Search Results (76)

Astaxanthin (ASX) is a xanthophyll carotenoid mainly derived from marine microalgae such as Haematococcus pluvialis and Chlorella zofingiensis, as well as the yeast Phaffia rhodozyma. Its chemical nature structure, rich in conjugated double bonds, carbonyl, and hydroxyl groups, confers potent antioxidant and anti-inflammatory properties. ASX modulates oxidative stress via the PI3K/Akt-Nrf2 pathway and suppresses NF-κB-mediated inflammatory responses, reducing cytokine levels such as TNF-α, IL-6, and iNOS. ASX exerts dual apoptotic effects, cytoprotective in non-transformed cells and pro-apoptotic in cancer cells through p53 activation. Sustainable extraction techniques, especially supercritical CO₂, have improved its industrial applicability. Recent findings highlight ASX’s role in stem cell biology, enhancing proliferation, supporting lineage-specific differentiation, and protecting against oxidative and inflammatory damage, which is a crucial issue for regenerative medicine applications. These multifaceted molecular effects support ASX’s therapeutic potential in chronic diseases, including diabetes, cardiovascular pathologies, and cancer. This review outlines ASX’s natural sources, extraction methods, and biological mechanisms, emphasizing its application in oxidative stress- and inflammation-related conditions. Full article

The yeast Saccharomyces cerevisiae is the paradigm of a eukaryotic model organism. In virtue of a substantial degree of functional conservation, it has been extensively exploited to understand multiple aspects of the genetic, molecular, and cellular biology of human disease. Many aspects of cell signaling in cancer, aging, or metabolic diseases have been tackled in yeast. Here, we review the strategies undertaken throughout the years for the development of humanized yeast models to study regulated cell death (RCD) pathways in general, and specifically, those related to innate immunity and inflammation, with an emphasis on pyroptosis and necroptosis. Such pathways involve the assembly of distinct modular signaling complexes such as the inflammasome and the necrosome. Like other supramolecular organizing centers (SMOCs), such intricate molecular arrangements trigger the activity of enzymes, like caspases or protein kinases, culminating in the activation of lytic pore-forming final effectors, respectively, Gasdermin D (GSDMD) in pyroptosis and MLKL in necroptosis. Even though pathways related to those governing innate immunity and inflammation in mammals are missing in fungi, the heterologous expression of their components in the S. cerevisiae model provides a “cellular test tube” to readily study their properties and interactions, thus constituting a valuable tool for finding novel therapies. Full article

The role of calcium, an essential secondary messenger, in cell division remains an outstanding question in cell biology despite several significant findings over the past few decades. Among them is the landmark discovery of intracellular calcium waves during cytokinesis, the last stage of cell division, in fish cells. Nevertheless, subsequent studies have been largely unable to determine the underlying molecular mechanism of these cytokinetic transients. At the center of this stalemate stands two challenging questions, how these calcium transients rise and what they do during cytokinesis. Yeast, despite its proven prowess as a model organism to study cell cycle, has not drawn much interest in addressing these questions. However, the recent discovery of cytokinetic calcium spikes in the fission yeast Schizosaccharomyces pombe has provided novel insights into how calcium regulates cytokinesis. In this review, I will primarily focus on our current understanding of the molecular mechanism of cytokinetic calcium transients in yeast cells. First, I will briefly recount the discovery of cytokinetic calcium transients in animal cells. This will be followed by an introduction to the intracellular calcium homeostasis. Next, I will discuss yeast cytokinetic calcium spikes, the ion channel Pkd2 that promotes these spikes, and the potential molecular targets of these spikes. I will also compare the calcium regulation of cytokinesis between yeast and animal cells. I will conclude by presenting a few critical questions in our continued quest to understand how calcium regulates cytokinesis. Full article

