Transcriptomic analysis of extensive changes in metabolic regulation in Kluyveromyces lactis strains

Novel Secreted Peptides From Rhizopus arrhizus var. delemar With Immunomodulatory Effects That Enhance Fungal Pathogenesis

Secreted fungal peptides are known to influence the interactions between the pathogen and host innate immunity. The aim of this study is to screen and evaluate secreted peptides from the fungus Rhizopus arrhizus var. delemar for their immunomodulatory activity. By using mass spectrometry and immuno-informatics analysis, we identified three secreted peptides CesT (S16), Colicin (S17), and Ca2+/calmodulin-dependent protein kinase/ligand (CAMK/CAMKL; S27). Culturing peripheral blood-derived monocytic macrophages (PBMMs) in the presence of S16 or S17 caused cell clumping, while culturing them with S27 resulted in the formation of spindle-shaped cells. S27-treated PBMMs showed cell cycle arrest at G0 phase and exhibited alternatively activated macrophage phenotype with pronounced reduction in scavenger receptors CD163 and CD206. Homology prediction indicated that IL-4/IL-13 is the immunomodulatory target of S27. Confirming this prediction, S27 initiated macrophage activation through phosphorylation of STAT-6; STAT-6 inhibition reversed the activity of S27 and reduced the formation of spindle-shaped PBMMs. Lastly, S27 treatment of PBMMs was associated with altered expression of key iron regulatory genes including hepcidin, ferroportin, transferrin receptor 1, and ferritin in a pattern consistent with increased cellular iron release; a condition known to enhance Rhizopus infection. Collectively, R. arrhizus var. delemar secretes peptides with immunomodulatory activities that support fungal pathogenesis. Targeting the IL-4/IL-13R/STAT-6 axis is a potential therapeutic approach to enhance the PBMM-mediated fungal phagocytosis. This represents a potential new approach to overcome lethal mucormycosis.

Omics Approaches to Assess Flavor Development in Cheese

Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.

A Novel Regulated Hybrid Promoter That Permits Autoinduction of Heterologous Protein Expression in Kluyveromyces lactis

The yeast Kluyveromyces lactis is an important host for the expression of recombinant proteins at both laboratory and industrial scales. However, the system lacks a tightly regulated promoter that permits controlled expression of heterologous proteins. In this study, we report the engineering of a highly regulated strong hybrid promoter (termed P₃₅₀) for use in K. lactis. P₃₅₀ is tightly repressed by glucose or glycerol in the medium but strongly promotes gene expression once the carbon source has been consumed by the cells. This feature permits heterologous protein expression to be “autoinduced” at any scale without the addition of a gratuitous inducer molecule or changing feed solutions.

The yeast Kluyveromyces lactis has been a successful host for the production of heterologous proteins for over 30 years. Currently, the galactose-/lactose-inducible and glucose-repressible LAC4 promoter (P_LAC4) is the most widely used promoter to drive recombinant protein expression in K. lactis. However, P_LAC4 is not fully repressed in the presence of glucose and significant protein expression still occurs. Thus, P_LAC4 is not suitable in processes where tight regulation of heterologous gene expression is required. In this study, we devised a novel K. lactis promoter system that is both strong and tightly controllable. We first tested several different endogenous K. lactis promoters for their ability to express recombinant proteins. A novel hybrid promoter (termed P₃₅₀) was created by combining segments of two K. lactis promoters, namely, the strong constitutive P_GAP1 promoter and the carbon source-sensitive P_ICL1 promoter. We demonstrate that P₃₅₀ is tightly repressed in the presence of glucose or glycerol and becomes derepressed upon depletion of these compounds by the growing cells. We further illustrate the utility of P₃₅₀-controlled protein expression in shake flask and high-cell-density bioreactor cultivation strategies. The P₃₅₀ hybrid promoter is a strong derepressible promoter for use in autoinduction of one-step fermentation processes for the production of heterologous proteins in K. lactis.

IMPORTANCE The yeast Kluyveromyces lactis is an important host for the expression of recombinant proteins at both laboratory and industrial scales. However, the system lacks a tightly regulated promoter that permits controlled expression of heterologous proteins. In this study, we report the engineering of a highly regulated strong hybrid promoter (termed P₃₅₀) for use in K. lactis. P₃₅₀ is tightly repressed by glucose or glycerol in the medium but strongly promotes gene expression once the carbon source has been consumed by the cells. This feature permits heterologous protein expression to be “autoinduced” at any scale without the addition of a gratuitous inducer molecule or changing feed solutions.

Quantitative physiology and elemental composition of Kluyveromyces lactis CBS 2359 during growth on glucose at different specific growth rates

The yeast Kluyveromyces lactis has received attention both from academia and industry due to some important features, such as its capacity to grow in lactose-based media, its safe status, its suitability for large-scale cultivation and for heterologous protein synthesis. It has also been considered as a model organism for genomics and metabolic regulation. Despite this, very few studies were carried out hitherto under strictly controlled conditions, such as those found in a chemostat. Here we report a set of quantitative physiological data generated during chemostat cultivations with the K. lactis CBS 2359 strain, obtained under glucose-limiting and fully aerobic conditions. This dataset serves [corrected] as a basis for the comparison of K. lactis with the model yeast Saccharomyces cerevisiae in terms of their elemental compositions, as well as for future metabolic flux analysis and metabolic modelling studies with K. lactis.

