RNA-seq analysis of Pichia anomala reveals important mechanisms required for survival at low pH

Effects of Environmentally Friendly Aquaculture Chamber Coatings on Enzyme Activities, Histology, and Transcriptome in the Liver of Larimichthys crocea

Aquaculture vessels have emerged as a sustainable alternative to traditional offshore aquaculture. However, the biological impacts of protective coatings used for vessel interiors are still poorly understood. This study assessed acute stress responses of Larimichthys crocea to epoxy-based aquaculture coatings using actual culture (1-fold) and high-exposure (80-fold) concentrations. Liver analyses included antioxidant enzymes, histopathology, and transcriptomics over 12-96 h. Firstly, the effect of the 80-fold concentration group on the activities of catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) was more significant in the liver of L. crocea compared to the 1-fold concentration group. Similarly, histological observations revealed that the 80-fold concentration group produced more significant pathological changes in the liver than the 1-fold concentration group, including hepatocyte damage and vacuolization. Subsequently, through high-throughput sequencing, a total of 714.02 million clean reads were obtained, with 693.71 million of these reads successfully mapped onto the reference genome of L. crocea, identifying 13,709 differentially expressed genes (DEGs). KEGG pathway enrichment analysis showed that many DEGs following coating-treated were involved in protein processing in endoplasmic reticulum, oxidative phosphorylation, cytokine-cytokine receptor interaction, FoxO signaling pathway, and toll-like receptor signaling pathway. Finally, fifteen DEGs were selected for quantitative real-time PCR (qRT-PCR) analysis, and the results showed a significant correlation with RNA-seq results, verifying the reliability and accuracy of the high-throughput sequencing data. This study preliminarily revealed the stress responses induced by aquaculture vessel coatings in L. crocea and provided fundamental data into the scientific use of coatings on aquaculture vessels.

Beer production potentiality of some non-Saccharomyces yeast obtained from a traditional beer starter emao

The recent realisation regarding the potentiality of the long-neglected non-Saccharomyces yeasts in improving the flavour profile and functionality of alcoholic beverages has pushed researchers to search for such potent strains in many sources. We studied the fungal diversity and the rice beer production capability of the fungal strains isolated from emao-a traditional rice beer starter culture of the Boro community. Fifty distinct colonies were picked from mixed-culture plates, of which ten representative morphotypes were selected for species identification, and simultaneous saccharification and beer fermentation (SSBF) assay. The representative isolates were identified as Hyphopichia burtonii (Hbur-FI38, Hbur-FI44, Hbur-FI47 & Hbur-FI68), Saccharomyces cerevisiae (Scer-FI51), Wickerhamomyces anomalus (Wano-FI52), Candida carpophila (Ccar-FI53), Mucor circinelloides (Mcir-FI60), and Saccharomycopsis malanga (Smal-FI77 and Smal-FI84). The non-Saccharomyces yeast strains Hbur-FI38, Hbur-FI44, Ccar-FI53, and Smal-FI77 showed SSBF capacity on rice substrate producing beer that contained 7-10% (v/v) ethanol. A scaled-up fermentation assay was performed to assess the strain-wise fermentation behaviour in large-scale production. The nutritional, functional, and sensory qualities of the SSBF strain fermented beer were compared to the beer produced by emao. All the strains produced beer with reduced alcohol and energy value while compared to the traditional starter emao. Beer produced by both the strains of H. burtonii stood out with higher ascorbic acid, phenol, and antioxidant property, and improved sensory profile in addition to reduced alcohol and energy value. Such SSBF strains are advantageous over the non-SSBF S. cerevisiae strains as the former can be used for direct beer production from rice substrates.