The Saccharomyces cerevisiae chromosomal architectural protein Hmo1 is categorized as an HMGB protein, as it contains two HMGB motifs that bind DNA in a structure-specific manner. However, Hmo1 has a basic C-terminal domain (CTD) that promotes DNA bending instead of an acidic one found in a canonical HMGB protein. Hmo1 has diverse functions in genome maintenance and gene regulation. It is implicated in DNA damage tolerance (DDT) that enables DNA replication to bypass lesions on the template. Hmo1 is believed to direct DNA lesions to the error-free template switching (TS) pathway of DDT and to aid in the formation of the key TS intermediate sister chromatid junction (SCJ), but the underlying mechanisms have yet to be resolved. In this work, we used genetic and molecular biology approaches to further investigate the role of Hmo1 in DDT. We found extensive functional interactions of Hmo1 with components of the genome integrity network in cellular response to the genotoxin methyl methanesulfonate (MMS), implicating Hmo1 in the execution or regulation of homology-directed DNA repair, replication-coupled chromatin assembly, and the DNA damage checkpoint. Notably, our data pointed to a role for Hmo1 in directing SCJ to the nuclease-mediated resolution pathway instead of the helicase/topoisomerase mediated dissolution pathway for processing/removal. They also suggested that Hmo1 modulates both the recycling of parental histones and the deposition of newly synthesized histones on nascent DNA at the replication fork to ensure proper chromatin formation. We found evidence that Hmo1 counteracts the function of histone H2A variant H2A.Z (Htz1 in yeast) in DDT possibly due to their opposing effects on DNA resection. We showed that Hmo1 promotes DNA negative supercoiling as a proxy of chromatin structure and MMS-induced DNA damage checkpoint signaling, which is independent of the CTD of Hmo1. Moreover, we obtained evidence indicating that whether the CTD of Hmo1 contributes to its function in DDT is dependent on the host’s genetic background. Taken together, our findings demonstrated that Hmo1 can contribute to, or regulate, multiple processes of DDT via different mechanisms. Full article

The community of epibiotic yeasts significantly influences the quality of Docynia delavayi (Franch.) Schneid. wine. The yeast diversity in four different Docynia delavayi (Franch.) Schneid. wines during the brewing stage was investigated using pure culture methods and high-throughput sequencing technology. A total of 229,381,292 sequencing bases were generated, yielding 323,820 valid sequences with an average length of 708 nt and identifying 93 operational taxonomic units (OTUs) from naturally fermented samples of Docynia delavayi (Franch.) Schneid. wine for classification purposes. At the early fermentation stage, Hanseniaspora sp. was identified as the dominant species, whereas at the late fermentation stage, Hanseniaspora sp., Saccharomyces sp., and Candida californica became predominant. From these samples, a total of 109 yeast strains were isolated from Docynia delavayi (Franch.) Schneid. wine. Three specific strains—LZX-76, LZX-89, and LZX-104—were further selected based on their growth characteristics along with hydrogen sulfide production, ester production, ethanol production, and tolerance levels. Through morphological examination and molecular biology techniques, these strains were identified as Pichia fermentans and Hanseniaspora spp. Additionally, a total of 29 volatile compounds were detected through simulated fermentation processes; these included 12 esters, 6 alcohols, 2 acids, 4 aldehydes, and 5 other compounds. When compared to commercial yeasts used as starters in winemaking processes, it was observed that utilizing yeast strains LZX-76, LZX-89, and LZX-104 resulted in an increased number of volatile compounds, which enhanced the aromatic profile characteristics of Docynia delavayi (Franch.) Schneid. wine by making its aroma richer and more complex. The findings from this study hold significant potential value for both the production practices and research endeavors related to Docynia delavayi (Franch.) Schneid. wine. Full article

Ubiquitylation is a post-translational modification that modulates protein function and stability. It is orchestrated by the concerted action of three types of enzymes, with substrate specificity governed by ubiquitin ligases (E3s), which may exist as single proteins or as part of multi-protein complexes. Although Cullin (CUL) proteins lack intrinsic enzymatic activity, they participate in the formation of active ubiquitin ligase complexes, known as Cullin-Ring ubiquitin Ligases (CRLs), through their association with ROC1 or ROC2, along with substrate adaptor and receptor proteins. Mammalian genomes encode several CUL proteins (CUL1–9), each contributing to distinct CRLs. Among these CUL proteins, CUL1, CUL3, and CUL4 are believed to be the most ancient and evolutionarily conserved from yeast to mammals, with CUL4 uniquely duplicated in vertebrates. Genetic evidence strongly implicates CUL4-based ubiquitin ligases (CRL4s) in chromatin regulation across various species and suggests that, in vertebrates, CRL4s have also acquired a cytosolic role, which is facilitated by a cytosol-localizing paralog of CUL4. Substrates identified through biochemical studies have elucidated the molecular mechanisms by which CRL4s regulate chromatin and cytosolic processes. The substantial body of knowledge on CUL4 biology amassed over the past two decades provides a unique opportunity to explore the functional evolution of CRL4. In this review, we synthesize the available structural, genetic, and biochemical data on CRL4 from various model organisms and discuss the conserved and novel functions of CRL4s. Full article

