Extraction of genomic DNA from yeasts for PCR-based applications

CRISPR/Cas9-based iterative multi-copy integration for improved metabolite yields in Saccharomyces cerevisiae

High-copy integration of key genes offers a promising strategy for efficient biosynthesis of valuable natural products in Saccharomyces cerevisiae. However, traditional multi-copy gene integration methods meet challenges including low efficiency and labor-intensive screening processes. In this study, we developed the IMIGE (Iterative Multi-copy Integration by Gene Editing) system, a CRISPR/Cas9-based approach that exploits both δ and rDNA repetitive sequences for simultaneous multi-copy integrations in S. cerevisiae. This system combines the mixture of Cas9-sgRNA expression vectors with a split-marker strategy for efficient donor DNA assembly in vivo and enables rapid, iterative screening through growth-related phenotypes. When applied to the biosynthesis of ergothioneine and cordycepin, the IMIGE system achieved significant yield improvements, with titers of 105.31 ± 1.53 mg/L and 62.01 ± 2.4 mg/L, respectively, within just two screening cycles (5.5-6 days in total). These yields represent increases of 407.39 % and 222.13 %, respectively, compared to the strains with episomal expression. By streamlining the integration process, utilizing growth-based selection, and minimizing screening demands in both equipment and labor, the IMIGE system could provide an efficient and scalable platform for high-throughput strain engineering, facilitating enhanced microbial production of a wide range of bioproducts.

Pichia Toolkit: Use of the combinatorial library screening system for expression of a marine laccase

Pnh_Lac1 (Lac1) gene from the marine-derived fungus Peniophora sp. CBMAI 1063 was expressed in Pichia pastoris using the Pichia Toolkit system. Constitutive (pGAP, pPET9, pG1, pG6, and pADH2) and methanol-inducible (pAOX1, pDAS1, and pPMP20) promoters were assessed in combination with 21 different signal peptides and His-tag about efficiency in laccase production. Next, 3,200 variants were screened, different culture conditions were evaluated, and an investigation was performed in a bench-scale bioreactor for the best variant selected. The influence of promoters and signal peptides on Lac1 expression was demonstrated in the constitutive libraries. The change from pG6 to pGAP resulted in a 171-fold increase in production. Changing the alpha-mating factor peptide by the native signal peptide of the Lac1 gene decreased laccase production 22-fold. The promoters pGAP (constitutive library) and pAOX1 (inductive library) performed best. The association with the signal peptide αAmylase-αMFD was more efficient for both promoters. The constitutive expression of Lac1 had a 1.37-fold greater production compared to the inducible expression achieved by pAOX1 and was considered more suitable for laccase expression. Culturing the best producer variant pGAP_αA1 at pH 6 and 18 °C resulted in the best production rate in deep-well plates (90 U/L). Constitutive laccase production in a 2-L bioreactor resulted in a peak production of 178 U/L after 78 h. Pichia Toolkit was efficient in the selection of the best molecular regulation and secretion of Lac1. Our findings contribute to the development of marine biotechnology and will serve as the basis for Lac1 production optimization.

Single cell protein production of co-culture Kodamaea ohmeri and Lactococcus lactis in corn straw hydrolysate

With the world population continuously increasing, the protein demand will double by 2050. Single cell protein (SCP) derived from lignocellulosic biomass offers a sustainable solution. Many inhibitors are produced during the pretreatment process of lignocellulosic biomass. Inhibitor-rich hydrolysates limit microorganisms cell growth and SCP yields. In this work, we report a co-culture consortium of Kodamaea ohmeri SSK (pentose-utilizing yeast) and Lactococcus lactis LX (probiotic bacterium) that efficiently converts real corn straw hydrolysate into SCP. K. ohmeri SSK can tolerate inhibitors such as furfural, 5-hydroxymethylfurfural (5-HMF), and acetic acid and consume glucose, xylose, and arabinose in real hydrolysate. L. lactis LX showed less growth in monoculture than that of co-culture. The total amino acid content from co-cultured K. ohmeri SSK and L. lactis LX was increased to 331.42 mg/g crude protein, but that of monocultured K. ohmeri SSK was 309.89 mg/g crude protein containing 17 amino acids. This work demonstrates a symbiotic microbial platform can produce SCP from non-detoxified lignocellulosic biomass. The co-culture robust inhibitor tolerance and balanced amino acid profile highlight its potential for industrial-scale protein production. These results will represent an attractive choice cell factory for lignocellulosic substrate utilization and provide a platform for biomass conversion to SCP.

Safety aspects and in vitro probiotic assessment of Kluyveromyces marxianus strains from neonatal faeces

The isolation and identification of probiotic yeasts is increasing rapidly. In this context, the present study aimed to isolate and identify yeast strains from neonatal faeces in Erzurum province, Türkiye and to determine their probiotic characteristics. A total of 12 yeast strains were isolated and genotypic characterization revealed the presence of seven different species, including Kluyveromyces marxianus, Candida spp. Clavispora lusitaniae, Geotrichum candidum, Trichophyton rubrum, Pichia cactophila, and Meyerozyma guilliermondii. The non-pathogenic and potentially probiotic characteristics of the K. marxianus M2, M9, and M10 strains were further investigated. Although yeast has been isolated from neonatal faeces before, K. marxianus was isolated for the first time in this study. The results revealed that the K. marxianus strains exhibited high resistance to simulated gastric juice and bile salts. The auto-aggregation percentages of the strains ranged from 92.55 to 94.78% after 4 h, while the co-aggregation percentages with pathogens ranged from 19.70 to 53.09%. The K. marxianus M2 strain exhibited the highest degree of hydrophobicity (74.97%), and none of the strains demonstrated DN-ase or haemolytic activity. Furthermore, M2 and M9 strains displayed bile salt hydrolase activity. In conclusion, based on in vitro probiotic test results, K. marxianus strains were selected as probiotic yeast candidates for further studies, especially in patients under antibiotic therapy.

Insights into urinary catheter colonisation and polymicrobial biofilms of Candida- bacteria under flow condition

Most hospital-acquired urinary tract infections are the result of implanted urinary catheter, with majority of studies focused on a single species colonisation, but recently polymicrobial colonisations are being reported. In this study, indwelling urinary catheters were collected from ICU patients and the colonising microbiome was isolated and identified by the traditional; culturing method and metagenomics. It was observed that majority of catheters were colonised by polymicrobial biofilms, containing both bacterial and fungal isolates making them diverse and complex. However, the metagenomics results were quite surprising showing the presence of multiple organisms of which only 1or 2 showed growth when cultured. Later, in vitro assays were performed by selecting 6 combinations, with each combination containing one Candida spp. - C. albicans or C. tropicalis with one bacteria K. pneumoniae, P. aeruginosa or E. coli. It was observed that polymicrobial biofilms were stronger than mono-microbial biofilms, suggesting their increased surface adhesion. Furthermore, to simulate the dynamic environment in which cells are exposed to a certain level of fluid movement, a flow system was established to imitate the flow generated in colonized urinary catheter. We have observed changes in biofilm architecture, adhesion and thickness under flow conditions compared with static conditions, with a uniformly adhered biofilm with increased thickness of polymicrobial biofilms as compared to mono-species biofilms. The biofilm formed under flow was more viable than the static biofilm with higher number of live cells in flow condition.

Phenotypic and Molecular Characterization of Candida albicans Isolates from Mexican Women with Vulvovaginitis

Vulvovaginal candidiasis (VVC) is an opportunistic mycosis that affects women of reproductive age. The most frequent etiological agent is Candida albicans. The development of VVC depends on factors related to the host and the fungus. Among the factors related to Candida spp. are virulence factors, but genotype may also be involved. The objective of this study was to evaluate the ABC genotypes and extracellular hydrolytic enzyme production in C. albicans isolates obtained from Mexican women with vulvovaginitis to determine if there is a correlation between these characteristics that allows the fungus to invade and cause damage to the host. Forty-three yeast isolates were obtained from vaginal exudates from women with symptoms of infection. The isolates were identified by germ tube tests and by Cand PCR. The ABC genotype of the isolates identified as C. albicans was determined through the isolates' DNA amplification using the oligonucleotides CA-INT-R and CA-INT-L. The activity of esterase, phospholipase, proteinase, and hemolysin was evaluated in specific culture media. The correlation between extracellular enzyme production and genotype was analyzed using a two-way ANOVA and the Sidak comparison test. A total of 57.5% of the yeast isolates were identified as C. albicans. The genotypes identified were A (82.6%) and B (17.4%). The activity of esterase, phospholipase, proteinase, and hemolysin was very strong. No statistically significant difference was found between enzyme production and genotypes. In conclusion, genotype A predominates among C. albicans vaginal isolates. The production of extracellular hydrolytic enzymes was widely expressed in C. albicans vaginal isolates, but no correlation with genotype was found.

