Expression analysis of systemically infected Nicotiana benthamiana infected by South African cassava mosaic virus (SACMV)
Ontology highlight
ABSTRACT:
ORGANISM(S): Nicotiana benthamiana
PROVIDER: GSE43584 | GEO | 2013/01/17
SECONDARY ACCESSION(S): PRJNA186756
REPOSITORIES: GEO
Similar Datasets
Project description:Micrarray analysis was used to identify gene expression changes associated with disease development and virus movement in N.benthamina plants induced by infection with the SACMV 1-Plex , 385K array Nicotiana benthamiana (NimbleGen design name: 110121_N_benthamiana_60mer_exp) was used in this study to monitor changes in gene expression levels in SACMV- infected leaf tissue. Three biological replicates were used for infected leaf tissue and one pooled mock-inoculated sample was used as a control/reference.
2013-01-17 | E-GEOD-43584 | biostudies-arrayexpress
Project description:Huh-7.5.1 cells were treated with 0.2% DMSO, 20 microM NeoB for 24 h. Treatment with 0.2% DMSO for 24h was prepared as non-treated Huh7.5.1 cells. Huh7.5.1 cells were kindly provided by Prof. Francis Chisari at The Scripps Research Institute.
2015-08-31 | GSE63026 | GEO
Project description:The production of cassava is threatened by the geminivirus South African cassava mosaic virus (SACMV), which causes cassava mosaic disease. Cassava landrace TME3 shows tolerance to SACMV, while T200 is highly susceptible. This study aimed to identify the leaf proteome involved in anti-viral defence. Liquid chromatography mass spectrometry (LC-MS) identified 2682 (54 differentially expressed) and 2817 (206 differentially expressed) proteins in both landraces at systemic infection (32 days post infection) and symptom recovery (67 days post infection), respectively. Differences in the number of differentially expressed proteins (DEPs) between the two landraces were observed. Gene ontology analysis showed that defence-associated pathways such as the chloroplast, proteasome, and ribosome were overrepresented at 67 days post infection (dpi) in SACMV-tolerant TME3. At 67 dpi, a high percentage (56%) of over-expressed proteins were localized in the chloroplast in TME3 compared to T200 (31% under-expressed), proposing that chloroplast proteins play a role in tolerance in TME3. Ribosomal_L7Ae domain-containing protein (Manes.12G139100) was over-expressed uniquely in TME3 at 67 dpi and interacts with the ribosomal protein Sac52 (RPL10). RPL10 is a known key player in the NIK1-mediated effector triggered immunity (ETI) response to geminivirus infection, indicating a possible role for Sac52 in SACMV recovery in TME3. In conclusion, differential protein expression responses in TME3 and T200 may be key to unravel tolerance to CMD.
| S-EPMC8628908 | biostudies-literature
Project description:Huh-7.5.1 cells were treated with 0.2% DMSO, 20 microM NeoB for 24 h. Treatment with 0.2% DMSO for 24h was prepared as non-treated Huh7.5.1 cells. Huh7.5.1 cells were kindly provided by Prof. Francis Chisari at The Scripps Research Institute. Total RNA obtained from NeoB-treated and un-treated Huh7.5.1 cells
2015-08-31 | E-GEOD-63026 | biostudies-arrayexpress
Project description:The serine/threonine kinase mammalian target of rapamycin (mTOR) governs growth, metabolism, and aging in response to insulin and amino acids (aa), and is often activated in metabolic disorders and cancer. Much is known about the regulatory signaling network around mTOR, but surprisingly few direct mTOR substrates have been established to date. To tackle this gap in our knowledge, we took advantage of a combined quantitative phosphoproteomic and interactomic strategy. We analyzed the insulin- and aa-responsive phosphoproteome upon inhibition of the mTOR complex 1 (mTORC1) component raptor, and analyzed in parallel the interactome of endogenous mTOR. By overlaying these two datasets, we identified acinus L as a potential novel mTORC1 target. We confirmed acinus L as a direct mTORC1 substrate by co-immunoprecipitation and MS-enhanced kinase assays. Our study delineates a triple proteomics strategy of combined phosphoproteomics, interactomics, and MS-enhanced kinase assays for the de novo-identification of mTOR network components, and provides a rich source of potential novel mTOR interactors and targets for future investigation.<br><br>Additional contact details:<br><a href="mailto:k.thedieck@umcg.nl">Prof. Dr. Kathrin Thedieck</a><br>Department of Pediatrics, University of Groningen, University Medical Center Groningen (UMCG), 9713 AV Groningen, The Netherlands.<br>Faculty VI - School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26111 Oldenburg, Germany.<br><br>Prof. Dr. Bettina Warscheid<br>Faculty of Biology, Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany.<br>BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.<br>