Fungi, which are widely distributed across the Earth, have successfully managed to colonize cold environments (e.g., polar regions, alpine ecosystems, and glaciers) despite the challenging conditions for life. They are capable of living in extremely harsh environments due to their ecological versatility and morphological plasticity. It is also believed that lower eukaryotes are the most adapted to life at low temperatures among microorganisms that thrive in cold environments. They play important ecological roles, contributing to nutrient recycling and organic matter mineralization. These highly specialized microorganisms have developed adaptation strategies to overcome the direct and indirect harmful influences of low temperatures. They have evolved a wide range of complex and cooperative adaptations at various cellular levels, including modifications to the cell envelope and enzymes, the production of cryoprotectants and chaperones, and the development of new metabolic functions. Adaptation to cold environments has made fungi an exciting source for the discovery of new cold-adapted enzymes (e.g., proteinases, lipases) and secondary metabolites (e.g., pigments, osmolytes, polyunsaturated fatty acids) for widespread use in biotechnology, food technology, agriculture, pharmaceutics, molecular biology, textile industry, and environmental bioremediation in cold climates. This review aims to provide a comprehensive overview of the adaptive strategies employed by psychrophilic yeasts and fungi, highlighting their ecological roles and biotechnological potential. Understanding these adaptive mechanisms not only sheds light on microbial life in extreme environments but also paves the way for innovative applications in the food industry and agriculture. Full article

In order to solve the problem of low and poor straw degradation in typical black soil areas of Northeast China, the present study was carried out to screen the potential of in situ strains with cellulose degradation ability from black soils of Northeast China to play a role in the resourceful utilization of straw and the development of sustainable agriculture. The straw degradation potential of the strains was evaluated by combining sodium carboxymethyl cellulose plate screening and cellulase viability assay; the species identification of the strains was carried out by morphology, physiology, biochemistry, and molecular biology; and the basic medium formulation of the strains was optimized by Box–Behnken response surface methodology. Ten cellulose-degrading strains were identified: ZL-5, ZL-69, ZL-88, ZL-95, ZL-111, ZL-137, ZL-139, ZL-140, ZL-187, and ZL-216, of which ZL-139 had the highest cellulase production capacity, with a cellulase secretion of 7.8781 U/mL in the enzyme-producing medium. ZL-139 was identified as Bacillus cereus; the optimized best formulation was glucose—4.284 g/L, yeast extract—1.454 g/L, MgSO₄—0.417 g/L, KH₂PO₄—0.5 g/L, KH₂PO₄—0.5 g/L, K₂HPO₄—1.5 g/L, and NaCl—1.0 g/L. In conclusion, strain ZL-139 has good potential for crop straw degradation and can be a candidate strain for a straw-rotting agent in northeast China, with promising prospects for development and utilization. Full article

Panax japonicus C. A. Meyer is renowned for its significant therapeutic effects and is commonly used worldwide. Its active ingredients, triterpenoid saponins, show variation in content among different tissues. The tissue-specific distribution of saponins is potentially related to the expression of vital genes in the biosynthesis pathway. In this study, the contents of five saponins (ginsenoside Ro, chikusetsusaponin IV, chikusetsusaponin IVa, ginsenoside Rg1, and ginsenoside Rb1) in three different tissues were determined by HPLC. Transcriptome sequencing analysis identified differentially expressed genes (DEGs) involved in triterpenoid saponin biosynthesis, highlighting significant correlations between saponin contents and the expression levels of 10 cytochrome p450 monooxygenase (CYP) and 3 UDP-glycosyltransferase (UGT) genes. Cloning, sequencing, and prokaryotic expression of UGT genes confirmed the molecular weights of UGT proteins. Gene sequence alignment and phylogenetic analysis provided preliminary insights into UGT gene functions. Meanwhile, the function of one UGT gene was characterized in the yeast. These findings advance our understanding of the triterpenoid saponin biosynthesis in P. japonicus and support future research in traditional Chinese medicine (TCM) and synthetic biology. Full article