The role of ATP citrate lyase, phosphoketolase, and malic enzyme in oleaginous Rhodotorula toruloides

Rhodotorula toruloides is an oleaginous yeast recognized for its robustness and the production of high content of neutral lipids. Early biochemical studies have linked ATP citrate lyase (ACL), phosphoketolase (PK), and cytosolic malic enzyme (cMAE) with de novo lipid synthesis. In this study, we discovered that upon a CRISPR/Cas9-mediated knockout of the ACL gene, lipid content in R. toruloides IFO0880 decreased from 50 to 9% of its dry cell weight (DCW) in glucose medium and caused severe growth defects (reduced specific growth rate, changes in cell morphology). In xylose medium, the lipid content decreased from 43 to 38% of DCW. However, when grown on acetate as the sole carbon source, the lipid content decreased from 45 to 20% of DCW. Significant growth defects as a result of ACL knockout were observed on all substrates. In contrast, PK knockout resulted in no change in growth or lipid synthesis. Knocking out cMAE gene resulted in lipid increase of 2.9% of DCW and 23% increase in specific growth rate on glucose. In xylose or acetate medium, no change in lipid production as a result of cMAE gene knockout was observed. These results demonstrated that ACL plays a crucial role in lipid synthesis in R. toruloides IFO0880, as opposed to PK pathway or cMAE, whose presence in some conditions even disfavors lipid production. These results provided valuable information for future metabolic engineering of R. toruloides. KEY POINTS: • ACL is crucial for the fatty acid synthesis and growth in R. toruloides IFO0880. • Lipid production and cell growth is are unchanged as a result of PK knockout. • Cytosolic malic enzyme does not play a significant role in lipogenesis.

Unveiling the fitness of Saccharomyces cerevisiae strains for lignocellulosic bioethanol: a genomic exploration through fermentation stress tests

Lignocellulosic biomass holds significant promise as a substrate for bioethanol production, yet the financial viability of lignocellulosic fermentation poses challenges. The pre-treatment step needed for lignocellulosic substrates generates inhibitors that impede Saccharomyces cerevisiae growth, affecting the fermentation process and overall yield. In modern sugarcane-to-ethanol plants, a rapid succession of yeast strains occurs, with dominant strains prevailing. Therefore, yeast strains with both dominance potential and inhibitor tolerance are crucial towards the development of superior strains with industrial fitness. This study adopted a hybrid approach combining biotechnology and bioinformatics to explore a cluster of 20 S. cerevisiae strains, including industrial and oenological strains exhibiting diverse phenotypic features. In-depth genomic analyses focusing on gene copy number variations (CNVs) and single nucleotide polymorphisms (SNPs) were conducted and compared with results from fermentation tests once inoculated in multiple strains kinetics under stressing conditions such as low nitrogen availability and high formic or acetic acid levels. Some strains showed high resistance to biotic stress and acetic acid. Moreover, four out of 20 strains - namely S. cerevisiae YI30, Fp89, Fp90 and CESPLG05 - displayed promising resistance also to formic acid, the most impactful weak acids in pre-treated lignocellulosic biomass. These strains have the potential to be used for the development of superior S. cerevisiae strains tailored for lignocellulosic bioethanol production.

Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex

Nuclear pore proteins (nucleoporins [Nups]) physically interact with hundreds of chromosomal sites, impacting transcription. In yeast, transcription factors mediate interactions between Nups and enhancers and promoters. To define the molecular basis of this mechanism, we exploited a separation-of-function mutation in the Gcn4 transcription factor that blocks its interaction with the nuclear pore complex (NPC). This mutation reduces the interaction of Gcn4 with the highly conserved nuclear export factor Crm1/Xpo1. Crm1 and Nups co-occupy enhancers, and Crm1 inhibition blocks interaction of the nuclear pore protein Nup2 with the genome. In vivo, Crm1 interacts stably with the NPC and in vitro, Crm1 binds directly to both Gcn4 and Nup2. Importantly, the interaction between Crm1 and Gcn4 requires neither Ran-guanosine triphosphate (GTP) nor the nuclear export sequence binding site. Finally, Crm1 and Ran-GTP stimulate DNA binding by Gcn4, suggesting that allosteric coupling between Crm1-Ran-GTP binding and DNA binding facilitates the docking of transcription-factor-bound enhancers at the NPC.

Establishment of a yeast essential protein conditional-degradation library and screening for autophagy-regulating genes

Macroautophagy/autophagy is an evolutionarily conserved intracellular degradation pathway that relies on vacuoles or lysosomes. Over 40 ATG genes have been identified in yeast cells as participants in various types of autophagy, although these genes are non-essential. While some essential genes involved in autophagy have been identified using temperature-sensitive yeast strains, systematic research on essential genes in autophagy remains lacking. To address this, we established an essential protein conditional degradation library using the auxin-inducible degron (AID) system. By introducing the GFP-Atg8 plasmid, we identified 29 essential yeast genes involved in autophagy, 19 of which had not been previously recognized. In summary, the yeast essential protein conditional degradation library we constructed will serve as a valuable resource for systematically investigating the roles of essential genes in autophagy and other biological functions.Abbreviation: AID: auxin-inducible degron; ALP: alkaline phosphatase; ATG: autophagy related; CSG: constitutive slow growth; DAmP: Decreased Abundance by mRNA Perturbation; GFP: green fluorescent protein; MMS: methyl methanesulfonate; ORF: open reading frame; PAS: phagophore assembly site; PCR: polymerase chain reaction; SD-G: glucose starvation medium; SD-N: nitrogen starvation medium; TOR: target of rapamycin kinase; YGRC: yeast genetic resource center; YPD: yeast extract peptone dextrose.

PCR-fingerprinting of culturable yeasts from commercially obtained beers: a simple and engaging applied microbiological laboratory exercise

Yeast and fermented products present an opportunity to introduce students to applied microbiology. We designed and implemented a project-oriented laboratory class where yeasts from bottled beverages were isolated and compared using DNA fingerprinting and Sanger-sequencing. We recovered 17 Saccharomyces isolates, and two non- Saccharomyces yeasts. Fingerprinting identified two groups of closely related Saccharomyces isolates in unrelated beer styles, later identified as diastatic and wine yeasts using phylogenomics. Isolates from traditional products thus may not represent the original fermentation. We believe that the interlinked nature of topics and the simple basis can elevate engagement and performance of students during such a class.

Cryptic genetic variation shapes the fate of gene duplicates in a protein interaction network

Paralogous genes are often functionally redundant for long periods of time. While their functions are preserved, paralogs accumulate cryptic changes in sequence and expression, which could modulate the impact of future mutations through epistasis. We examine the impact of mutations on redundant myosin proteins that have maintained the same binding preference despite having accumulated differences in expression levels and amino acid substitutions in the last 100 million years. By quantifying the impact of all single-amino acid substitutions in their SH3 domains on the physical interaction with their interaction partners, we show that the same mutations in the paralogous SH3s change binding in a paralog-specific and interaction partner-specific manner. This contingency is explained by the difference in promoter strength of the two paralogous myosin genes and epistatic interactions between the mutations introduced and cryptic divergent sites within the SH3s. One significant consequence of this contingency is that while some mutations would be sufficient to nonfunctionalize one paralog, they would have minimal impact on the other. Our results reveal how cryptic divergence, which accumulates while maintaining functional redundancy in cellular networks, could bias gene duplicates to specific fates.

