Abstract
The concepts, methodologies and applications of some of the major molecular or DNA markers commonly used in plant science have been presented. The general principles of molecular marker techniques have been elucidated with detailed explanation of some notable basic concepts associated with marker applications: marker polymorphism, dominant or co-dominant mode of inheritance, agronomic trait-marker linkage, genetic mutations and variation. The molecular marker methods that have been extensively reviewed are RFLP, RAPD, SCAR, AFLP, SSR, CpSSR, ISSR, RAMP, SAMPL, SRAP, SSCP, CAPS, SNP, DArT, EST, and STS. In addition, the practicality of the retrotransposon-based marker methods, IRAP, REMAP, RBIP, and IPBS, have been discussed. Moreover, some salient characteristics of DNA markers have been compared and the various marker systems classified as PCR- or non-PCR-based, dominantly or co-dominantly inherited, locus specific or non-specific as well as at the levels of marker polymorphism and efficiency of marker reproducibility. Furthermore, the principles and methods of the following DNA markers have been highlighted: Penta-primer amplification refractory mutation system (PARMS), Conserved DNA-Derived Polymorphism (CDDP), P450-based analogue (PBA) markers, Tubulin-Based Polymorphism (TBP), Inter-SINE amplified polymorphism (ISAP), Sequence specific amplified polymorphism (S-SAP), Intron length polymorphisms (ILPs), Inter small RNA polymorphism (iSNAP), Direct amplification of length polymorphisms (DALP), Promoter anchored amplified polymorphism (PAAP), Target region amplification polymorphism (TRAP), Conserved region amplification polymorphism (CoRAP), Start Codon Targeted (SCoT) Polymorphism, and Directed Amplification of Minisatellite DNA (DAMD). Some molecular marker applications that have been recently employed to achieve various objectives in plant research have also been outlined. This review will serve as a useful reference resource for plant breeders and other scientists, as well as technicians and students who require basic know-how in the use of molecular or DNA marker technologies.
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Affiliation(s)
- Samuel Amiteye
- Department of Nuclear Agriculture and Radiation Processing (NARP), Graduate School of Nuclear and Allied Sciences (SNAS), College of Basic and Applied Sciences, University of Ghana, P. O. Box AE 1, Accra, Ghana
- Biotechnology Centre, Biotechnology and Nuclear Agriculture Research Institute (BNARI), Ghana Atomic Energy Commission (GAEC), P. O. Box AE 50, Accra, Ghana
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5
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Pandey J, Scheuring DC, Koym JW, Coombs J, Novy RG, Thompson AL, Holm DG, Douches DS, Miller JC, Vales MI. Genetic diversity and population structure of advanced clones selected over forty years by a potato breeding program in the USA. Sci Rep 2021; 11:8344. [PMID: 33863959 PMCID: PMC8052460 DOI: 10.1038/s41598-021-87284-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 03/24/2021] [Indexed: 01/12/2023] Open
Abstract
Knowledge regarding genetic diversity and population structure of breeding materials is essential for crop improvement. The Texas A&M University Potato Breeding Program has a collection of advanced clones selected and maintained in-vitro over a 40-year period. Little is known about its genetic makeup and usefulness for the current breeding program. In this study, 214 potato clones were genotyped with the Infinium Illumina 22 K V3 Potato Array. After filtering, a total of 10,106 single nucleotide polymorphic (SNP) markers were used for analysis. Heterozygosity varied by SNP, with an overall average of 0.59. Three groups of tetraploid clones primarily based on potato market classes, were detected using STRUCTURE software and confirmed by discriminant analysis of principal components.
The highest coefficient of differentiation observed between the groups was 0.14. Signatures of selection were uncovered in genes controlling potato flesh and skin color, length of plant cycle and tuberization, and carbohydrate metabolism. A core set of 43 clones was obtained using Core Hunter 3 to develop a sub-collection that retains similar genetic diversity as the whole population, minimize redundancies, and facilitates long-term conservation of genetic resources. The comprehensive molecular characterization of our breeding clone bank collection contributes to understanding the genetic diversity of existing potato resources. This analysis could be applied to other breeding programs and assist in the selection of parents, fingerprinting, protection, and management of the breeding collections.
