Transcriptomic Analysis of Oenococcus oeni SD-2a Response to Acid Shock by RNA-Seq

Abstract

Oenococcus oeni can be applied to conduct malolactic fermentation (MLF), but also is the main species growing naturally in wine. Due to the high stress tolerance, it is an interesting model for investigating acid response mechanisms. In this study, the changes in the transcriptome of O.oeni SD-2a during the adaptation period have been studied. RNA-seq was introduced for the transcriptomic analysis of O. oeni samples treated with pH 4.8 and pH 3.0 at 0 and 1 h, respectively. Gene ontology (GO) and Kyoto encyclopedia of genes and genome (KEGG) were performed to compare the transcriptome data between different treatments. From GO analysis, the majority of differentially expressed genes (DEGs) (pH 3.0_1 h-VS-pH 4.8_1 h, pH 3.0_1 h-VS-pH 4.8_0 h, and pH 4.8_1 h-VS-pH 4.8_0 h) were found to be involved in the metabolic process, catalytic activity, cellular process, and binding. KEGG analysis reveals that the most functional gene categories affected by acid are membrane transport, amino acid metabolism and carbohydrate metabolism. Some genes, like the heat shock protein Hsp20, malate transporter and malate permease, were also over-expressed in response to acid stress. In addition, a considerable proportion of gene indicate a significantly different expression in this study, are novel, which needs to be investigated further. These results provide a new viewpoint and crucial resource on the acid stress response in O. oeni.

Selection and Validation of Reference Genes for Quantitative Real-Time PCR Normalization Under Ethanol Stress Conditions in Oenococcus oeni SD-2a

“…In 16% ethanol, the top-ranked gene was proC , which was not evaluated in the previous studies of O. oeni , whereas gyrB and dnaG were ranked second and third respectively. In our study, dpoIII, dnaG, gyrB , and gyrA showed better expression stability, while in some studies, they were used together as reference genes for RT-qPCR normalization in O. oeni , but not evaluated particularly (Costantini et al, 2011 ; Margalef-Català et al, 2016 ; Liu et al, 2017 ). Moreover, the traditional reference genes in O. oeni , such as ddlA and ldhD varied greatly in our experimental conditions.…”

“…The O. oeni SD-2a was cultured at 28°C and pH 4.8 in three flasks with 100 mL FMATB broth, which contains glucose 5 g/L, D, L-malate 5 g/L, yeast extract 5 g/L, peptone 10 g/L, MgSO4 •7H 2 O 0.2 g/L, MnSO4 •4H 2 O 0.05 g/L, Cysteine/HCl 0.5 g/L, and tomato juice 250 mL (Li et al, 2009 ; Liu et al, 2017 ). The growth of cultures was monitored by measuring OD value using a spectrophotometer (Cary 60 UV-Vis, Agilent Technologies, USA).…”

“…Several stress-related genes such as hsp18, citE, ctsR, clpP, ftsH , have been studied using RT-qPCR analysis in O. oeni under different stress conditions, however only one common reference gene, ldhD , was used for normalization (Bourdineaud et al, 2003 ; Beltramo et al, 2006 ; Olguín et al, 2009 , 2010 ; Capozzi et al, 2010 ). Recently, some studies attempted to elucidate the mechanisms of the adaptation and tolerance of O. oeni under stress conditions through transcriptomic and proteomic analysis, in which RT-qPCR was applied to confirm transcriptomic analysis results using the multiple common reference genes for normalization (Olguín et al, 2015 ; Margalef-Català et al, 2016 ; Liu et al, 2017 ). However, in these studies, the evaluation of reference genes was not performed in advance.…”

Mapping the Physiological Response of Oenococcus oeni to Ethanol Stress Using an Extended Genome-Scale Metabolic Model

“…For example, a similar approach can be employed to tackle the metabolic response to acidic conditions in this bacterium, which, together with alcohol and SO 2 stresses, are the most relevant conditions that affect the growth of O. oeni. For instance, Liu et al (2017) recently showed, using RNA-seq, that in O. oeni SD-2a strain grown at pH of 4.8 and pH 3.0, several genes related with the metabolism of amino acids, carbohydrates, membrane transport and energy metabolism were differentially expressed. Therefore, the resulting quantitative transcriptomics can be incorporated into the iSM454 metabolic model as restrictions and, together with experimental data, could allow to simulate the redistribution of metabolic fluxes resulting from this environmental perturbation.…”

Transcriptomic and metabolomic analyses of Lycium ruthenicum and Lycium barbarum fruits during ripening

“…Proline iminopeptidase (pip), associated with arginine and proline metabolism, was highly downregulated in LR in all stages. As proline (and pip) concentrations tend to increase under stress in a broad range of living organisms 40,54,55 , we would expect the pip gene to be upregulated. It should be noted that we did observe a high accumulation of L-proline in the ripe LR fruit.…”