Photoinduced electron transfer enables cytochrome P450 enzyme-catalyzed reaction cycling

Cytochrome P450 enzymes (CYPs), the members of the largest superfamily of enzymes in plant kingdom, catalyze a variety of functional group transformations involved in metabolite biosynthesis, end-product derivatization, and exogeneous molecule detoxification. Nevertheless, CYPs' functional characterization and practically industrial application have been largely encumbered by their critical dependency on the reducing equivalent for the catalytic cycling, driven by the tedious electron relay mediated by CYP reductase (CPR). Here, we report a photoinduced electron transfer system that initiates and sustains the CYP-catalyzed reaction cycling. Using Camptotheca acuminata CYP72A565-catalyzed carbon-carbon cleavage reaction, a key biosynthetic reaction in the biosynthesis of plant-derived antitumor monoterpene indole alkaloid camptothecin, as a representative CYP-catalyzed reaction model, we identified eosin Y (EY) and triethanolamine (TEOA) as an efficient photosensitizer/sacrificial reagent pair for the photoinduced electron generating system. The C. acuminata camptothecin 10-hydroxylase-catalyzed regioselective C10-hydroxylation of camptothecin into 10-hydroxycamptothecin could be enabled by the photoinduced electron transfer system, demonstrating that the EY/TEOA pair serves as an efficient surrogate for membranous CPR and can be expanded to other CYP-catalyzed reaction cycling. The catalytic efficiency of the photoinduced electron transfer-driven CYP-catalyzed cycling exceeds that of the native NADPH-dependent CPR-supported CYP-catalyzed reaction, thereby circumventing the dependency on both NADPH and the reductase CPR. The present study provides a photoinduced electron generating and transferring system as an efficient and facile alternative to membranous NADPH-dependent CPR, offering a new avenue for CYP-mediated conversion of complex bioactive natural products using synthetic biology approaches.

Characterizing heterologous protein burden in Komagataella phaffii

Yeast is a widely utilized chassis for heterologous protein production, with Komagataella phaffii well-established as a prominent nonconventional yeast in this field. Despite its widespread recognition, there remains considerable potential to further optimize these cell factories to meet high production demands in a cost-effective and sustainable manner. Understanding the cellular response to the challenges of heterologous protein production can equip genetic engineers with crucial knowledge to develop enhanced strategies for constructing more efficient cell factories. In this study, we explore the molecular response of various K. phaffii strains that produce either the human insulin precursor or Mambalgin-1, examining changes in transcription and changes in intra- and extracellular protein levels. Our findings provide valuable insights into the molecular mechanisms that regulate the behaviour of K. phaffii production strains under the stress of producing different heterologous proteins. We believe that these results will serve as a foundation for identifying new genetic targets to improve strain robustness and productivity. In conclusion, we present new cellular and molecular insights into the response of K. phaffii cell factories to the challenges of burdensome heterologous protein production and our findings point to different engineering strategies for improved cell factory performance.

Challenges in elucidating ethylene glycol metabolism in Saccharomyces cerevisiae

Polyethylene terephthalate (PET) is one of the most used polymers in the packaging industry; enzymatic recycling is emerging as a sustainable strategy to deal with waste PET, producing the virgin monomers terephthalic acid and ethylene glycol (EG). These monomers can be feedstocks for further microbial transformations. While EG metabolism has been uncovered in bacteria, in yeast the pathway for the oxidation to glycolic acid (GA) has only been proposed, but never experimentally elucidated. In this work, we investigated in Saccharomyces cerevisiae the potential contribution to this metabolism of two endogenous genes, YLL056C (a putative alcohol dehydrogenase) and GOR1 (glyoxylate reductase). Secondly, the possible role of alcohol dehydrogenases (ADHs) was considered, too. Finally, two heterologous genes (gox0313 from Gluconobacter oxydans and AOX1 from Komagataella phaffii) were expressed with the intent to push EG oxidation toward GA. Our main findings revealed that (i) Gor1, Yll056c, and ADHs are not involved in EG oxidation and (ii) the bottleneck of the catabolism is the first step in the pathway, due to the endogenous mechanisms for aldehyde detoxification. Multiomics studies are required to completely elucidate the pathway for EG catabolism, while further engineering directed toward relieving the bottleneck is needed to fully unleash the potential of yeasts for the upcycling of EG to GA.

Construction and iterative redesign of synXVI a 903 kb synthetic Saccharomyces cerevisiae chromosome

The Sc2.0 global consortium to design and construct a synthetic genome based on the Saccharomyces cerevisiae genome commenced in 2006, comprising 16 synthetic chromosomes and a new-to-nature tRNA neochromosome. In this paper we describe assembly and debugging of the 902,994-bp synthetic Saccharomyces cerevisiae chromosome synXVI of the Sc2.0 project. Application of the CRISPR D-BUGS protocol identified defective loci, which were modified to improve sporulation and recover wild-type like growth when grown on glycerol as a sole carbon source when grown at 37˚C. LoxPsym sites inserted downstream of dubious open reading frames impacted the 5' UTR of genes required for optimal growth and were identified as a systematic cause of defective growth. Based on lessons learned from analysis of Sc2.0 defects and synXVI, an in-silico redesign of the synXVI chromosome was performed, which can be used as a blueprint for future synthetic yeast genome designs. The in-silico redesign of synXVI includes reduced PCR tag frequency, modified chunk and megachunk termini, and adjustments to allocation of loxPsym sites and TAA stop codons to dubious ORFs. This redesign provides a roadmap into applications of Sc2.0 strategies in non-yeast organisms.

Heterologous Production of Antimicrobial Peptides in Yeast Allows for Massive Assessment of the Activity of DNA-Encoded Antimicrobials In Situ

Antibiotic resistance threatens global healthcare. In clinical practice, conventional antibiotics are becoming gradually less effective. Moreover, the introduction of new antimicrobial agents into clinical practice leads to the emergence of resistant pathogenic strains within just a few years. Hence, the development of platforms for massive creation and screening of new antimicrobial agents is of particular importance. Massive parallel screening will greatly reduce the time required to identify the most promising drug candidates. Meanwhile, DNA-encoded antimicrobial agents offer unique opportunities for the high-throughput development of new antibiotics. Here, the yeast Pichia pastoris was engineered to produce a panel of antimicrobial peptides (AMPs), followed by high-throughput screening of AMP producers that inhibit bacterial growth in situ. Yeast clones producing thanatin and protegrin-1 exhibited the highest level of antimicrobial activity among the panel of AMPs under investigation. The production level of recombinant thanatin was significantly higher than that of protegrin-1, which correlates with its low toxicity. The designed technique of massive assessment of the activity of DNA-encoded antimicrobial agents enables the identification of drug candidates with an increased therapeutic index. Further development of methods for a rational design of artificial diversity in AMPs, followed by deep functional profiling of antimicrobial activity, will yield new AMPs with improved therapeutic characteristics.

The Yeast Optogenetic Toolkit (yOTK) for Spatiotemporal Control of Gene Expression in Budding Yeast

Optogenetic systems utilize genetically encoded light-sensitive proteins to control cellular processes such as gene expression and protein localization. Like most synthetic systems, generation of an optogenetic system with desirable properties requires multiple design-test-build cycles. A yeast optogenetic toolkit (yOTK) allows rapid assembly of optogenetic constructs using Modular Cloning, or MoClo. In this protocol, we describe how to assemble, integrate, and test optogenetic systems in the budding yeast Saccharomyces cerevisiae. Generating an optogenetic system requires the user to first define the structure of the final construct and identify all basic parts and vectors required for the construction strategy, including light-sensitive proteins that need to be domesticated into the toolkit. The assembly is then defined following a set of standard rules. Multigene constructs are assembled using a series of one-pot assembly steps with the identified parts and vectors and transformed into yeast. Screening of the transformants allows optogenetic systems with optimal properties to be selected.

Anchor-Away: Efficient, Conditional Depletion of Nuclear Proteins in Saccharomyces cerevisiae

For functional studies of proteins in cells, effective tools that trigger rapid and efficient inactivation of the proteins are indispensable. The anchor-away (AA) system is designed to deplete nuclear-localized proteins through cellular relocation. The target protein is sequestered by an anchor receptor protein from the nucleus to the cytoplasm. The depletion is achieved through the formation of a stable complex that is solely driven by the addition of rapamycin, between the FRB domain of human mTOR and the FKBP12-binding domain of the FRP protein. The target protein and the receptor protein are fused through genetic recombination with the FRB and FKBP12 domains, respectively, to mediate the interaction. The export of the nuclear protein of interest is executed by the receptor protein, i.e., ribosomal protein RPL13A, which is transiently imported into the nucleus and then exported to the cytoplasm within the pre-ribosome. The proteins of interest can be depleted within minutes although the depleting conditions need to be optimized. AA is a valuable tool to help dissect the biological functions of nuclear proteins, especially ones that are essential for cell viability. In this chapter, we describe the steps to construct the necessary strains and several biochemical and functional experiments to confirm the functional abrogation of target proteins by AA.