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Affiliation(s)
- Jeewan Pandey
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843-2133, USA
| | - Douglas C Scheuring
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843-2133, USA
| | - Jeffrey W Koym
- Texas A&M AgriLife Research and Extension Center, Lubbock, TX, 79403, USA
| | - Joseph Coombs
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Richard G Novy
- USDA-Agricultural Research Service, Small Grains and Potato Germplasm Research, Aberdeen, ID, 83210, USA
| | - Asunta L Thompson
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - David G Holm
- San Luis Valley Research Center, Department of Horticulture and Landscape Architecture, Colorado State University, Center, CO, 81125, USA
| | - David S Douches
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - J Creighton Miller
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843-2133, USA
| | - M Isabel Vales
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843-2133, USA.
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6
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Zhang K, He M, Fan Y, Zhao H, Gao B, Yang K, Li F, Tang Y, Gao Q, Lin T, Quinet M, Janovská D, Meglič V, Kwiatkowski J, Romanova O, Chrungoo N, Suzuki T, Luthar Z, Germ M, Woo SH, Georgiev MI, Zhou M. Resequencing of global Tartary buckwheat accessions reveals multiple domestication events and key loci associated with agronomic traits. Genome Biol 2021; 22:23. [PMID: 33430931 PMCID: PMC7802136 DOI: 10.1186/s13059-020-02217-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 12/03/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Tartary buckwheat (Fagopyrum tataricum) is a nutritionally balanced and flavonoid-rich crop plant that has been in cultivation for 4000 years and is now grown globally. Despite its nutraceutical and agricultural value, the characterization of its genetics and its domestication history is limited. RESULTS Here, we report a comprehensive database of Tartary buckwheat genomic variation based on whole-genome resequencing of 510 germplasms. Our analysis suggests that two independent domestication events occurred in southwestern and northern China, resulting in diverse characteristics of modern Tartary buckwheat varieties. Genome-wide association studies for important agricultural traits identify several candidate genes, including FtUFGT3 and FtAP2YT1 that significantly correlate with flavonoid accumulation and grain weight, respectively. CONCLUSIONS We describe the domestication history of Tartary buckwheat and provide a detailed resource of genomic variation to allow for genomic-assisted breeding in the improvement of elite cultivars.
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Affiliation(s)
- Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Ming He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Yu Fan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Hui Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Bin Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Keli Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Faliang Li
- Research Station of Alpine Crop, Xichang Institute of Agricultural Sciences, Liangshan, 616150 Sichuan China
| | - Yu Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 58083 Guangdong China
| | - Tao Lin
- College of Horticulture, China Agricultural University, Beijing, 100083 China
| | - Muriel Quinet
- Groupe de Recherche en Physiologie Végétale (GRPV), Earth and Life Institute-Agronomy (ELI-A), Université catholique de Louvain, Croix du Sud 45, boîte L7.07.13, B-1348 Louvain-la-Neuve, Belgium
| | - Dagmar Janovská
- Gene Bank, Crop Research Institute, Drnovská 507, Prague 6, Czech Republic
| | - Vladimir Meglič
- Agricultural Institute of Slovenia, Hacquetova ulica, Ljubljana, Slovenia
| | - Jacek Kwiatkowski
- Department of Plant Breeding and Seed Production, University of Warmia and Mazury in Olsztyn, Plac Łódzki 3, 10-724 Olsztyn, Poland
| | - Olga Romanova
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), Bol’shaya Morskaya, 42-44, St. Petersburg, Russia 190000
| | - Nikhil Chrungoo
- Department of Botany, North Eastern Hill University, Shillong, 793022 India
| | - Tatsuro Suzuki
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Suya 2421, Koshi, Kumamoto 861-1192 Japan
| | - Zlata Luthar
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Mateja Germ
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Sun-Hee Woo
- Department of Crop Science, Chungbuk National University, Cheong-ju, Republic of Korea
| | - Milen I. Georgiev
- Group of Plant Cell Biotechnology and Metabolomics, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Plovdiv, Bulgaria
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
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7
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Ramos MJN, Coito JL, Faísca-Silva D, Cunha J, Costa MMR, Amâncio S, Rocheta M. Portuguese wild grapevine genome re-sequencing (Vitis vinifera sylvestris). Sci Rep 2020; 10:18993. [PMID: 33149248 PMCID: PMC7642406 DOI: 10.1038/s41598-020-76012-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 10/06/2020] [Indexed: 12/30/2022] Open
Abstract
The first genome of Vitis vinifera vinifera (PN40024), published in 2007, boosted grapevine related studies. While this reference genome is a suitable tool for the overall studies in the field, it lacks the ability to unveil changes accumulated during V. v. vinifera domestication. The subspecies V. v. sylvestris preserves wild characteristics, making it a good material to provide insights into V. v. vinifera domestication. The difference in the reproductive strategy between both subspecies is one of the characteristics that set them apart. While V. v. vinifera flowers are hermaphrodite, V. v. sylvestris is mostly dioecious. In this paper, we compare the re-sequencing of the genomes from a male and a female individual of the wild sylvestris, against the reference vinifera genome (PN40024). Variant analysis reveals a low number but with high impact modifications in coding regions, essentially non-synonymous single nucleotide polymorphisms and frame shifts caused by insertions and deletions. The sex-locus was manually inspected, and the results obtained are in line with the most recent works related with wild grapevine sex. In this paper we also describe for the first time RNA editing in transcripts of 14 genes in the sex-determining region, including VviYABBY and VviPLATZ.
