{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T06:17:04Z","timestamp":1772173024958,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1009539","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,6,29]],"date-time":"2022-06-29T00:00:00Z","timestamp":1656460800000}}],"reference-count":75,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2022,6,16]],"date-time":"2022-06-16T00:00:00Z","timestamp":1655337600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    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\n                    <jats:italic>Arabidopsis<\/jats:italic>\n                    plant. Specific amino acid changes in the ACD11 protein\u2019s 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.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1009539","type":"journal-article","created":{"date-parts":[[2022,6,16]],"date-time":"2022-06-16T13:54:27Z","timestamp":1655387667000},"page":"e1009539","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":4,"title":["Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach"],"prefix":"10.1371","volume":"18","author":[{"given":"Mahmudul Hasan","family":"Rifat","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4573-5196","authenticated-orcid":true,"given":"Jamil","family":"Ahmed","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1708-6165","authenticated-orcid":true,"given":"Milad","family":"Ahmed","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9322-6831","authenticated-orcid":true,"given":"Foeaz","family":"Ahmed","sequence":"additional","affiliation":[]},{"given":"Airin","family":"Gulshan","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4761-2111","authenticated-orcid":true,"given":"Mahmudul","family":"Hasan","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,6,16]]},"reference":[{"key":"pcbi.1009539.ref001","doi-asserted-by":"crossref","first-page":"826","DOI":"10.1038\/35081161","article-title":"Plant pathogens and integrated defence responses to infection","volume":"411","author":"JL Dangl","year":"2001","journal-title":"Nature"},{"key":"pcbi.1009539.ref002","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1146\/annurev.genet.37.110801.142628","article-title":"Recognition and response in the plant immune system","volume":"37","author":"Z Nimchuk","year":"2003","journal-title":"Annu Rev Genet"},{"key":"pcbi.1009539.ref003","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1146\/annurev.genet.31.1.547","article-title":"Use of Arabidopsis for genetic dissection of plant defense responses","volume":"31","author":"J Glazebrook","year":"1997","journal-title":"Annu Rev Genet"},{"key":"pcbi.1009539.ref004","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1105\/tpc.9.7.1157","article-title":"Programmed cell death in plants","volume":"9","author":"RI Pennell","year":"1997","journal-title":"Plant Cell"},{"key":"pcbi.1009539.ref005","doi-asserted-by":"crossref","first-page":"3321","DOI":"10.1093\/jxb\/err031","article-title":"Salicylic acid beyond defence: its role in plant growth and development","volume":"62","author":"M Rivas-San Vicente","year":"2011","journal-title":"J Exp Bot"},{"key":"pcbi.1009539.ref006","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1016\/j.celrep.2013.12.023","article-title":"Arabidopsis accelerated cell death 11, ACD11, is a ceramide-1-phosphate transfer protein and intermediary regulator of phytoceramide levels","volume":"6","author":"DK Simanshu","year":"2014","journal-title":"Cell Rep"},{"key":"pcbi.1009539.ref007","first-page":"713","article-title":"Sphingolipids and cell signaling: involvement in apoptosis and atherogenesis","volume":"71","author":"OM Ipatova","year":"2006","journal-title":"Biochemistry"},{"key":"pcbi.1009539.ref008","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1101\/gad.218202","article-title":"Knockout of Arabidopsis accelerated-cell-death11 encoding a sphingosine transfer protein causes activation of programmed cell death and defense","volume":"16","author":"P Brodersen","year":"2002","journal-title":"Genes Dev"},{"key":"pcbi.1009539.ref009","doi-asserted-by":"crossref","first-page":"68","DOI":"10.3389\/fpls.2012.00068","article-title":"Sphingolipids and plant defense\/disease: the \u201cdeath\u201d connection and beyond","volume":"3","author":"R Berkey","year":"2012","journal-title":"Front Plant Sci"},{"key":"pcbi.1009539.ref010","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/j.ydbio.2007.07.021","article-title":"Disruption of sphingolipid metabolism elicits apoptosis-associated reproductive defects in Drosophila","volume":"309","author":"VH Phan","year":"2007","journal-title":"Dev Biol"},{"key":"pcbi.1009539.ref011","doi-asserted-by":"crossref","first-page":"4378","DOI":"10.1111\/j.1742-4658.2008.06584.x","article-title":"Human GLTP and mutant