Stress-inducible phosphoprotein 1 (Sti1/Stip1/Hop) sequesters misfolded proteins during stress

Co-chaperones are key elements of cellular protein quality control. They cooperate with the major heat shock proteins Hsp70 and Hsp90 in folding proteins and preventing the toxic accumulation of misfolded proteins upon exposure to stress. Hsp90 interacts with the co-chaperone stress-inducible phosphoprotein 1 (Sti1/Stip1/Hop) and activator of Hsp90 ATPase protein 1 (Aha1) among many others. Sti1 and Aha1 control the ATPase activity of Hsp90, but Sti1 also facilitates the transfer of client proteins from Hsp70 to Hsp90, thus connecting these two major branches of protein quality control. We find that misbalanced expression of Sti1 and Aha1 in yeast and mammalian cells causes severe growth defects. Also, deletion of STI1 causes an accumulation of soluble misfolded ubiquitinated proteins and a strong activation of the heat shock response. We discover that, during proteostatic stress, Sti1 forms cytoplasmic inclusions in yeast and mammalian cells that overlap with misfolded proteins. Our work indicates a key role of Sti1 in proteostasis independent of its Hsp90 ATPase regulatory functions by sequestering misfolded proteins during stress.

High-throughput single-cell sorting by stimulated Raman-activated cell ejection

Raman-activated cell sorting isolates single cells in a nondestructive and label-free manner, but its throughput is limited by small spontaneous Raman scattering cross section. Coherent Raman scattering integrated with microfluidics enables high-throughput cell analysis, but faces challenges with small cells (<3 μm) and tissue sections. Here, we report stimulated Raman-activated cell ejection (S-RACE) that enables high-throughput single-cell sorting by integrating stimulated Raman imaging, in situ image decomposition, and laser-induced cell ejection. S-RACE allows ejection of live bacteria or fungi guided by their Raman signatures. Furthermore, S-RACE successfully sorted lipid-rich Rhodotorula glutinis cells from a cell mixture with a throughput of ~13 cells per second, and the sorting results were confirmed by downstream quantitative polymerase chain reaction. Beyond single cells, S-RACE shows high compatibility with tissue sections. Incorporating a closed-loop feedback control circuit further enables real-time SRS imaging-identification-ejection. In summary, S-RACE opens exciting opportunities for diverse single-cell sorting applications.

Physiological relevance, localization and substrate specificity of the alternative (type II) mitochondrial NADH dehydrogenases of Ogataea parapolymorpha

Mitochondria from Ogataea parapolymorpha harbor a branched electron-transport chain containing a proton-pumping Complex I NADH dehydrogenase and three Type II NADH dehydrogenases (NDH-2). To investigate the physiological role, localization and substrate specificity of these enzymes, the growth of various NADH dehydrogenase knockout mutants was quantitatively characterized in shake-flask and chemostat cultures, followed by oxygen-uptake experiments with isolated mitochondria. NAD(P)H:quinone oxidoreduction of the three NDH-2 were individually assessed. Our findings reveal that the O. parapolymorpha respiratory chain contains an internal NADH-accepting NDH-2 (Ndh2-1/OpNdi1), at least one external NAD(P)H-accepting enzyme, and likely additional mechanisms for respiration-linked oxidation of cytosolic NADH. Metabolic regulation appears to prevent competition between OpNdi1 and Complex I for mitochondrial NADH. With the exception of OpNdi1, the respiratory chain of O. parapolymorpha exhibits metabolic redundancy and tolerates deletion of multiple NADH-dehydrogenase genes without compromising fully respiratory metabolism.

Pretreated sugarcane bagasse matches performance of synthetic media for lipid production with Yarrowia lipolytica

Engineered strains of Yarrowia lipolytica with modified lipid profiles and other desirable properties for microbial oil production are widely reported but are almost exclusively characterized in synthetic laboratory-grade media. Ensuring translatable performance between synthetic media and industrially scalable lignocellulosic feedstocks is a critical challenge. Yarrowia lipolytica growth and lipid production were characterized in media derived from two-step acid-catalyzed glycerol pretreatment of sugarcane bagasse. Fermentation performance was benchmarked against laboratory-grade synthetic growth media, including detailed characterization of media composition, nitrogen utilization, biomass and lipid production, and fatty acid product profile. A Yarrowia lipolytica strain modified to enable xylose consumption consumed all sugars, glycerol, and acetic acid, accumulating lipids to 34-44 % of cell dry weight. Growth and lipid content when grown in sugarcane bagasse-derived media were equivalent to or better than that observed with synthetic media. These sugarcane bagasse-derived media are suitable for transferable development of Yarrowia lipolytica fermentations from synthetic media.

Inhibition of diastatic yeasts by Saccharomyces killer toxins to prevent hyperattenuation during brewing

Secondary fermentation in beer can result in undesirable consequences, such as off-flavors, increased alcohol content, hyperattenuation, gushing, and the spontaneous explosion of packaging. Strains of Saccharomyces cerevisiae var. diastaticus are a major contributor to such spoilage due to their production of extracellular glucoamylase enzyme encoded by the STA1 gene. Saccharomyces yeasts can naturally produce antifungal proteins named "killer" toxins that inhibit the growth of competing yeasts. Challenging diastatic yeasts with killer toxins revealed that 91% of strains are susceptible to the K1 killer toxin produced by S. cerevisiae. Screening of 192 killer yeasts identified novel K2 toxins that could inhibit all K1-resistant diastatic yeasts. Variant K2 killer toxins were more potent than the K1 and K2 toxins, inhibiting 95% of diastatic yeast strains tested. Brewing trials demonstrated that adding killer yeast during a simulated diastatic contamination event could prevent hyperattenuation. Currently, most craft breweries can only safeguard against diastatic yeast contamination by good hygiene and monitoring for the presence of diastatic yeasts. The detection of diastatic yeasts will often lead to the destruction of contaminated products and the aggressive decontamination of brewing facilities. Using killer yeasts in brewing offers an approach to safeguard against product loss and potentially remediate contaminated beer.IMPORTANCEThe rise of craft brewing means that more domestic beer in the marketplace is being produced in facilities lacking the means for pasteurization, which increases the risk of microbial spoilage. The most damaging spoilage yeasts are "diastatic" strains of Saccharomyces cerevisiae that cause increased fermentation (hyperattenuation), resulting in unpalatable flavors such as phenolic off-flavor, as well as over-carbonation that can cause exploding packaging. In the absence of a pasteurizer, there are no methods available that would avert the loss of beer due to contamination by diastatic yeasts. This manuscript has found that diastatic yeasts are sensitive to antifungal proteins named "killer toxins" produced by Saccharomyces yeasts, and in industrial-scale fermentation trials, killer yeasts can remediate diastatic yeast contamination. Using killer toxins to prevent diastatic contamination is a unique and innovative approach that could prevent lost revenue to yeast spoilage and save many breweries the time and cost of purchasing and installing a pasteurizer.

Lifespan Extension by Retrotransposons under Conditions of Mild Stress Requires Genes Involved in tRNA Modifications and Nucleotide Metabolism

Retrotransposons are mobile DNA elements that are more active with increasing age and exacerbate aging phenotypes in multiple species. We previously reported an unexpected extension of chronological lifespan in the yeast, Saccharomyces paradoxus, due to the presence of Ty1 retrotransposons when cells were aged under conditions of mild stress. In this study, we tested a subset of genes identified by RNA-seq to be differentially expressed in S. paradoxus strains with a high-copy number of Ty1 retrotransposons compared with a strain with no retrotransposons and additional candidate genes for their contribution to lifespan extension when cells were exposed to a moderate dose of hydroxyurea (HU). Deletion of ADE8, NCS2, or TRM9 prevented lifespan extension, while deletion of CDD1, HAC1, or IRE1 partially prevented lifespan extension. Genes overexpressed in high-copy Ty1 strains did not typically have Ty1 insertions in their promoter regions. We found that silencing genomic copies of Ty1 prevented lifespan extension, while expression of Ty1 from a high-copy plasmid extended lifespan in medium with HU or synthetic medium. These results indicate that cells adapt to expression of retrotransposons by changing gene expression in a manner that can better prepare them to remain healthy under mild stress.