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Affiliation(s)
- Miguel J N Ramos
- LEAF (Linking Landscape, Environment, Agriculture and Food) Research Center, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal.
| | - João L Coito
- LEAF (Linking Landscape, Environment, Agriculture and Food) Research Center, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - David Faísca-Silva
- LEAF (Linking Landscape, Environment, Agriculture and Food) Research Center, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Jorge Cunha
- Instituto Nacional de Investigação Agrária E Veterinária, Quinta d'Almoinha, 2565-191, Dois Portos, Portugal
| | - M Manuela R Costa
- Plant Functional Biology Centre, Biosystems and Integrative Sciences Institute, University of Minho, 4710-057, Braga, Portugal
| | - Sara Amâncio
- LEAF (Linking Landscape, Environment, Agriculture and Food) Research Center, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Margarida Rocheta
- LEAF (Linking Landscape, Environment, Agriculture and Food) Research Center, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal.
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Genome-Wide Development and Validation of Cost-Effective KASP Marker Assays for Genetic Dissection of Heat Stress Tolerance in Maize. Int J Mol Sci 2020; 21:ijms21197386. [PMID: 33036291 PMCID: PMC7582619 DOI: 10.3390/ijms21197386] [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: 07/15/2020] [Revised: 08/24/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023] Open
Abstract
Maize is the third most important cereal crop worldwide. However, its production is vulnerable to heat stress, which is expected to become more and more severe in coming years. Germplasm resilient to heat stress has been identified, but its underlying genetic basis remains poorly understood. Genomic mapping technologies can fill the void, provided robust markers are available to tease apart the genotype-phenotype relationship. In the present investigation, we used data from an RNA-seq experiment to identify single nucleotide polymorphisms (SNPs) between two contrasting lines, LM11 and CML25, sensitive and tolerant to heat stress, respectively. The libraries for RNA-seq were made following heat stress treatment from three separate tissues/organs, comprising the top leaf, ovule, and pollen, all of which are highly vulnerable to damage by heat stress. The single nucleotide variants (SNVs) calling used STAR mapper and GATK caller pipelines in a combined approach to identify highly accurate SNPs between the two lines. A total of 554,423, 410,698, and 596,868 SNVs were discovered between LM11 and CML25 after comparing the transcript sequence reads from the leaf, pollen, and ovule libraries, respectively. Hundreds of these SNPs were then selected to develop into genome-wide Kompetitive Allele-Specific PCR (KASP) markers, which were validated to be robust with a successful SNP conversion rate of 71%. Subsequently, these KASP markers were used to effectively genotype an F2 mapping population derived from a cross of LM11 and CML25. Being highly cost-effective, these KASP markers provide a reliable molecular marker toolkit to not only facilitate the genetic dissection of the trait of heat stress tolerance but also to accelerate the breeding of heat-resilient maize by marker-assisted selection (MAS).
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9
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Guajardo V, Solís S, Almada R, Saski C, Gasic K, Moreno MÁ. Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function. Sci Rep 2020; 10:1467. [PMID: 32001784 PMCID: PMC6992769 DOI: 10.1038/s41598-020-58271-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/15/2019] [Indexed: 01/09/2023] Open
Abstract
Genotyping-by-Sequencing (GBS) was applied in a set of 53 diploid Prunus rootstocks and five scion cultivars from three subgenera (Amygdalus, Prunus and Cerasus) for genome-wide SNP identification and to assess genetic diversity of both Chilean and Spanish germplasm collections. A group of 45,382 high quality SNPs (MAF >0.05; missing data <5%) were selected for analysis of this group of 58 accessions. These SNPs were distributed in genic and intergenic regions in the eight pseudomolecules of the peach genome (Peach v2.0), with an average of 53% located in exonic regions. The genetic diversity detected among the studied accessions divided them in three groups, which are in agreement with their current taxonomic classification. SNPs were classified based on their putative effect on annotated genes and KOG analysis was carried out to provide a deeper understanding of the function of 119 genes affected by high-impact SNPs. Results demonstrate the high utility for Prunus rootstocks identification and studies of diversity in Prunus species. Also, given the high number of SNPs identified in exonic regions, this strategy represents an important tool for finding candidate genes underlying traits of interest and potential functional markers for use in marker-assisted selection.