Physiological characterization and transcriptome analysis of Pichia pastoris reveals its response to lignocellulose-derived inhibitors

The negative effects of lignocellulose-derived inhibitors such as acetic acid and furaldehydes on microbial metabolism constitute a significant drawback to the usage of biomass feedstocks for the production of fuels and chemicals. The yeast Pichia pastoris has shown a great biotechnological potential for producing heterologous proteins and renewable chemicals. Despite its relevance, the performance of P. pastoris in presence of lignocellulose-derived inhibitors remains unclear. In this work, our results show for the first time the dose-dependent response of P. pastoris to acetic acid, furaldehydes (HMF and furfural), and sugarcane biomass hydrolysate, both at physiological and transcriptional levels. The yeast was able to grow in synthetic media with up to 6 g.L-1 acetic acid, 1.75 g.L-1 furaldehydes or hydrolysate diluted to 10% (v/v). However, its metabolism was completely hindered in presence of hydrolysate diluted to 30% (v/v). Additionally, the yeast was capable to co-consume acetic acid and glucose. At the transcriptional level, P. pastoris response to lignocellulose-derived inhibitors relays on the up-regulation of genes related to transmembrane transport, oxidoreductase activities, RNA processing, and the repression of pathways related to biosynthetic processes and central carbon metabolism. These results demonstrate a polygenetic response that involves detoxification activities, and maintenance of energy and cellular homeostasis. In this context, ALD4, OYE3, QOR2, NTL100, YCT1, and PPR1 were identified as target genes to improve P. pastoris tolerance. Altogether, this work provides valuable insights into the P. pastoris stress tolerance, which can be useful to expand its use in different bioprocesses.

Cooperative Response of Pichia kudriavzevii and Saccharomyces cerevisiae to Lactic Acid Stress in Baijiu Fermentation

Lactic acid is a universal metabolite, as well as a growth inhibitor of ethanol producers in Baijiu fermentation. Revealing the mechanism of lactic acid tolerance is essential for the yield of fermented foods. Here, we employed reverse transcription-quantitative polymerase chain reaction to explore the degradation mechanism of lactic acid, based on the coculture of Pichia kudriavzevii and Saccharomyces cerevisiae. Under high lactic acid stress, P. kudriavzevii decreased lactic acid from 40.00 to 35.46 g L^-1 within 24 h. Then, S. cerevisiae restored its capacity to degrade lactic acid. Finally, lactic acid decreased to 26.29 g L^-1. Coculture significantly enhanced lactic acid consumption compared to the monoculture of P. kudriavzevii (90% higher) or S. cerevisiae (209% higher). We found that lactate catabolism, H⁺ extrusion, and glycerol transport were the lactic acid tolerance pathways in yeasts. This study reveals the novel acid tolerance mechanisms of microbiota and would provide new strategies for ethanol production under acid stress.

Distinct Regioselectivity of Fungal P450 Enzymes for Steroidal Hydroxylation

In this study, we identified two P450 enzymes (CYP5150AP3 and CYP5150AN1) from Thanatephorus cucumeris NBRC 6298 by combination of transcriptome sequencing and heterologous expression in Pichia pastoris The biotransformation of 11-deoxycortisol and testosterone by Pichia pastoris whole cells coexpressing the cyp5150ap3 and por genes demonstrated that the CYP5150AP3 enzyme possessed steroidal 7β-hydroxylase activities toward these substrates, and the regioselectivity was dependent on the structures of steroidal compounds. CYP5150AN1 catalyzed the 2β-hydroxylation of 11-deoxycortisol. It is interesting that they display different regioselectivity of hydroxylation from that of their isoenzyme, CYP5150AP2, which possesses 19- and 11β-hydroxylase activities.IMPORTANCE The steroidal hydroxylases CYP5150AP3 and CYP5150AN1 together with the previously characterized CYP5150AP2 belong to the CYP5150A family of P450 enzymes with high amino acid sequence identity, but they showed completely different regioselectivities toward 11-deoxycortisol, suggesting the regioselectivity diversity of steroidal hydroxylases of CYP5150 family. They are also distinct from the known bacterial and fungal steroidal hydroxylases in substrate specificity and regioselectivity. Biocatalytic hydroxylation is one of the important transformations for the functionalization of steroid nucleus rings but remains a very challenging task in organic synthesis. These hydroxylases are useful additions to the toolbox of hydroxylase enzymes for the functionalization of steroids at various positions.