forms of ACD11 suppress cell death in the Arabidopsis ACD11 mutant","volume":"275","author":"NH Petersen","year":"2008","journal-title":"FEBS J"},{"key":"pcbi.1009539.ref012","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1016\/S1369-5266(02)00240-6","article-title":"Applications of single nucleotide polymorphisms in crop genetics","volume":"5","author":"A. Rafalski","year":"2002","journal-title":"Curr Opin Plant Biol"},{"key":"pcbi.1009539.ref013","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1007\/s100380200086","article-title":"SNP alleles in human disease and evolution","volume":"47","author":"BS Shastry","year":"2002","journal-title":"J Hum Genet"},{"key":"pcbi.1009539.ref014","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1038\/sj.ejhg.5201987","article-title":"Singleton SNPs in the human genome and implications for genome-wide association studies","volume":"16","author":"X Ke","year":"2008","journal-title":"Eur J Hum Genet"},{"key":"pcbi.1009539.ref015","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1007\/s00122-003-1531-6","article-title":"Mapping, genetic effects, and epistatic interaction of two bacterial canker resistance QTLs from Lycopersicon hirsutum","volume":"108","author":"GL Coaker","year":"2004","journal-title":"Theor Appl 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Assoc"},{"key":"pcbi.1009539.ref025","doi-asserted-by":"crossref","first-page":"e0188143","DOI":"10.1371\/journal.pone.0188143","article-title":"Identification and in silico analysis of functional SNPs of human TAGAP protein: A comprehensive study","volume":"13","author":"M Arshad","year":"2018","journal-title":"PloS One"},{"key":"pcbi.1009539.ref026","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1101\/gr.131201.111","article-title":"Effects of sequence variation on differential allelic transcription factor occupancy and gene expression","volume":"22","author":"TE Reddy","year":"2012","journal-title":"Genome Res"},{"key":"pcbi.1009539.ref027","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1007\/s00439-016-1654-x","article-title":"Allele-specific transcription factor binding to common and rare variants associated with disease and gene expression","volume":"135","author":"M Cavalli","year":"2016","journal-title":"Hum Genet"},{"issue":"28","key":"pcbi.1009539.ref028","first-page":"E2655","article-title":"Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato","volume":"110","author":"D Koenig","year":"2013","journal-title":"Proce Acad Sci"},{"key":"pcbi.1009539.ref029","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"HM Berman","year":"2000","journal-title":"Nucleic acids research"},{"key":"pcbi.1009539.ref030","doi-asserted-by":"crossref","first-page":"1806","DOI":"10.1105\/tpc.17.00073","article-title":"ePlant: visualizing and exploring multiple levels of data for hypothesis generation in plant biology","volume":"29","author":"J Waese","year":"2017","journal-title":"Plant Cell"},{"key":"pcbi.1009539.ref031","doi-asserted-by":"crossref","first-page":"1064","DOI":"10.1093\/nar\/gkw1041","article-title":"SUBA4: the interactive data analysis centre for Arabidopsis 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epigenetic and genetic regulation of transcription in seed","volume":"41","author":"K Nakabayashi","year":"2005","journal-title":"Plant J"},{"key":"pcbi.1009539.ref039","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1111\/j.1365-313X.2005.02355.x","article-title":"Laser capture microdissection for the analysis of gene expression during embryogenesis of Arabidopsis","volume":"42","author":"S Casson","year":"2005","journal-title":"Plant J"},{"key":"pcbi.1009539.ref040","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-7-137","article-title":"How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results","volume":"7","author":"FF Millenaar","year":"2006","journal-title":"BMC Bioinform"},{"key":"pcbi.1009539.ref041","doi-asserted-by":"crossref","first-page":"D575","DOI":"10.1093\/nar\/gkh133","article-title":"NASCArrays: a repository for microarray data generated by NASC\u2019s transcriptomics service","volume":"32","author":"DJ Craigon","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1009539.ref042","doi-asserted-by":"crossref","first-page":"1649","DOI":"10.1104\/pp.105.070805","article-title":"Cuticular lipid composition, surface structure, and gene expression in Arabidopsis stem epidermis","volume":"139","author":"MC Suh","year":"2005","journal-title":"Plant Physiol"},{"key":"pcbi.1009539.ref043","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1007\/s00497-005-0009-x","article-title":"Expression profiling of Arabidopsis stigma tissue identifies stigma-specific genes","volume":"18","author":"R Swanson","year":"2005","journal-title":"Sex Plant