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Affiliation(s)
| | - Simón Solís
- Centro de Estudios Avanzados en Fruticultura (CEAF), Rengo, Chile
| | - Rubén Almada
- Centro de Estudios Avanzados en Fruticultura (CEAF), Rengo, Chile
| | - Christopher Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Ksenija Gasic
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, 29634, USA
| | - María Ángeles Moreno
- Department of Pomology, Estación Experimental de Aula Dei-CSIC, 50059, Zaragoza, Spain.
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Kolli V, Paul S, Guttula PK, Sarkar N. Elucidating the Role of Val-Asn 95 and Arg-Gly 52 Mutations on Structure and Stability of Fibroblast Growth Factor Homologous Factor 2. Protein Pept Lett 2019; 26:848-859. [PMID: 37020363 DOI: 10.2174/0929866526666190503092718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/11/2019] [Accepted: 04/19/2019] [Indexed: 11/22/2022]
Abstract
Background:
Fibroblast growth Factor Homologous Factors (FHFs) belong to a subclass
of Fibroblast Growth Factor (FGF) family owing to their high sequence and structural similarities
with FGFs. However, despite these similarities, there are properties which set them apart from
FGFs. FHFs lack the secretion signal sequence unlike other FGF members, except FGF1 and 2.
Unlike FGFs, FHFs are not able to bind to FGF Receptors (FGFRs) and instead have been
implicated in binding to Voltage-Gated Sodium Channels (VGSCs), neuronal MAP kinase scaffold
protein and islet-brain-2 (IB2). The two amino acids Arg-52 and Val95 are conserved in all FHFs
and mutation of these residues lead to its inability to bind with VGSC/IB2. However, it is not clear
whether the loss of binding is due to destabilization of the protein on mutation or due to
involvement of Arg52 and Val95 in conferring functionality to FHFs.
Objective:
In the present study, we have mutated these two conserved residues of FHF2 with its
corresponding FGF counterpart amino acids and studied the effects of the mutations on the
structure and stability of the protein.
Methods:
Several biophysical methods like isothermal equilibrium denaturation study, ANS
fluorescence, intrinsic fluorescence, acrylamide quenching, circular dichroism studies as well as
using computational approaches were employed.
Results:
The single mutations were found to affect the overall stability, conformation and
functionality of the protein.
Conclusion:
Thus, the studies throw light on the role of specific amino acids in deciding the
stability, structure and functionality of proteins and will be useful for development of
therapeutically engineered proteins.
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Affiliation(s)
- Vidyalatha Kolli
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela- 769008, Odisha, India
| | - Subhankar Paul
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela- 769008, Odisha, India
| | - Praveen Kumar Guttula
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela- 769008, Odisha, India
| | - Nandini Sarkar
- Department of Biotechnology and Medical Engineering, National Institute of Technology Rourkela, Rourkela- 769008, Odisha, India
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Zhou Y, Cho WK, Byun HS, Kil EJ, Bak SI, Moon DH, Chavan V, Park TS, Lee S, Hong SW. Transcriptome profiles of tomato plants after neutron irradiation and infection with TYLCV. PHYSIOLOGIA PLANTARUM 2019; 165:427-441. [PMID: 30575049 DOI: 10.1111/ppl.12913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
Ionizing radiation is ubiquitous in the environment and can cause mutagenesis in living organisms. In this study, we examined the effects of neutron irradiation on tomato plants. Neutron irradiation decreased tomato germination rates, but most irradiated tomato plants did not show any significant phenotype. However, tomato mutants infected by Tomato yellow leaf curl virus (TYLCV) displayed resistance against TYLCV compared to the wild type (WT), which showed disease symptoms. RNA-Seq data demonstrated that the expression profiles of eight tomato mutants were significantly different from that of the WT. The transcriptomes obtained from presoaked seeds were highly altered compared to those of dry seeds. Increased irradiation time resulted in severe changes in the tomato transcriptome; however, different neutron irradiation intensities affected the expressions of different sets of genes. A high number of single-nucleotide polymorphisms in tomato transcriptomes suggest that neutron irradiation strongly impacts plant transcriptomes. The transition/transversion values among mutants were almost constant and were lower than that of the non-irradiated sample (WT), suggesting that neutron irradiation caused an effect. Taken together, this is the first report showing the effects of neutron irradiation on tomato plants by transcriptome analyses.