2015-04-28 | PXD001244 | Pride
Project description:The serine/threonine kinase mammalian target of rapamycin (mTOR) governs growth, metabolism, and aging in response to insulin and amino acids (aa), and is often activated in metabolic disorders and cancer. Much is known about the regulatory signaling network around mTOR, but surprisingly few direct mTOR substrates have been established to date. To tackle this gap in our knowledge, we took advantage of a combined quantitative phosphoproteomic and interactomic strategy. We analyzed the insulin- and aa-responsive phosphoproteome upon inhibition of the mTOR complex 1 (mTORC1) component raptor, and analyzed in parallel the interactome of endogenous mTOR. By overlaying these two datasets, we identified acinus L as a potential novel mTORC1 target. We confirmed acinus L as a direct mTORC1 substrate by co-immunoprecipitation and MS-enhanced kinase assays. Our study delineates a triple proteomics strategy of combined phosphoproteomics, interactomics, and MS-enhanced kinase assays for the de novo-identification of mTOR network components, and provides a rich source of potential novel mTOR interactors and targets for future investigation.<br><br>Additional contact details:<br><a href="mailto:k.thedieck@umcg.nl">Prof. Dr. Kathrin Thedieck</a><br>Department of Pediatrics, University of Groningen, University Medical Center Groningen (UMCG), 9713 AV Groningen, The Netherlands.<br>Faculty VI - School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26111 Oldenburg, Germany.<br><br>Prof. Dr. Bettina Warscheid<br>Faculty of Biology, Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany.<br>BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.<br>
2015-04-28 | PXD001196 | Pride
Project description:The serine/threonine kinase mammalian target of rapamycin (mTOR) governs growth, metabolism, and aging in response to insulin and amino acids (aa), and is often activated in metabolic disorders and cancer. Much is known about the regulatory signaling network around mTOR, but surprisingly few direct mTOR substrates have been established to date. To tackle this gap in our knowledge, we took advantage of a combined quantitative phosphoproteomic and interactomic strategy. We analyzed the insulin- and aa-responsive phosphoproteome upon inhibition of the mTOR complex 1 (mTORC1) component raptor, and analyzed in parallel the interactome of endogenous mTOR. By overlaying these two datasets, we identified acinus L as a potential novel mTORC1 target. We confirmed acinus L as a direct mTORC1 substrate by co-immunoprecipitation and MS-enhanced kinase assays. Our study delineates a triple proteomics strategy of combined phosphoproteomics, interactomics, and MS-enhanced kinase assays for the de novo-identification of mTOR network components, and provides a rich source of potential novel mTOR interactors and targets for future investigation.<br><br>Additional contact details:<br><a href="mailto:k.thedieck@umcg.nl">Prof. Dr. Kathrin Thedieck</a><br>Department of Pediatrics, University of Groningen, University Medical Center Groningen (UMCG), 9713 AV Groningen, The Netherlands.<br>Faculty VI - School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26111 Oldenburg, Germany.<br><br>Prof. Dr. Bettina Warscheid<br>Faculty of Biology, Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany.<br>BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.<br>
2015-04-28 | PXD001245 | Pride
Project description:BACKGROUND: Cassava mosaic disease is caused by several distinct geminivirus species, including South African cassava mosaic virus-[South Africa:99] (SACMV). To date, there is limited gene regulation information on viral stress responses in cassava, and global transcriptome profiling in SACMV-infected cassava represents an important step towards understanding natural host responses to plant geminiviruses. RESULTS: A RNA-seq time course (12, 32 and 67 dpi) study, monitoring gene expression in SACMV-challenged susceptible (T200) and tolerant (TME3) cassava landraces, was performed using the Applied Biosystems (ABI) SOLiD next-generation sequencing platform. The multiplexed paired end sequencing run produced a total of 523 MB and 693 MB of paired-end reads for SACMV-infected susceptible and tolerant cDNA libraries, respectively. Of these, approximately 50.7% of the T200 reads and 55.06% of TME3 reads mapped