There have been massive technological advances in molecular biology and genetics over the past five decades. I have personally experienced these advances and here I reflect on those origins, from my perspective, studying yeast mitochondrial genetics leading up to deciphering the functions of the mitochondrial genome. The yeast contributions commenced in the middle of the last century with pure genetics, correlating mutants with phenotypes, in order to discover genes, just like the early explorations to discover new lands. The quest was to explore the mitochondrial genome and find its genes and their products. It was most fortunate that DNA sequencing technologies became available in the late 1970s, and laboratories were restructured enormously to keep pace with the emerging technologies. There were considerable costs in equipping laboratories, purchasing ultracentrifuges and restriction endonucleases, and undertaking DNA sequencing; additionally, workers required special safety gear. Full article

Onychomycosis (OM) is a widespread infection requiring prolonged treatment with potential side effects. Diagnostic certainty is therefore essential before initiating antifungal therapy. Molecular biology has already shown benefits in reducing the time to diagnosis, providing technical ease, and increasing sensitivity for the respective species that molecular tests can detect. Nevertheless, causative agents are numerous, and culture remains essential, particularly for detecting non-dermatophytes mold infections. This study compared the performance of three different diagnostic strategies: conventional culture technique, the multiplex DermaGenius^® 2.0 PCR (DG), and a mixed PCR/culture algorithm guided by the result of direct examination with calcofluor (DEC). The mixed algorithm (MA) prioritizes DG PCR and DEC as the primary diagnostic tools, supplemented by selective sample inoculation when mycelial elements are visualized in DEC and when DG PCR fails to detect any fungus or identifies a fungus with morphology differing from that observed in DEC (filamentous fungi versus yeasts). With only 13% of samples requiring inoculation, MA emerged as the most effective strategy, demonstrating significantly higher sensitivity (98.18%; p < 0.001) compared to single-method approaches (78.18% for DG PCR alone and 74.55% for culture alone) while maintaining a specificity comparable to DG PCR (100%). This new approach saves time in result delivery, requires fewer human resources, and increases diagnostic accuracy to better meet the needs of clinicians. Full article

Despite the current appreciation of pulque as a probiotic fermented beverage, pulque has been also regarded as a poor-quality product, particularly due to the lack of sanitary control during its elaboration. To address this problem, a semi-continuous fermentation system was established, emulating the artisanal production process. Microfiltration-sterilized aguamiel was employed as the substrate, whereas a good-quality pulque was used as the fermentation inoculum. During the fermentation, the physicochemical, microbiological (lactic acid and Leuconostoc-type bacteria and yeasts) and sensory characteristics of the must were monitored. The isolated microorganisms were identified by molecular biology and MALDI-MS techniques. The sterilization of aguamiel by microfiltration did not negatively affect its physicochemical attributes. After 6–8 days of operation of the semi-continuous bioreactor, the fermentation reached a quasi-stationary state considering most of the parameters monitored during the experiment. The final fermentation product presented similar physicochemical, microbial and sensory properties to those of the pulque inoculum. The genera identified were Leuconostoc, Lentilactobacillus, Lactobacillus, Liquorilactobacillus, Fructilactobacillus and Saccharomyces. The strains Lentilactobacillus diolivorans and Liquorilactobacillus capillatus and uvarum have not been previously isolated from pulque. In conclusion, the fermentation system developed in this work was effective to standardize the quality of pulque while preserving the positive attributes of the artisanal process, thus harnessing the probiotic properties of pulque. Full article