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Affiliation(s)
- Yujie Zhou
- Department of Energy Science, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Won Kyong Cho
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hee-Seong Byun
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Eui-Joon Kil
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sang-In Bak
- Department of Energy Science, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Dal-Ho Moon
- Department of Physics, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Vivek Chavan
- Department of Physics, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Tae-Sun Park
- Department of Physics, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Seung-Woo Hong
- Department of Physics, Sungkyunkwan University, Suwon 16419, Republic of Korea
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Kim J, Manivannan A, Kim DS, Lee ES, Lee HE. Transcriptome sequencing assisted discovery and computational analysis of novel SNPs associated with flowering in Raphanus sativus in-bred lines for marker-assisted backcross breeding. HORTICULTURE RESEARCH 2019; 6:120. [PMID: 31700647 PMCID: PMC6823433 DOI: 10.1038/s41438-019-0200-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 05/08/2023]
Abstract
The sequencing of radish genome aids in the better understanding and tailoring of traits associated with economic importance. In order to accelerate the genomics assisted breeding and genetic selection, transcriptomes of 33 radish inbred lines with diverse traits were sequenced for the development of single nucleotide polymorphic (SNP) markers. The sequence reads ranged from 2,560,543,741 bp to 20,039,688,139 bp with the GC (%) of 47.80-49.34 and phred quality score (Q30) of 96.47-97.54%. A total of 4951 polymorphic SNPs were identified among the accessions after stringent filtering and 298 SNPs with efficient marker assisted backcross breeding (MAB) markers were generated from the polymorphic SNPs. Further, functional annotations of SNPs revealed the effects and importance of the SNPs identified in the flowering process. The SNPs were predominantly associated with the four major flowering related transcription factors such as MYB, MADS box (AG), AP2/EREB, and bHLH. In addition, SNPs in the vital flowering integrator gene (FT) and floral repressors (EMBRYONIC FLOWER 1, 2, and FRIGIDA) were identified among the radish inbred lines. Further, 50 SNPs were randomly selected from 298 SNPs and validated using Kompetitive Allele Specific PCR genotyping system (KASP) in 102 radish inbred lines. The homozygosity of the inbred lines varied from 56 to 96% and the phylogenetic analysis resulted in the clustering of inbred lines into three subgroups. Taken together, the SNP markers identified in the present study can be utilized for the discrimination, seed purity test, and adjusting parental combinations for breeding in radish.
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Affiliation(s)
- Jinhee Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
| | - Abinaya Manivannan
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
| | - Eun-Su Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
| | - Hye-Eun Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, 55365 Republic of Korea
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Ramakrishna G, Kaur P, Nigam D, Chaduvula PK, Yadav S, Talukdar A, Singh NK, Gaikwad K. Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits. BMC PLANT BIOLOGY 2018; 18:141. [PMID: 29986650 PMCID: PMC6038289 DOI: 10.1186/s12870-018-1341-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 06/05/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Water permeability governed by seed coat is a major facet of seed crops, especially soybean, whose seeds lack physiological dormancy and experience rapid deterioration in seed viability under prolonged storage. Moreover, the physiological and chemical characteristics of soybean seeds are known to vary with seed coat color. Thus, to underpin the genes controlling water permeability in soybean seeds, we carried out an in-depth characterization of the associated genomic variation. RESULTS In the present study, we have analyzed genomic variation between cultivated soybean and its wild progenitor with implications on seed permeability, a trait related to seed storability. Whole genome resequencing of G.max and G. soja, identified SNPs and InDels which were further characterized on the basis of their genomic location and impact on gene expression. Chromosomal density distribution of the variation was assessed across the genome and genes carrying SNPs and InDels were characterized into different metabolic pathways. Seed hardiness is a complex trait that is affected by the allelic constitution of a genetic locus as well as by a tricky web of plant hormone interactions. Seven genes that hold a probable role in the determination of seed permeability were selected and their expression differences at different stages of water imbibition were analyzed. Variant interaction network derived 205 downstream interacting partners of 7 genes confirmed their role in seed related traits. Interestingly, genes encoding for Type I- Inositol polyphosphate 5 phosphatase1 and E3 Ubiquitin ligase could differentiate parental genotypes, revealed protein conformational deformations and were found to segregate among RILs in coherence with their permeability scores. The 2 identified genes, thus showed a preliminary association with the desirable permeability characteristics. CONCLUSION In the light of above outcomes, 2 genes were identified that revealed preliminary, but a relevant association with soybean seed permeability trait and hence could serve as a primary material for understanding the molecular pathways controlling seed permeability traits in soybean.