Reprod"},{"key":"pcbi.1009539.ref044","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2004-5-11-r85","article-title":"Transcriptome analysis of haploid male gametophyte development in Arabidopsis","volume":"5","author":"D Honys","year":"2004","journal-title":"Genome Biol"},{"key":"pcbi.1009539.ref045","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1017\/S0007485307005160","article-title":"Exploring plant responses to aphid feeding using a full Arabidopsis microarray reveals a small number of genes with significantly altered expression","volume":"97","author":"C Couldridge","year":"2007","journal-title":"Bull Entomol Res"},{"key":"pcbi.1009539.ref046","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1111\/j.1365-313X.2007.03052.x","article-title":"The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses","volume":"50","author":"J Kilian","year":"2007","journal-title":"Plant J"},{"key":"pcbi.1009539.ref047","doi-asserted-by":"crossref","first-page":"W452","DOI":"10.1093\/nar\/gks539","article-title":"SIFT web server: predicting effects of amino acid substitutions on proteins","volume":"40","author":"NL Sim","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1009539.ref048","doi-asserted-by":"crossref","first-page":"3812","DOI":"10.1093\/nar\/gkg509","article-title":"SIFT: Predicting amino acid changes that affect protein function","volume":"31","author":"PC Ng","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1009539.ref049","doi-asserted-by":"crossref","first-page":"D394","DOI":"10.1093\/nar\/gkaa1106","article-title":"PANTHER Version 16: A Revised Family Classification, Tree-Based Classification Tool, Enhancer Regions and Extensive API","volume":"49","author":"H Mi","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1009539.ref050","doi-asserted-by":"crossref","first-page":"2745","DOI":"10.1093\/bioinformatics\/btv195","article-title":"PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels","volume":"31","author":"Y Choi","year":"2015","journal-title":"Bioinformatics"},{"key":"pcbi.1009539.ref051","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/nmeth0410-248","article-title":"A method and server for predicting damaging missense mutations","volume":"7","author":"IA Adzhubei","year":"2010","journal-title":"Nat Methods"},{"key":"pcbi.1009539.ref052","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1093\/protein\/12.5.387","article-title":"PSIC: profile extraction from sequence alignments with position-specific counts of independent observations","volume":"12","author":"SR Sunyaev","year":"1999","journal-title":"Protein Eng"},{"key":"pcbi.1009539.ref053","doi-asserted-by":"crossref","first-page":"D465","DOI":"10.1093\/nar\/gkr1181","article-title":"Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis","volume":"40","author":"J Lees","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1009539.ref054","doi-asserted-by":"crossref","first-page":"D380","DOI":"10.1093\/nar\/gkn762","article-title":"SUPERFAMILY-comparative genomics, datamining and sophisticated visualisation","volume":"37","author":"D Wilson","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1009539.ref055","doi-asserted-by":"crossref","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: The protein families database in 2021","volume":"49","author":"J Mistry","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1009539.ref056","doi-asserted-by":"crossref","first-page":"D387","DOI":"10.1093\/nar\/gkn750","article-title":"The SWISS-MODEL Repository and associated resources","volume":"37","author":"F Kiefer","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1009539.ref057","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1002\/0471250953.bi0508s52","article-title":"Protein structure and function prediction using I-TASSER","volume":"52","author":"J Yang","year":"2015","journal-title":"Curr Protoc Bioinformatics"},{"key":"pcbi.1009539.ref058","first-page":"1511","article-title":"ERRAT: an empirical atom-based method for validating protein structures","volume":"2","author":"C Colovos","year":"1993","journal-title":"Protein Sci"},{"key":"pcbi.1009539.ref059","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1126\/science.1853201","article-title":"A method to identify protein sequences that fold into a known three-dimensional structure","volume":"253","author":"JU Bowie","year":"1991","journal-title":"Science"},{"key":"pcbi.1009539.ref060","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1038\/356083a0","article-title":"Assessment of protein models with three-dimensional profiles","volume":"356","author":"R L\u00fcthy","year":"1992","journal-title":"Nature"},{"key":"pcbi.1009539.ref061","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1107\/S0021889892009944","article-title":"PROCHECK: a program to check the