(1) Background: The identification of microorganisms includes traditional biochemical methods, molecular biology methods evaluating the conserved regions of rRNA, and the molecular biology of proteins (proteomics), such as MALDI-TOF MS mass spectrometry. This work aimed to identify the biodiversity of yeasts associated with stingless bee species’ honey and pollen, Melipona scutellaris, Nannotrigona testaceicornes, and Tetragonisca angustula, from the region of São Gonçalo dos Campos-Bahia (BA) state, Brazil. (2) Methods: Cellular proteins were extracted from 2837 microbial isolates (pollen and honey) and identified via MALDI-TOF MS. The identified yeast species were also compared to the mass spectra of taxonomically well-characterized reference strains, available from the National Center of Biotechnology Information (NCBI) database. (3) Results: Nine yeast species were identified: Candida maltosa, Candida norvegica, Kazachstania telluris, Schizosaccharomyces pombe, Scheffersomyces insectosus, Meyerozyma guilliermondii, Brettanomyces bruxellensis, Kazachstania exigua, and Starmerella lactis-condensi. Nannotrigona testaceicornes pollen had the highest number of yeast colonies. The yeasts Brettanomyces bruxellensis and Kazachstania telluris showed high populations in the samples of Nannotrigona testaceicornes and Melipona scutellaris, respectively. This work shows that there is some sharing of the same species of yeast between honey and pollen from the same beehive. (4) Conclusions: A total of 71.84% of the identified species present a high level of confidence at the species level. Eight yeast species (Candida maltosa, Candida norvegica, Kazachstania telluris, Schizosaccharomyces pombe, Scheffersomyces insectosus, Meyerozyma guilliermondii, Kazachstania exigua, and Starmerella lactis-condensi) were found for the first time in the samples that the authors inspected. This contributes to the construction of new knowledge about the diversity of yeasts associated with stingless bee products, as well as to the possibility of the biotechnological application of some yeast species. Full article

Tausonia pullulans 6A7 is a low-temperature yeast strain that can produce lipases. Yeast, which is made up of chassis cells, is an important part of synthetic biology, and the use of the lipase-producing properties of T. pullulans 6A7 for the production of fatty acids provides a new pathway for targeted synthesis in yeast cell factories. In this study, we performed RNA-seq on lipase-producing T. pullulans 6A7 at different temperatures (15 °C, 20 °C, 20 °C without corn oil, and 25 °C). Therefore, a total of 8455 differentially expressed genes were screened, and 16 of them were FAD candidate genes. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of group A (15 °C) vs. group D (25 °C) showed that the pathways of fatty acid biosynthesis (map00061) and the biosynthesis of unsaturated fatty acids (map01040) were significantly enriched. In the proposed temporal analysis of differentially expressed genes among the four temperature modulations, we found differentially expressed genes in nine clusters that had the same expression trends; these genes may be jointly involved in multiple biological processes in T. pullulans 6A7. In addition, we found 16 FAD candidate genes involved in fatty acid biosynthesis, and the expression of these genes had similar expression in the transcriptome trends with the different temperature treatments. These findings will help in future in-depth studies of the function and molecular mechanisms of these important FAD genes involved in fatty acid metabolism in yeast, and they could also be conducive to the establishment of a cellular factory for targeted fatty acid production by using yeast. Full article

Bread is the oldest and most essential food consumed by humans, with its consumption exceeding nutritional needs and becoming part of cultural habits. Fermentation is an important step in the bread-making process, giving it its rheological, organoleptic, aromatic, and nutritional properties. Lactic acid bacteria and yeasts are both responsible for the fermentation step and part of the natural flour microbiota. In this study, we aimed to characterize LAB in three types of flour, namely, wheat, oat, and rice flour, using conventional phenotypic and biochemical assays and to carry out molecular-biology-based characterization via studying the rrn Operon using RFLP of the ITS region and via PCR using species-specific primers. Additionally, the effect of LAB diversity among the three types of flour and their influence on dough characteristics were assessed. Also, we evaluated the antagonistic effects of LAB on two bacterial (E. coli and S. aureus) and two fungal (Botrytis and Fusarium) pathogens. This study showed that LAB are not the predominant species in rice flour, while they were predominant in wheat and oat flour. Additionally, Lactobacillus sanfranciscencis was found to be the predominant species in wheat flour, while its presence in oat flour was minor. Finally, through their production of soluble substances, LAB exerted antagonistic effects on the four types of pathogenic microorganisms. Full article