Characteristics of Candida albicans Derived From HIV-Positive Individuals With Oral Candidiasis: Genotyping, Phenotypic Variation, Antifungal Susceptibility, and Biofilm Formation

BACKGROUND

Oral candidiasis (OC) is one of the most common mucosal infections in those afflicted with HIV/AIDS. This study aimed to provide detailed information on the phenotype, genotype, antifungal susceptibility, and biofilm formation ability of oral Candida albicans isolated from HIV-infected patients with OC.

METHODS

A total of 25 C. albicans isolates were collected from oral lesions of HIV-infected patients referred to Behavioral Diseases Counseling Center affiliated with Ahvaz Jundishapur University of Medical Sciences, Iran. The antifungal susceptibility testing was done according to CLSI M27 guideline (fourth edition). The crystal violet method was used to evaluate the biofilm formation ability of isolates. Different phenotypes were identified on yeast extract-peptone-dextrose agar medium supplemented with phloxine B. Genotyping analysis of the isolates was performed using high-resolution melting (HRM) assays and ABC genotyping.

RESULTS

The highest and lowest susceptibility of the C. albicans isolates was found for fluconazole 24 (96%) and ITC 18 (72%), respectively. Forty-eight percent of the isolates had high biofilm formation ability and exhibited gray cell type. The most common genotype was genotype B (52%). HRM analysis of HIS3, EF3, and CDC3 markers showed three, four, and five different groups, respectively.

CONCLUSION

Investigating the phenotype, antifungal susceptibility and biofilm formation ability of the C. albicans isolates obtained from oral lesions of HIV-infected patients revealed that the dominant genotypes in the current research could cause more serious infections from the oral source. We recommend further research with a larger sample size to determine the molecular epidemiology of C. albicans among HIV patients in Iran.

The yeast gene ECM9 regulates cell wall maintenance and cell division in stress conditions

Saccharomyces cerevisiae , Baker's yeast, is a well-studied model eukaryotic organism. Much of our knowledge about eukaryotic cell function comes from yeast studies, though nearly 10% of yeast genes remain uncharacterized. This study focuses on YKR004C, a verified gene of unknown function named ECM9 , predicted to be involved in cell division and cell wall maintenance or composition based on previous studies. We investigated the sensitivity in stress conditions of an ECM9 deletion strain, compared to wild-type, to cell wall integrity. These results suggest that ECM9 is involved in cell wall maintenance and the regulatory pathway determining cell division readiness under stress.

Physiological responses contributing to multiple stress tolerance in Pichia kudriavzevii with potential enhancement for ethanol fermentation

Economically feasible ethanol production requires efficient hydrolysis of lignocellulosic biomass and high-temperature processing to enable simultaneous saccharification and fermentation. During the lignocellulolysic hydrolysate, the yeast must encounter with a multiple of inhibitors such as heat and furfural. To solve this problem, a potential fermentative yeast strain that tolerated simultaneous multistress and enhance ethanol concentration was investigated. Twenty yeast isolates were classified into two major yeast species, namely Pichia kudriavzevii (twelve isolates) and Candida tropicalis (eight isolates). All P. kudriavzevii isolates were able to grow at high temperature (45 °C) and exhibited stress tolerance toward furfural. Among P. kudriavzevii isolates, NUCG-S3 presented the highest specific growth rate under each stress condition of heat and furfural, and multistress. Morphological changes in P. kudriavzevii isolates (NUCG-S2, NUCG-S3, NUKL-P1, NUKL-P3, and NUOR-J1) showed alteration in mean cell length and width compared to the non-stress condition. Ethanol production by glucose was also determined. The yeast strain, NUCG-S3, gave the highest ethanol concentrations at 99.46 ± 0.82, 62.23 ± 0.96, and 65.80 ± 0.62 g/l (P < 0.05) under temperature of 30 °C, 40 °C, and 42 °C, respectively. The tolerant isolated yeast NUCG-S3 achieved ethanol production of 53.58 ± 3.36 and 48.06 ± 3.31 g/l (P < 0.05) in the presence of 15 mM furfural and multistress (42 °C with 15 mM furfural), respectively. Based on the results of the present study, the novel thermos and furfural-tolerant yeast strain P. kudriavzevii NUCG-S3 showed promise as a highly proficient yeast for high-temperature ethanol fermentation.

CRISPR-Cas9 mediated genome editing of Kluyveromyces marxianus for iterative, multiplexed gene disruption and pathway integration

Kluyveromyces marxianus, a thermotolerant, fast-growing, Crabtree-negative yeast, is a promising chassis for the manufacture of various bioproducts. Although several genome editing tools are available for this yeast, these tools still require refinement to enable more convenient and efficient genetic modification. In this study, we engineered the K. marxianus NBRC 104275 strain by impairing the nonhomologous end joining and enhancing the homologous recombination machinery, which resulted in improved homology-directed repair effective on homology arms of up to 40 bp in length. Additionally, we simplified the CRISPR-Cas9 editing system by constructing a strain for integrative expression of Cas9 nuclease and plasmids bearing different selection markers for gRNA expression, thereby facilitating iterative genome editing without the need for plasmid curing. We demonstrated that tRNA was more effective than the hammerhead ribozyme for processing gRNA primary transcripts, and readily assembled tRNA-gRNA arrays were used for multiplexed editing of at least four targets. This editing tool was further employed for simultaneous scarless in vivo assembly of a 12-kb cassette from three fragments and marker-free integration for expressing a fusion variant of fatty acid synthase, as well as the integration of genes for starch hydrolysis. Together, the genome editing tool developed in this study makes K. marxianus more amenable to genetic modification and will facilitate more extensive engineering of this nonconventional yeast for chemical production.

Protocol for rapid and cost-effective extraction of genomic DNA from a wide range of wild yeast species for use in PCR-based applications

Isolation of amplifiable genomic DNA is a prerequisite for the implementation of PCR-based techniques. Here we present a protocol for isolating the genomic DNA from a variety of wild yeast species. This can be completed in approximately 1 h and does not require sophisticated laboratory equipment. We describe steps for growing yeast cells, genomic data extraction, and downstream assay for amplification of specific sequences from the genomic DNA. We then detail procedures for gel electrophoresis and analysis of the results. For complete details on the use and execution of this protocol, please refer to Kristjuhan et al.1.

Dynamically Regulating Homologous Recombination Enables Precise Genome Editing in Ogataea polymorpha

Methylotrophic yeast Ogataea polymorpha has become a promising cell factory due to its efficient utilization of methanol to produce high value-added chemicals. However, the low homologous recombination (HR) efficiency in O. polymorpha greatly hinders extensive metabolic engineering for industrial applications. Overexpression of HR-related genes successfully improved HR efficiency, which however brought cellular stress and reduced chemical production due to constitutive expression of the HR-related gene. Here, we engineered an HR repair pathway using the dynamically regulated gene ScRAD51 under the control of the l-rhamnose-induced promoter PLRA3 based on the previously constructed CRISPR-Cas9 system in O. polymorpha. Under the optimal inducible conditions, the appropriate expression level of ScRAD51 achieved up to 60% of HR rates without any detectable influence on cell growth in methanol, which was 10-fold higher than that of the wild-type strain. While adopting as the chassis strain for bioproductions, the dynamically regulated recombination system had 50% higher titers of fatty alcohols than that static regulation system. Therefore, this study provided a feasible platform in O. polymorpha for convenient genetic manipulation without perturbing cellular fitness.

The bacterial and yeast microbiota in livestock forages in Hungary

BACKGROUND

Along bacteria, yeasts are common in forages and forage fermentations as spoilage microbes or as additives, yet few studies exist with species-level data on these fungi's occurrence in feedstuff. Active dry yeast and other yeast-based products are also common feed additives in animal husbandry. Here, we aimed to characterize both fermented and non-fermented milking cow feedstuff samples from Hungary to assess their microbial diversity in the first such study from Central Europe.