stereochemical quality of protein structures","volume":"26","author":"RA Laskowski","year":"1993","journal-title":"J Appl Crystallogr"},{"key":"pcbi.1009539.ref062","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1016\/j.jmb.2016.12.004","article-title":"Arpeggio: a web server for calculating and visualising interatomic interactions in protein structures","volume":"429","author":"HC Jubb","year":"2017","journal-title":"J Mol Biol"},{"key":"pcbi.1009539.ref063","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1006\/meth.1999.0922","article-title":"Automated docking of ligands to antibodies: methods and applications","volume":"20","author":"CA Sotriffer","year":"2000","journal-title":"Methods"},{"key":"pcbi.1009539.ref064","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1016\/j.jplph.2008.08.003","article-title":"Identification of proteins interacting with Arabidopsis ACD11","volume":"166","author":"NH Petersen","year":"2009","journal-title":"J Plant Physiol"},{"key":"pcbi.1009539.ref065","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gb-2009-10-5-107","article-title":"The 1001 genomes project for Arabidopsis thaliana","volume":"10","author":"D Weigel","year":"2009","journal-title":"Genome Biol"},{"key":"pcbi.1009539.ref066","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1038\/nrg.2016.99","article-title":"1001 genomes and epigenomes","volume":"17","author":"L. Koch","year":"2016","journal-title":"Nat Rev Genet"},{"key":"pcbi.1009539.ref067","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2164-13-S4-S4","article-title":"Predict impact of single amino acid change upon protein structure","volume":"13","author":"C Schaefer","year":"2012","journal-title":"BMC Genom"},{"key":"pcbi.1009539.ref068","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.sbi.2015.01.003","article-title":"Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins","volume":"32","author":"TG Kucukkal","year":"2015","journal-title":"Curr Opin Struct Biol"},{"key":"pcbi.1009539.ref069","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1016\/j.jmb.2005.10.031","article-title":"Structural evidence for adaptive ligand binding of glycolipid transfer protein","volume":"355","author":"TT Airenne","year":"2006","journal-title":"J Mol Biol"},{"key":"pcbi.1009539.ref070","doi-asserted-by":"crossref","first-page":"2531","DOI":"10.1074\/jbc.M116.760256","article-title":"Phosphatidylserine stimulates ceramide 1-phosphate (C1P) intermembrane transfer by C1P transfer proteins","volume":"292","author":"X Zhai","year":"2017","journal-title":"J Biol Chem"},{"key":"pcbi.1009539.ref071","doi-asserted-by":"crossref","first-page":"746","DOI":"10.1016\/j.bbalip.2007.01.011","article-title":"Glycolipid transfer proteins","volume":"1771","author":"RE Brown","year":"2007","journal-title":"Biochim Biophys Acta Mol Cell Biol Lipids"},{"key":"pcbi.1009539.ref072","doi-asserted-by":"crossref","first-page":"e1001137","DOI":"10.1371\/journal.ppat.1001137","article-title":"Autoimmunity in Arabidopsis acd11 is mediated by epigenetic regulation of an immune receptor","volume":"6","author":"K Palma","year":"2010","journal-title":"PLoS Pathog"},{"key":"pcbi.1009539.ref073","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-11-548","article-title":"Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces","volume":"11","author":"H Venselaar","year":"2010","journal-title":"BMC Bioinform"},{"key":"pcbi.1009539.ref074","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1111\/jfbc.12058","article-title":"The Role of Ethylene and Calcium in Programmed Cell Death of Cold-Stored Cucumber Fruit","volume":"38","author":"J Chen","year":"2014","journal-title":"J Food Biochem"},{"key":"pcbi.1009539.ref075","doi-asserted-by":"crossref","first-page":"1392","DOI":"10.1126\/science.1126410","article-title":"An SNP caused loss of seed shattering during rice domestication","volume":"312","author":"S Konishi","year":"2006","journal-title":"Science"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1009539","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,6,29]],"date-time":"2022-06-29T00:00:00Z","timestamp":1656460800000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1009539","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,6,29]],"date-time":"2022-06-29T13:43:09Z","timestamp":1656510189000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1009539"}},"subtitle":[],"editor":[{"given":"Inna","family":"Lavrik","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,6,16]]},"references-count":75,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2022,6,16]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1009539","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.10.08.463616","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,6,16]]}}}