Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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Article Citation - WoS: 14Citation - Scopus: 16Transcriptomic Analysis of Boron Hyperaccumulation Mechanisms in Puccinellia Distans(Elsevier Ltd., 2018) Öztürk, Saniye Elvan; Göktay, Mehmet; Has, Canan; Babaoğlu, Mehmet; Allmer, Jens; Doğanlar, Sami; Frary, AnnePuccinellia distans, common alkali grass, is found throughout the world and can survive in soils with boron concentrations that are lethal for other plant species. Indeed, P. distans accumulates very high levels of this element. Despite these interesting features, very little research has been performed to elucidate the boron tolerance mechanism in this species. In this study, P. distans samples were treated for three weeks with normal (0.5 mg L−1) and elevated (500 mg L−1) boron levels in hydroponic solution. Expressed sequence tags (ESTs) derived from shoot tissue were analyzed by RNA sequencing to identify genes up and down-regulated under boron stress. In this way, 3312 differentially expressed transcripts were detected, 67.7% of which were up-regulated and 32.3% of which were down-regulated in boron-treated plants. To partially confirm the RNA sequencing results, 32 randomly selected transcripts were analyzed for their expression levels in boron-treated plants. The results agreed with the expected direction of change (up or down-regulation). A total of 1652 transcripts had homologs in A. thaliana and/or O. sativa and mapped to 1107 different proteins. Functional annotation of these proteins indicated that the boron tolerance and hyperaccumulation mechanisms of P. distans involve many transcriptomic changes including: alterations in the malate pathway, changes in cell wall components that may allow sequestration of excess boron without toxic effects, and increased expression of at least one putative boron transporter and two putative aquaporins. Elucidation of the boron accumulation mechanism is important in developing approaches for bioremediation of boron contaminated soils.Article Citation - WoS: 2Citation - Scopus: 5Pgminer: Complete Proteogenomics Workflow; From Data Acquisition To Result Visualization(Elsevier Ltd., 2017) Has, Canan; Allmer, JensIn parallel with the development of nucleotide sequencing an equally important interest in further describing the sequence in terms of function arose and the latter represents the current bottleneck in the overall research question. Sequencing the transcriptome allows determination of expressed nucleotide sequences and using mass spectrometry allows sequencing on the protein level. Both approaches can only sequence a subset of the existing transcripts. Moreover, for example post translational modification events can only be determined on the proteomics level. Therefore, it is essential to combine proteomics and genomics. For that purpose, proteogenomics data analysis pipelines have been described. Here, we describe a novel proteogenomics workflow which encompasses everything from the acquisition of data to result visualization in the Konstanz Information Miner (KNIME), a state of the art workflow management and data analytics platform. We amended KNIME with a number of processes like peptide consensus prediction, peptide mapping, and database equalizing, as well as result visualization. This enabled construction of our new workflow, entitled PGMiner, which not only includes all data analysis steps, but is highly customizable which is rather cumbersome for most existing pipelines. Furthermore, no burdensome installation processes have to be performed making PGMiner the most user friendly tool available.