RESULTS

We applied long-read bacterial metabarcoding to 10 fermented and 25 non-fermented types of samples to assess bacterial communities and their characteristics, surveyed culturable mold and yeast abundance, and identified culturable yeast species. Fermented forages showed the abundance of Aerococcaceae, Bacillaceae, Brucellaceae, Lactobacillaceae, Staphylococcaceae, and Thermoactinomycetaceae, non-fermented ones had Cyanothecaceae, Enterobacteriaceae, Erwiniaceae, Gomontiellaceae, Oxalobacteraceae, Rhodobiaceae, Rickettsiaceae, and Staphylococcaceae. Abundances of bacterial families showed mostly weak correlation with yeast CFU numbers, only Microcoleaceae (positive) and Enterococcaceae and Alcaligenaceae (negative correlation) showed moderate correlation. We identified 14 yeast species, most commonly Diutina rugosa, Pichia fermentans, P. kudriavzevii, and Wickerhahomyces anomalus. We recorded S. cerevisiae isolates only from animal feed mixes with added active dry yeast, while the species was completely absent from fermented forages. The S. cerevisiae isolates showed high genetic uniformity.

CONCLUSION

Our results show that both fermented and non-fermented forages harbor diverse bacterial microbiota, with higher alpha diversity in the latter. The bacterial microbiome had an overall weak correlation with yeast abundance, but yeasts were present in the majority of the samples, including four new records for forages as a habitat for yeasts. Yeasts in forages mostly represented common species including opportunistic pathogens, along with a single strain of Saccharomyces used as a feed mix additive.

Differential effects of 40S ribosome recycling factors on reinitiation at regulatory uORFs in GCN4 mRNA are not dictated by their roles in bulk 40S recycling

Recycling of 40S ribosomal subunits following translation termination, entailing release of deacylated tRNA and dissociation of the empty 40S from mRNA, involves yeast Tma20/Tma22 heterodimer and Tma64, counterparts of mammalian MCTS1/DENR and eIF2D. MCTS1/DENR enhance reinitiation (REI) at short upstream open reading frames (uORFs) harboring penultimate codons that confer heightened dependence on these factors in bulk 40S recycling. Tma factors, by contrast, inhibited REI at particular uORFs in extracts; however, their roles at regulatory uORFs in vivo were unknown. We examined effects of eliminating Tma proteins on REI at regulatory uORFs mediating translational control of GCN4 optimized for either promoting (uORF1) or preventing (uORF4) REI. We found that the Tma proteins generally impede REI at native uORF4 and its variants equipped with various penultimate codons regardless of their Tma-dependence in bulk recycling. The Tma factors have no effect on REI at native uORF1 and equipping it with Tma-hyperdependent penultimate codons generally did not confer Tma-dependent REI; nor did converting the uORFs to AUG-stop elements. Thus, effects of the Tma proteins vary depending on the REI potential of the uORF and penultimate codon, but unlike in mammals, are not principally dictated by the Tma-dependence of the codon in bulk 40S recycling.

Unlocking lager's flavour palette by metabolic engineering of Saccharomyces pastorianus for enhanced ethyl ester production

Despite being present in trace amounts, ethyl esters play a crucial role as flavour compounds in lager beer. In yeast, ethyl hexanoate, ethyl octanoate and ethyl decanoate, responsible for fruity and floral taste tones, are synthesized from the toxic medium chain acyl-CoA intermediates released by the fatty acid synthase complex during the fatty acid biosynthesis, as a protective mechanism. The aim of this study was to enhance the production of ethyl esters in the hybrid lager brewing yeast Saccharomyces pastorianus by improving the medium chain acyl-CoA precursor supply. Through CRISPR-Cas9-based genetic engineering, specific FAS1 and FAS2 genes harbouring mutations in domains of the fatty acid synthesis complex were overexpressed in a single and combinatorial approach. These mutations in the ScFAS genes led to specific overproduction of the respective ethyl esters: overexpression of ScFAS1I306A and ScFAS2G1250S significantly improved ethyl hexanoate production and ScFAS1R1834K boosted the ethyl octanoate production. Combinations of ScFAS1 mutant genes with ScFAS2G1250S greatly enhanced predictably the final ethyl ester concentrations in cultures grown on full malt wort, but also resulted in increased levels of free medium chain fatty acids causing alterations in flavour profiles. Finally, the elevated medium chain fatty acid pool was directed towards the ethyl esters by overexpressing the esterase ScEEB1. The genetically modified S. pastorianus strains were utilized in lager beer production, and the resulting beverage exhibited significantly altered flavour profiles, thereby greatly expanding the possibilities of the flavour palette of lager beers.

Compensatory mutations potentiate constructive neutral evolution by gene duplication

The functions of proteins generally depend on their assembly into complexes. During evolution, some complexes have transitioned from homomers encoded by a single gene to heteromers encoded by duplicate genes. This transition could occur without adaptive evolution through intermolecular compensatory mutations. Here, we experimentally duplicated and evolved a homodimeric enzyme to determine whether and how this could happen. We identified hundreds of deleterious mutations that inactivate individual homodimers but produce functional enzymes when coexpressed as duplicated proteins that heterodimerize. The structure of one such heteromer reveals how both losses of function are buffered through the introduction of asymmetry in the complex that allows them to subfunctionalize. Constructive neutral evolution can thus occur by gene duplication followed by only one deleterious mutation per duplicate.

De novo biosynthesis of anthocyanins in Saccharomyces cerevisiae using metabolic pathway synthases from blueberry

BACKGROUND

Anthocyanins are water-soluble flavonoids in plants, which give plants bright colors and are widely used as food coloring agents, nutrients, and cosmetic additives. There are several limitations for traditional techniques of collecting anthocyanins from plant tissues, including species, origin, season, and technology. The benefits of using engineering microbial production of natural products include ease of use, controllability, and high efficiency.

RESULTS

In this study, ten genes encoding enzymes involved in the anthocyanin biosynthetic pathway were successfully cloned from anthocyanin-rich plant materials blueberry fruit and purple round eggplant rind. The Yeast Fab Assembly technology was utilized to construct the transcriptional units of these genes under different promoters. The transcriptional units of PAL and C4H, 4CL and CHS were fused and inserted into Chr. XVI and IV of yeast strain JDY52 respectively using homologous recombination to gain Strain A. The fragments containing the transcriptional units of CHI and F3H, F3'H and DFR were inserted into Chr. III and XVI to gain Strain B1. Strain B2 has the transcriptional units of ANS and 3GT in Chr. IV. Several anthocyanidins, including cyanidin, peonidin, pelargonidin, petunidin, and malvidin, were detected by LC-MS/MS following the predicted outcomes of the de novo biosynthesis of anthocyanins in S. cerevisiae using a multi-strain co-culture technique.

CONCLUSIONS

We propose a novel concept for advancing the heterologous de novo anthocyanin biosynthetic pathway, as well as fundamental information and a theoretical framework for the ensuing optimization of the microbial synthesis of anthocyanins.

Yeast perilipin Pet10p/Pln1p interacts with Erg6p in ergosterol metabolism

Lipid droplets (LD) are highly dynamic organelles specialized for the regulation of energy storage and cellular homeostasis. LD consist of a neutral lipid core surrounded by a phospholipid monolayer membrane with embedded proteins, most of which are involved in lipid homeostasis. In this study, we focused on one of the major LD proteins, sterol C24-methyltransferase, encoded by ERG6. We found that the absence of Erg6p resulted in an increased accumulation of yeast perilipin Pet10p in LD, while the disruption of PET10 was accompanied by Erg6p LD over-accumulation. An observed reciprocal enrichment of Erg6p and Pet10p in pet10Δ and erg6Δ mutants in LD, respectively, was related to specific functional changes in the LD and was not due to regulation on the expression level. The involvement of Pet10p in neutral lipid homeostasis was observed in experiments that focused on the dynamics of neutral lipid mobilization as time-dependent changes in the triacylglycerols (TAG) and steryl esters (SE) content. We found that the kinetics of SE hydrolysis was reduced in erg6Δ cells and the mobilization of SE was completely lost in mutants that lacked both Erg6p and Pet10p. In addition, we observed that decreased levels of SE in erg6Δpet10Δ was linked to an overexpression of steryl ester hydrolase Yeh1p. Lipid analysis of erg6Δpet10Δ showed that PET10 deletion altered the composition of ergosterol intermediates which had accumulated in erg6Δ. In conclusion, yeast perilipin Pet10p functionally interacts with Erg6p during the metabolism of ergosterol.