to the cassava reference genome available in phytozome. Using a log2 fold cut-off (p<0.05), comparative analysis between the six normalized cDNA libraries showed that 4181 and 1008 transcripts in total were differentially expressed in T200 and TME3, respectively, across 12, 32 and 67 days post infection, compared to mock-inoculated. The number of responsive transcripts increased dramatically from 12 to 32 dpi in both cultivars, but in contrast, in T200 the levels did not change significantly at 67 dpi, while in TME3 they declined. GOslim functional groups illustrated that differentially expressed genes in T200 and TME3 were overrepresented in the cellular component category for stress-related genes, plasma membrane and nucleus. Alterations in the expression of other interesting genes such as transcription factors, resistance (R) genes, and histone/DNA methylation-associated genes, were observed. KEGG pathway analysis uncovered important altered metabolic pathways, including phenylpropanoid biosynthesis, sucrose and starch metabolism, and plant hormone signalling. CONCLUSIONS: Molecular mechanisms for TME3 tolerance are proposed, and differences in patterns and levels of transcriptome profiling between T200 and TME3 with susceptible and tolerant phenotypes, respectively, support the hypothesis that viruses rearrange their molecular interactions in adapting to hosts with different genetic backgrounds.
| S-EPMC4253015 | biostudies-literature
Project description:Cassava brown streak disease (CBSD) is a severe virus disease of cassava and prevalent in the eastern regions of Africa. The disease is characterized by distinct vein chlorosis and streak symptoms on leaves and stems and necrosis of storage roots. This necrosis can encompass large areas of the root, rendering it inedible so that the entire cassava harvest can be lost. African cassava varieties are susceptible to either of the two viruses causing the disease, cassava brown streak virus (CBSV) and Uganda cassava brown streak virus, and while there are less sensitive varieties, all cassava eventually succumb to the disease. The lack of CBSD resistance in African cassava varieties prompted this search for new sources of virus resistance in the diversity of South American cassava germplasm held in the collection at International Center for Tropical Agriculture, Columbia. Our search for CBSD resistance in South American cassava germplasm accessions revealed that most of the 238 South American cassava lines infected with CBSV established systemic virus infections with moderate to severe disease symptoms on leaves and stems. Fifteen cassava accessions did not become virus infected, remained free of symptoms, and CBSV was undetected by qRT-PCR. When tuberous roots of those lines were examined, necrotic tissue was found in eight lines and CBSV was detected. The remaining seven cassava accessions remained clear of symptoms on all tissues and organs and were virus free. A broad spectrum of virus resistance also including other virus isolates was confirmed for the breeding lines DSC167 and DSC118. While detailed infection experiments with other cassava lines selected for resistance are still ongoing, this indicates that the resistance identified may also hold against a broader diversity of CBSVs. Taken together, we present the results of a comprehensive study on CBSV resistance and susceptibility in cassava germplasm accessions from South America. The virus resistance in cassava germplasm identified provides compelling evidence for the invaluable contribution of germplasm collections to supply the genetic resources for the improvement of our crops.
| S-EPMC6523400 | biostudies-literature
Project description:Wilms tumour (nephroblastoma) is the most common paediatric renal tumour, affecting 1 in 10,000 children. Despite the excellent survival of patients treated with a combination of surgery, chemotherapy and radiotherapy, approximately 15% will relapse and die of this disease. We have identified CACNA1E to be significantly overexpressed in relapsing tumours compared to non-relapsing. To investigate the involvement of CACNA1E in Wilms tumorigenesis, CACNA1E stably transfected HEK293 cell line and parental lines were obtained, grown and RNA extracted. To assess differential gene expression between the two cell lines, RNA was hybridised to Affymetrix Human Genome U133 Plus 2.0 GeneChip. Human embryonic kidney HEK293 parental and HEK2C6, (CACNA1E stably transfected cells) were kindly provided by Prof. Schneider, Cologne (Pereverzev et al., 1998).
2006-12-01 | E-MEXP-587 | biostudies-arrayexpress