Acid stress induces cross-protection for cadmium tolerance of multi-stress-tolerant Pichia kudriavzevii by regulating cadmium transport and antioxidant defense system

The toxicity of cadmium (Cd) is the major limitation to its removal using microorganisms. The Cd tolerance of Pichia kudriavzevii was obviously enhanced by acid stress based on multi-stress cross-protection. RNA-Seq showed that most differentially expressed genes (DEGs) in the Pentose phosphate pathway, Citrate cycle (TCA cycle), Glycolysis/Gluconeogenesis, Peroxisome and Glutathione metabolism were up-regulated by acid stress. The up-regulated expression of genes related to ATP synthesis (GOR1, ALD5, ADH4, ADH6, MDH2, IDH1, IDH2, and ATP19) and Cd transport (GSTY2, GTO2, GLO2, and YOR1), and the improvement of intracellular GSH level and GST activity, reduced the Cd toxicity towards P. kudriavzevii. Cd efflux by YOR1 played a key role in the decline of intracellular Cd level. Acid stress obviously improved the gene expression levels and activities of antioxidant enzymes (SOD, POD, and CAT), which inhibited the Cd-induced ROS outburst and oxidative damage of proteins and membrane lipids. In addition, the enhanced expression of HSP12 protected P. kudriavzevii from the damage of Cd stress. These results provide some important clues to reconstruct robust strains using for Cd removal in aquatic environments.

The regulation of oxidative phosphorylation pathway on Vibrio alginolyticus adhesion under adversities

Vibrio alginolyticus is one of the most important pathogens in mariculture and leading to heavy losses. After treatment with Cu²⁺, Pb²⁺, and low pH, the expression of oxidative phosphorylation pathway genes, including coxA, coxB, coxC, ccoN, ccoO, and ccoQ, was found commonly downregulated by RNA‐seq as well as quantitative real‐time PCR. RNAi significantly reduced the expression of coxA, coxB, coxC, ccoN, ccoO, and ccoQ in V. alginolyticus. Compared with the wild‐type strain, the adhesion abilities of RNAi strains of V. alginolyticus were significantly impaired, as well as their cytochrome C oxidase activity. ccoQ appeared to be more important in the regulation of bacterial adhesion in these target genes, while ccoO was relatively weak in the regulation of the adhesion. Meanwhile, the changes of temperature, salinity, pH, and starvation affected coxA, coxB, coxC, ccoN, ccoO, and ccoQ expression remarkably. These findings indicated that: the oxidative phosphorylation pathway is a critical regulator of adhesion in V. alginolyticus; coxA, coxB, coxC, ccoN, ccoO, and ccoQ regulate the bacterial adhesion in response to environmental changes such as temperature, salinity, pH, and starvation.

Challenges of the Non-Conventional Yeast Wickerhamomyces anomalus in Winemaking

Nowadays it is widely accepted that non-Saccharomyces yeasts, which prevail during the early stages of alcoholic fermentation, contribute significantly to the character and quality of the final wine. Among these yeasts, Wickerhamomyces anomalus (formerly Pichia anomala, Hansenula anomala, Candida pelliculosa) has gained considerable importance for the wine industry since it exhibits interesting and potentially exploitable physiological and metabolic characteristics, although its growth along fermentation can still be seen as an uncontrollable risk. This species is widespread in nature and has been isolated from different environments including grapes and wines. Its use together with Saccharomyces cerevisiae in mixed culture fermentations has been proposed to increase wine particular characteristics. Here, we review the ability of W. anomalus to produce enzymes and metabolites of oenological relevance and we discuss its potential as a biocontrol agent in winemaking. Finally, biotechnological applications of W. anomalus beyond wine fermentation are briefly described.