Mushroom Tyrosinase: Six Isoenzymes Catalyzing Distinct Reactions

"Mushroom tyrosinase" from the common button mushroom is the most frequently used source of tyrosinase activity, both for basic and applied research. Here, the complete tyrosinase family from Agaricus bisporus var. bisporus (abPPO1-6) was cloned from mRNA and expressed heterologously using a single protocol. All six isoenzymes accept a wide range of phenolic and catecholic substrates, but display pronounced differences in their specificity and enzymatic reaction rate. AbPPO3 ignores γ-l-glutaminyl-4-hydroxybenzene (GHB), a natural phenol present in mM concentrations in A. bisporus, while AbPPO4 processes 100 μM GHB at 4-times the rate of the catechol l-DOPA. All six AbPPOs are biochemically distinct enzymes fit for different roles in the fungal life cycle, which challenges the traditional concept of isoenzymes as catalyzing the same physiological reaction and varying only in secondary properties. Transferring this approach to other enzymes and organisms will greatly stimulate both the study of the in vivo function(s) of enzymes and the application of these highly efficient catalysts.

What are the 100 most cited fungal genera?

The global diversity of fungi has been estimated between 2 to 11 million species, of which only about 155 000 have been named. Most fungi are invisible to the unaided eye, but they represent a major component of biodiversity on our planet, and play essential ecological roles, supporting life as we know it. Although approximately 20 000 fungal genera are presently recognised, the ecology of most remains undetermined. Despite all this diversity, the mycological community actively researches some fungal genera more commonly than others. This poses an interesting question: why have some fungal genera impacted mycology and related fields more than others? To address this issue, we conducted a bibliometric analysis to identify the top 100 most cited fungal genera. A thorough database search of the Web of Science, Google Scholar, and PubMed was performed to establish which genera are most cited. The most cited 10 genera are Saccharomyces, Candida, Aspergillus, Fusarium, Penicillium, Trichoderma, Botrytis, Pichia, Cryptococcus and Alternaria. Case studies are presented for the 100 most cited genera with general background, notes on their ecology and economic significance and important research advances. This paper provides a historic overview of scientific research of these genera and the prospect for further research. Citation: Bhunjun CS, Chen YJ, Phukhamsakda C, Boekhout T, Groenewald JZ, McKenzie EHC, Francisco EC, Frisvad JC, Groenewald M, Hurdeal VG, Luangsa-ard J, Perrone G, Visagie CM, Bai FY, Błaszkowski J, Braun U, de Souza FA, de Queiroz MB, Dutta AK, Gonkhom D, Goto BT, Guarnaccia V, Hagen F, Houbraken J, Lachance MA, Li JJ, Luo KY, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe DN, Wang DQ, Wei DP, Zhao CL, Aiphuk W, Ajayi-Oyetunde O, Arantes TD, Araujo JC, Begerow D, Bakhshi M, Barbosa RN, Behrens FH, Bensch K, Bezerra JDP, Bilański P, Bradley CA, Bubner B, Burgess TI, Buyck B, Čadež N, Cai L, Calaça FJS, Campbell LJ, Chaverri P, Chen YY, Chethana KWT, Coetzee B, Costa MM, Chen Q, Custódio FA, Dai YC, Damm U, de Azevedo Santiago ALCM, De Miccolis Angelini RM, Dijksterhuis J, Dissanayake AJ, Doilom M, Dong W, Alvarez-Duarte E, Fischer M, Gajanayake AJ, Gené J, Gomdola D, Gomes AAM, Hausner G, He MQ, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena RS, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin CG, Liu JK, Liu XB, Loizides M, Luangharn T, Maharachchikumbura SSN, Makhathini Mkhwanazi GJ, Manawasinghe IS, Marin-Felix Y, McTaggart AR, Moreau PA, Morozova OV, Mostert L, Osiewacz HD, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips AJL, Phonemany M, Promputtha I, Rathnayaka AR, Rodrigues AM, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe SJ, Scholler M, Scott P, Shivas RG, Silar P, Souza-Motta CM, Silva-Filho AGS, Spies CFJ, Stchigel AM, Sterflinger K, Summerbell RC, Svetasheva TY, Takamatsu S, Theelen B, Theodoro RC, Thines M, Thongklang N, Torres R, Turchetti B, van den Brule T, Wang XW, Wartchow F, Welti S, Wijesinghe SN, Wu F, Xu R, Yang ZL, Yilmaz N, Yurkov A, Zhao L, Zhao RL, Zhou N, Hyde KD, Crous PW (2024). What are the 100 most cited fungal genera? Studies in Mycology 108: 1-411. doi: 10.3114/sim.2024.108.01.

Efficient CRISPR-mediated C-to-T base editing in Komagataella phaffii

The nonconventional methylotrophic yeast Komagataella phaffii is widely applied in the production of industrial enzymes, pharmaceutical proteins, and various high-value chemicals. The development of robust and versatile genome editing tools for K. phaffii is crucial for the design of increasingly advanced cell factories. Here, we first developed a base editing method for K. phaffii based on the CRISPR-nCas9 system. We engineered 24 different base editor constructs, using a variety of promoters and cytidine deaminases (CDAs). The optimal base editor (PAOX2*-KpA3A-nCas9-KpUGI-DAS1TT) comprised a truncated AOX2 promoter (PAOX2*), a K. phaffii codon-optimized human APOBEC3A CDA (KpA3A), human codon-optimized nCas9 (D10A), and a K. phaffii codon-optimized uracil glycosylase inhibitor (KpUGI). This optimal base editor efficiently performed C-to-T editing in K. phaffii, with single-, double-, and triple-locus editing efficiencies of up to 96.0%, 65.0%, and 5.0%, respectively, within a 7-nucleotide window from C-18 to C-12. To expand the targetable genomic region, we also replaced nCas9 in the optimal base editor with nSpG and nSpRy, and achieved 50.0%-60.0% C-to-T editing efficiency for NGN-protospacer adjacent motif (PAM) sites and 20.0%-93.2% C-to-T editing efficiency for NRN-PAM sites, respectively. Therefore, these constructed base editors have emerged as powerful tools for gene function research, metabolic engineering, genetic improvement, and functional genomics research in K. phaffii.

A high-throughput synthetic biology approach for studying combinatorial chromatin-based transcriptional regulation

The construction of synthetic gene circuits requires the rational combination of multiple regulatory components, but predicting their behavior can be challenging due to poorly understood component interactions and unexpected emergent behaviors. In eukaryotes, chromatin regulators (CRs) are essential regulatory components that orchestrate gene expression. Here, we develop a screening platform to investigate the impact of CR pairs on transcriptional activity in yeast. We construct a combinatorial library consisting of over 1,900 CR pairs and use a high-throughput workflow to characterize the impact of CR co-recruitment on gene expression. We recapitulate known interactions and discover several instances of CR pairs with emergent behaviors. We also demonstrate that supervised machine learning models trained with low-dimensional amino acid embeddings accurately predict the impact of CR co-recruitment on transcriptional activity. This work introduces a scalable platform and machine learning approach that can be used to study how networks of regulatory components impact gene expression.

Analyzing the quality differences between healthy and moldy cigar tobacco leaves during the air-curing process through fungal communities and physicochemical components

Introduction

The air-curing process of cigar tobacco, as a key step in enhancing the quality of cigars, is often susceptible to contamination by mold spores, which severely constrains the quality of cigar tobacco.

Methods

This study employed high-throughput Illumina sequencing technology and a continuous flow analysis system to analyze the differences between the microbial communities and physicochemical components of moldy and healthy cigar tobacco leaves. Furthermore, correlation analysis was performed to reveal the impact of mold on the quality of cigar tobacco.

Results

The differences between the microbial flora and physicochemical compositions of moldy (MC) and healthy (HC) tobacco leaves were analyzed, revealing significant disparities between the two groups. Aspergillus spp. represented the dominant mold in MC, with nine out of twelve isolated molds showing higher quantities on MC than on HC. Mold contamination notably decreased the total nitrogen (TN), total phosphorus (TP), total alkaloids (TA), starch, protein, and flavor constituents while increasing the total fatty acid esters (TFAA), which was accompanied by a shift towards weakly acidic pH in the leaves. Fungal community analysis indicated a significant reduction in the fungal operational taxonomic unit (OUT) numbers and diversity indices in MC, contrasting with the bacterial trends. Aspergillus exhibited significantly higher relative abundance in MC, with LEfSe analysis pinpointing it as the primary driver of differentiation. Furthermore, significant negative correlations were observed between Aspergillus and TP, starch, TA, and protein, while a significant positive association was evident with TFAA. Network analysis underscored the pivotal role of Aspergillus as the species influencing disparities between HC and MC, with its abundance serving as a critical determinant during the air-curing process.