A tool kit for molecular genetics of Kluyveromyces lactis comprising a congenic strain series and a set of versatile vectors

A set of different marker deletions starting with a ura3 derivative of the Kluyveromyces lactis type strain CBS2359 was constructed. After a first cross to obtain a strain with the opposite mating type that also carried a leu2 allele, continuous back-crosses were used to obtain a congenic strain series with different marker combinations, including deletions in KlHIS3, KlADE2 and KlLAC4. Enzymes involved in carbohydrate metabolism were shown to behave very similarly to the original type strain and other K. lactis strains investigated previously. Moreover, a vector series of Saccharomyces cerevisiae genes flanked by loxP sites was constructed to be used as heterologous deletion cassettes in K. lactis, together with two plasmids for expression of Cre-recombinase for marker regeneration. To increase the frequency of homologous recombination, the Klku80 deletion was also introduced into the congenic strain series. A PCR-based method for determination of mating type is provided.

Fungal regulatory evolution: cis and trans in the balance

Regulatory divergence is likely a major driving force in evolution. Comparative genomics is being increasingly used to infer the evolution of gene regulation. Ascomycota fungi are uniquely suited among eukaryotes for regulatory evolution studies, due to broad phylogenetic scope, many sequenced genomes, and tractability of genomic analysis. Here we review recent advances in the identification of the contribution of cis- and trans-factors to expression divergence. Whereas current strategies have led to the discovery of surprising signatures and mechanisms, we still understand very little about the adaptive role of regulatory evolution. Empirical studies including experimental evolution, comparative functional genomics and hybrid and engineered strains are showing early promise toward deciphering the contribution of regulatory divergence to adaptation.

From elements to modules: regulatory evolution in Ascomycota fungi

Regulatory divergence is likely a major driving force in evolution. Comparative transcriptomics provides a new glimpse into the evolution of gene regulation. Ascomycota fungi are uniquely suited among eukaryotes for studies of regulatory evolution, because of broad phylogenetic scope, many sequenced genomes, and facility of genomic analysis. Here we review the substantial divergence in gene expression in Ascomycota and how this is reconciled with the modular organization of transcriptional networks. We show that flexibility and redundancy in both cis-regulation and trans-regulation can lead to changes from altered expression of single genes to wholesale rewiring of regulatory modules. Redundancy thus emerges as a major driving force facilitating expression divergence while preserving the coherent functional organization of a transcriptional response.

Production of ethanol from the mixture of beet molasses and cheese whey by a 2-deoxyglucose-resistant mutant of Kluyveromyces marxianus

Fourteen lactose-fermenting strains of Kluyveromyces marxianus, including its anamorph, Candida kefyr, were grown in two media containing 20% (w/v) sugar as either beet molasses or cheese whey. Strain NBRC 1963 of K. marxianus converted sucrose and lactose to ethanol in both media most efficiently. However, ethanol was produced from sucrose and not from lactose by strain NBRC 1963 in the medium containing equal amounts of sugar from beet molasses and cheese whey. The spontaneous mutants resistant to 2-deoxyglucose in the minimal medium composed of galactose as the sole carbon source were isolated from strain NBRC 1963. Among them, strain KD-15 vigorously produced ethanol in the media containing beet molasses, cheese whey, or both. The mutant strain KD-15 was insensitive to catabolite repression, as shown by the observation that beta-galactosidase was not repressed in the presence of sucrose from beet molasses.

Gene expression and biochemical analysis of cheese-ripening yeasts: focus on catabolism of L-methionine, lactate, and lactose

DNA microarrays of 86 genes from the yeasts Debaryomyces hansenii, Kluyveromyces marxianus, and Yarrowia lipolytica were developed to determine which genes were expressed in a medium mimicking a cheese-ripening environment. These genes were selected for potential involvement in lactose/lactate catabolism and the biosynthesis of sulfur-flavored compounds. Hybridization conditions to follow specifically the expression of homologous genes belonging to different species were set up. The microarray was first validated on pure cultures of each yeast; no interspecies cross-hybridization was observed. Expression patterns of targeted genes were studied in pure cultures of each yeast, as well as in coculture, and compared to biochemical data. As expected, a high expression of the LAC genes of K. marxianus was observed. This is a yeast that efficiently degrades lactose. Several lactate dehydrogenase-encoding genes were also expressed essentially in D. hansenii and K. marxianus, which are two efficient deacidifying yeasts in cheese ripening. A set of genes possibly involved in l-methionine catabolism was also used on the array. Y. lipolytica, which efficiently assimilates l-methionine, also exhibited a high expression of the Saccharomyces cerevisiae orthologs BAT2 and ARO8, which are involved in the l-methionine degradation pathway. Our data provide the first evidence that the use of a multispecies microarray could be a powerful tool to investigate targeted metabolism and possible metabolic interactions between species within microbial cocultures.