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Affiliation(s)
- G. Ramakrishna
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Parampreet Kaur
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Deepti Nigam
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Pavan K. Chaduvula
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Sangita Yadav
- ICAR- IARI, Division of Seed Science and Technology, Pusa Campus, New Delhi, 110012 India
| | - Akshay Talukdar
- ICAR- IARI, Division of Genetics, Pusa Campus, New Delhi, India
| | - Nagendra Kumar Singh
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Kishor Gaikwad
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
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14
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Agrahari AK, Sneha P, George Priya Doss C, Siva R, Zayed H. A profound computational study to prioritize the disease-causing mutations in PRPS1 gene. Metab Brain Dis 2018; 33:589-600. [PMID: 29047041 DOI: 10.1007/s11011-017-0121-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 10/04/2017] [Indexed: 01/16/2023]
Abstract
Charcot-Marie-Tooth disease (CMT) is one of the most commonly inherited congenital neurological disorders, affecting approximately 1 in 2500 in the US. About 80 genes were found to be in association with CMT. The phosphoribosyl pyrophosphate synthetase 1 (PRPS1) is an essential enzyme in the primary stage of de novo and salvage nucleotide synthesis. The mutations in the PRPS1 gene leads to X-linked Charcot-Marie-Tooth neuropathy type 5 (CMTX5), PRS super activity, Arts syndrome, X-linked deafness-1, breast cancer, and colorectal cancer. In the present study, we obtained 20 missense mutations from UniProt and dbSNP databases and applied series of comprehensive in silico prediction methods to assess the degree of pathogenicity and stability. In silico tools predicted four missense mutations (D52H, M115 T, L152P, and D203H) to be potential disease causing mutations. We further subjected the four mutations along with native protein to 50 ns molecular dynamics simulation (MDS) using Gromacs package. The resulting trajectory files were analyzed to understand the stability differences caused by the mutations. We used the Root Mean Square Deviation (RMSD), Radius of Gyration (Rg), solvent accessibility surface area (SASA), Covariance matrix, Principal Component Analysis (PCA), Free Energy Landscape (FEL), and secondary structure analysis to assess the structural changes in the protein upon mutation. Our study suggests that the four mutations might affect the PRPS1 protein function and stability of the structure. The proposed study may serve as a platform for drug repositioning and personalized medicine for diseases that are caused by the PRPS1 deficiency.
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Affiliation(s)
- Ashish Kumar Agrahari
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - P Sneha
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - C George Priya Doss
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India.
| | - R Siva
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar.
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15
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Laddach A, Ng JCF, Chung SS, Fraternali F. Genetic variants and protein-protein interactions: a multidimensional network-centric view. Curr Opin Struct Biol 2018; 50:82-90. [PMID: 29306755 DOI: 10.1016/j.sbi.2017.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 01/18/2023]
Abstract
We review recent progress in the mapping of genetic variants to proteins, in the context of their interactions, as measured from experiments and/or computational predictions. Such variants can impact on the molecular mechanisms underlying an interaction and its stability. We highlight recent work which relies on the effective use of protein-protein interaction networks (PPINs), integrated with 3D structural information, for evaluating disease-associated variants. Furthermore, we discuss how the integration of multiple layers of biological information, in the context of PPINs, can improve the interpretation of genetic variants and inspire new therapeutic strategies.
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Affiliation(s)
- Anna Laddach
- Randall Division of Cell and Molecular Biophysics, King's College London, UK
| | - Joseph Chi-Fung Ng
- Randall Division of Cell and Molecular Biophysics, King's College London, UK
| | - Sun Sook Chung
- Randall Division of Cell and Molecular Biophysics, King's College London, UK; Department of Haematological Medicine, King's College London, UK
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, King's College London, UK.
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