Análise integrativa de dados de expressão gênica de Rhodosporidium toruloides em condições relevantes para a indústria biotecnológica

Abstract

INTEGRATIVE ANALYSIS OF GENE EXPRESSION DATA OF RHODOSPORIDIUM TORULOIDES UNDER RELEVANT CONDITIONS TO THE BIOTECHNOLOGICAL INDUSTRY"Rhodosporidium toruloides (R. toruloides) has been highlighted as an alternative to model organisms already used to conduct industrial bioprocesses due to some characteristics such as: (i) efficient processing of complex carbon sources, (ii) high storage and production of lipids, (iii) carotenogenesis, (iv) innate resistance to some chemical inhibitors present in lignocellulosic hydrolisates, and (v) absence of pathogenicity. However, to better exploit the potentials of this yeast and improve the efficiency of these bioprocesses, it is needed to know how it biologically deals with different growth conditions. Thus, our work aimed to understand the landscape of the transcriptional response of R. toruloides under different culture conditions through the integration of gene expression data.For this purpose, 54 RNA-Seq data of R. toruloides IFO0880 ∆ku70 strain were analysed. The quality control of raw reads was performed by FastQC and Trimmomatic softwares, as well as read alignment was done by Hisat2, transcripts assembly was done by Stringtie, differential expression analysis was performed by DESeq2, transcripts functional annotation and functional enrichment analysis was performed by Blast2GO. The results of the growth profile analysis indicate that the yeast is able to grow even in the presence of stresses induced by 5% ethanol, 0.15% acetic acid and 40º C. By analyzing the total number of differentially expressed genes (DEGs) of each condition we can infer that the number of DEGs changes in function of the culture conditions as a result of the level of system disturbance caused by each condition. Despite this difference in total DEGs number between conditions, the number of up-regulated and down-regulated DEGs inside each condition is really near to the balance, supposedly as a result of a fight to achieve a system homeostasis. Furthermore, our enrichment analysis results of the stress conditions provide some evidences that the major players in the response to stress are placed at the cell membrane and the main molecular functions associated to this response are the oxidoreductase activity and transmembrane transporter activity. Considering the carbon source conditions, the response is associated with carbohydrate metabolism, ATP production, ribosome biogenesis, translation and cell division. Thus, this work provides a more integrated biological knowledge of the transcriptional response of R. toruloides under conditions relevant to the biotechnology industry.

Cupuassu (Theobroma grandiflorum [Willd. ex Sprengel] Schumann) Fruit Development: Key Genes Involved in Primary Metabolism and Stress Response

“…Total RNA was extracted from the samples described in 2.1 using the cethyltrimethylammonium bromide (CTAB) method [18,19] with modifications [20]. The cupuassu tissues were macerated in liquid nitrogen, and the extraction was carried out with a buffer containing 2% CTAB (w/v), 2 M NaCl, 100 mM Tris-HCl pH 8.0, 25 mM EDTA, pH 8.0, 2% PVP 10,000 (w/v), and 2% β-mercaptoethanol (v/v).…”