title: Organellar proteome analyses of ricin toxin-treated HeLa cells.
abstract: Apoptosis triggered by ricin toxin (RT) has previously been associated with certain cellular organellar compartments, but the diversity in the composition of the organellar proteins remains unclear. Here, we applied a shotgun proteomics strategy to examine the differential expression of proteins in the mitochondria, nuclei, and cytoplasm of HeLa cells treated and not treated with RT. Data were combined with a global bioinformatics analysis and experimental confirmations. A total of 3107 proteins were identified. Bioinformatics predictors (Proteome Analyst, WoLF PSORT, TargetP, MitoPred, Nucleo, MultiLoc, and k-nearest neighbor) and a Bayesian model that integrated these predictors were used to predict the locations of 1349 distinct organellar proteins. Our data indicate that the Bayesian model was more efficient than the individual implementation of these predictors. Additionally, a Biomolecular Interaction Network (BIN) analysis was used to identify 149 BIN subnetworks. Our experimental confirmations indicate that certain apoptosis-related proteins (e.g. cytochrome c, enolase, lamin B, Bax, and Drp1) were found to be translocated and had variable expression levels. These results provide new insights for the systematic understanding of RT-induced apoptosis responses.
authors.affiliation: Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, People's Republic of China Institute of Military Veterinary Science, Academy of Military Medical Science, Changchun, Jilin Province, People's Republic of China.
authors.forename: Peng
authors.initials: P
authors.lastname: Liao
authors.affiliation: Hunan Biological and Electromechanical Polytechnic, The Party and Government Office, Changsha, Hunan Province, People's Republic of China.
authors.forename: Yunhu
authors.initials: Y
authors.lastname: Li
authors.affiliation: Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan Province, People's Republic of China.
authors.forename: Hongyang
authors.initials: H
authors.lastname: Li
authors.affiliation: Institute of Military Veterinary Science, Academy of Military Medical Science, Changchun, Jilin Province, People's Republic of China liuwensen85952@163.com.
authors.forename: Wensen
authors.initials: W
authors.lastname: Liu
mesh_terms: D017209:Apoptosis / Q000187:drug effects; D001499:Bayes Theorem; D002467:Cell Nucleus / Q000187:drug effects / Q000235:genetics; D002619:Chemical Warfare Agents / Q000633:toxicity*; D019295:Computational Biology; D045304:Cytochromes c / Q000235:genetics; D003593:Cytoplasm / Q000187:drug effects / Q000235:genetics; D034281:Dynamins; D020558:GTP Phosphohydrolases / Q000235:genetics; D006367:HeLa Cells; D006801:Humans; D034921:Lamin Type B / Q000235:genetics; D008869:Microtubule-Associated Proteins / Q000235:genetics; D008928:Mitochondria / Q000187:drug effects / Q000235:genetics; D024101:Mitochondrial Proteins / Q000235:genetics; D015388:Organelles / Q000187:drug effects / Q000235:genetics*; D010751:Phosphopyruvate Hydratase / Q000235:genetics; D020543:Proteome / Q000235:genetics*; D040901:Proteomics / Q000379:methods*; D012276:Ricin / Q000633:toxicity*; D053719:Tandem Mass Spectrometry; D051028:bcl-2-Associated X Protein / Q000235:genetics
chemical_list: C494826:BAX protein, human; D002619:Chemical Warfare Agents; D034921:Lamin Type B; D008869:Microtubule-Associated Proteins; D024101:Mitochondrial Proteins; D020543:Proteome; D051028:bcl-2-Associated X Protein; D045304:Cytochromes c; D012276:Ricin; D020558:GTP Phosphohydrolases; C110768:DNM1L protein, human; D034281:Dynamins; D010751:Phosphopyruvate Hydratase
keywords: Bayesian model; Biomolecular Interaction Networks (BINs).; Ricin toxin (RT); apoptosis; organellar localization; organellar proteome