Transcriptional Response to Lactic Acid Stress in the Hybrid Yeast Zygosaccharomyces parabailii

Lactic acid has a wide range of applications starting from its undissociated form, and its production using cell factories requires stress-tolerant microbial hosts. The interspecies hybrid yeast Zygosaccharomyces parabailii has great potential to be exploited as a novel host for lactic acid production, due to high organic acid tolerance at low pH and a fermentative metabolism with a high growth rate. Here we used mRNA sequencing (RNA-seq) to analyze Z. parabailii's transcriptional response to lactic acid added exogenously, and we explore the biological mechanisms involved in tolerance. Z. parabailii contains two homeologous copies of most genes. Under lactic acid stress, the two genes in each homeolog pair tend to diverge in expression to a significantly greater extent than under control conditions, indicating that stress tolerance is facilitated by interactions between the two gene sets in the hybrid. Lactic acid induces downregulation of genes related to cell wall and plasma membrane functions, possibly altering the rate of diffusion of lactic acid into cells. Genes related to iron transport and redox processes were upregulated, suggesting an important role for respiratory functions and oxidative stress defense. We found differences in the expression profiles of genes putatively regulated by Haa1 and Aft1/Aft2, previously described as lactic acid responsive in Saccharomyces cerevisiae. Furthermore, formate dehydrogenase (FDH) genes form a lactic acid-responsive gene family that has been specifically amplified in Z. parabailii in comparison to other closely related species. Our study provides a useful starting point for the engineering of Z. parabailii as a host for lactic acid production.

IMPORTANCE Hybrid yeasts are important in biotechnology because of their tolerance to harsh industrial conditions. The molecular mechanisms of tolerance can be studied by analyzing differential gene expression under conditions of interest and relating gene expression patterns to protein functions. However, hybrid organisms present a challenge to the standard use of mRNA sequencing (RNA-seq) to study transcriptional responses to stress, because their genomes contain two similar copies of almost every gene. Here we used stringent mapping methods and a high-quality genome sequence to study the transcriptional response to lactic acid stress in Zygosaccharomyces parabailii ATCC 60483, a natural interspecies hybrid yeast that contains two complete subgenomes that are approximately 7% divergent in sequence. Beyond the insights we gained into lactic acid tolerance in this study, the methods we developed will be broadly applicable to other yeast hybrid strains.

Omics analysis of acetic acid tolerance in Saccharomyces cerevisiae

Acetic acid is an inhibitor in industrial processes such as wine making and bioethanol production from cellulosic hydrolysate. It causes energy depletion, inhibition of metabolic enzyme activity, growth arrest and ethanol productivity losses in Saccharomyces cerevisiae. Therefore, understanding the mechanisms of the yeast responses to acetic acid stress is essential for improving acetic acid tolerance and ethanol production. Although 329 genes associated with acetic acid tolerance have been identified in the Saccharomyces genome and included in the database ( http://www.yeastgenome.org/observable/resistance_to_acetic_acid/overview ), the cellular mechanistic responses to acetic acid remain unclear in this organism. Post-genomic approaches such as transcriptomics, proteomics, metabolomics and chemogenomics are being applied to yeast and are providing insight into the mechanisms and interactions of genes, proteins and other components that together determine complex quantitative phenotypic traits such as acetic acid tolerance. This review focuses on these omics approaches in the response to acetic acid in S. cerevisiae. Additionally, several novel strains with improved acetic acid tolerance have been engineered by modifying key genes, and the application of these strains and recently acquired knowledge to industrial processes is also discussed.

Industrial systems biology and its impact on synthetic biology of yeast cell factories

Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal of developing improved yeast cell factories. Biotechnol. Bioeng. 2016;113: 1164-1170. © 2015 Wiley Periodicals, Inc.