Discussion

This study elucidated substantial quality distinctions between MC and HC during air-curing, with Aspergillus emerging as the key species contributing to leaf mold.

Bioprospecting of sourdough microbial species from artisan bakeries in the city of Valencia

This work describes the characterization of an artisanal sourdough set of bakeries located in the city of Valencia. Culture-dependent and -independent analyses detected Fructilactobacillus sanfranciscensis, Saccharomyces cerevisiae and Kazachstania humilis as dominant species. Nevertheless, specific technological parameters, including backslopping temperature, dough yield, or the addition of salt affected microbial counting, LAB/Yeast ratio, and gassing performance, favouring the appearance of several species of Lactobacillus sp., Limosilactobacillus pontis or Torulaspora delbrueckii as additional players. Sourdough leavening activity was affected positively by yeast counts and negatively by the presence of salt. In addition, the predominance of a particular yeast species appeared to impact the dynamics of CO2 release. Seven important flavour-active compounds (ethyl acetate, 1-hexanol, 2-penthylfuran, 3-ethyl-2-methyl-1,3-hexadiene, 2-octen-1-ol, nonanal and 1-nonanol) were detected in all samples and together with 3-methyl butanol and hexyl acetate represented more than the 53% of volatile abundancy in nine of the ten sourdoughs analysed. Even so, the specific microbial composition of each sample influenced the volatile profile. For example, the occurrence of K. humilis or S. cerevisiae as dominant yeast influenced the composition of major alcohol species, while F. sanfranciscensis and L. pontis positively correlated with aldehydes and octanoic acid content. In addition, relevant correlations could be also found among different technological parameters and between these, volatile compounds and microbial species. Overall, our study emphasises on how differences in technological parameters generate biodiversity in a relatively small set of artisan sourdoughs providing opportunities for excellence and quality baking products.

An engineered Pichia pastoris platform for the biosynthesis of silk-based nanomaterials with therapeutic potential

Silk fibroin (SF) from the cocoon of silkworm has exceptional mechanical properties and biocompatibility and is used as a biomaterial in a variety of fields. Sustainable, affordable, and scalable manufacturing of SF would enable its large-scale use. We report for the first time the high-level secretory production of recombinant SF peptides in engineered Pichia pastoris cell factories and the processing thereof to nanomaterials. Two SF peptides (BmSPR3 and BmSPR4) were synthesized and secreted by P. pastoris using signal peptides and appropriate spacing between hydrophilic sequences. By strain engineering to reduce protein degradation, increase glycyl-tRNA supply, and improve protein secretion, we created the optimized P. pastoris chassis PPGSP-8 to produce BmSPR3 and BmSPR4. The SF fed-batch fermentation titers of the resulting two P. pastoris cell factories were 11.39 and 9.48 g/L, respectively. Protein self-assembly was inhibited by adding Tween 80 to the medium. Recombinant SF peptides were processed to nanoparticles (NPs) and nanofibrils. The physicochemical properties of nanoparticles R3NPs and R4NPs from the recombinant SFs synthesized in P. pastoris cell factories were similar or superior to those of RSFNPs (Regenerated Silk Fibroin NanoParticles) originating from commercially available SF. Our work will facilitate the production by microbial fermentation of functional SF for use as a biomaterial.

Exploring class III cellobiose dehydrogenase: sequence analysis and optimized recombinant expression

BACKGROUND

Cellobiose dehydrogenase (CDH) is an extracellular fungal oxidoreductase with multiple functions in plant biomass degradation. Its primary function as an auxiliary enzyme of lytic polysaccharide monooxygenase (LPMO) facilitates the efficient depolymerization of cellulose, hemicelluloses and other carbohydrate-based polymers. The synergistic action of CDH and LPMO that supports biomass-degrading hydrolases holds significant promise to harness renewable resources for the production of biofuels, chemicals, and modified materials in an environmentally sustainable manner. While previous phylogenetic analyses have identified four distinct classes of CDHs, only class I and II have been biochemically characterized so far.

RESULTS

Following a comprehensive database search aimed at identifying CDH sequences belonging to the so far uncharacterized class III for subsequent expression and biochemical characterization, we have curated an extensive compilation of putative CDH amino acid sequences. A sequence similarity network analysis was used to cluster them into the four distinct CDH classes. A total of 1237 sequences encoding putative class III CDHs were extracted from the network and used for phylogenetic analyses. The obtained phylogenetic tree was used to guide the selection of 11 cdhIII genes for recombinant expression in Komagataella phaffii. A small-scale expression screening procedure identified a promising cdhIII gene originating from the plant pathogen Fusarium solani (FsCDH), which was selected for expression optimization by signal peptide shuffling and subsequent production in a 5-L bioreactor. The purified FsCDH exhibits a UV-Vis spectrum and enzymatic activity similar to other characterized CDH classes.

CONCLUSION

The successful production and functional characterization of FsCDH proved that class III CDHs are catalytical active enzymes resembling the key properties of class I and class II CDHs. A detailed biochemical characterization based on the established expression and purification strategy can provide new insights into the evolutionary process shaping CDHs and leading to their differentiation into the four distinct classes. The findings have the potential to broaden our understanding of the biocatalytic application of CDH and LPMO for the oxidative depolymerization of polysaccharides.

Cryptic genetic variation shapes the fate of gene duplicates in a protein interaction network

Paralogous genes are often redundant for long periods of time before they diverge in function. While their functions are preserved, paralogous proteins can accumulate mutations that, through epistasis, could impact their fate in the future. By quantifying the impact of all single-amino acid substitutions on the binding of two myosin proteins to their interaction partners, we find that the future evolution of these proteins is highly contingent on their regulatory divergence and the mutations that have silently accumulated in their protein binding domains. Differences in the promoter strength of the two paralogs amplify the impact of mutations on binding in the lowly expressed one. While some mutations would be sufficient to non-functionalize one paralog, they would have minimal impact on the other. Our results reveal how functionally equivalent protein domains could be destined to specific fates by regulatory and cryptic coding sequence changes that currently have little to no functional impact.

Codon-tRNA Coadaptation Bias for Identifying Strong Native Promoters in Komagataella phaffii

Promoters are crucial elements for engineering microbial production strains used in bioprocesses. For the increasingly popular chassis Komagataella phaffii (formerly Pichia pastoris), a limited number of well-characterized promoters constrain the data-driven engineering of production strains. Here, we present an in silico approach for condition-independent de novo identification of strong native promoters. The method relies on tRNA-codon coadaptation of coding sequences in the K. phaffii genome and is based on two complementary scores: the number of effective codons and the tRNA adaptation index. Genes with high codon bias are expected to be translated efficiently and, thus, also be under control of strong promoters. Using this approach, we identified promising strong promoter candidates and experimentally assessed their activity using fluorescent reporter assays characterizing 50 promoters spanning a 76-fold difference in expression levels in a glucose medium. Overall, we report several promoters that should be added to the molecular toolbox for engineering of K. phaffii and present an approach for identifying promoters in microbial genomes.

Impacts of yeast Tma20/MCTS1, Tma22/DENR and Tma64/eIF2D on translation reinitiation and ribosome recycling

Recycling of 40S ribosomal subunits following translation termination, entailing release of deacylated tRNA and dissociation of the empty 40S subunit from mRNA, involves yeast Tma20/Tma22 heterodimer and Tma64, counterparts of mammalian MCTS1/DENR and eIF2D. MCTS1/DENR enhance reinitiation at short upstream open reading frames (uORFs) harboring penultimate codons that confer dependence on these factors in bulk 40S recycling. Tma factors, by contrast, inhibited reinitiation at particular uORFs in extracts; however, their roles at regulatory uORFs in vivo were unknown. We examined effects of eliminating Tma proteins on reinitiation at regulatory uORFs mediating translational control of GCN4 optimized for either promoting (uORF1) or preventing (uORF4) reinitiation. We found that the Tma proteins generally impede reinitiation at native uORF4 and uORF4 variants equipped with various penultimate codons regardless of their Tma-dependence in bulk recycling. The Tma factors have no effect on reinitiation at native uORF1, and equipping uORF1 with Tma-dependent penultimate codons generally did not confer Tma-dependent reinitiation; nor did converting the uORFs to AUG-stop elements. Thus, effects of the Tma proteins vary depending on the reinitiation potential of the uORF and the penultimate codon, but unlike in mammals, are not principally dictated by the Tma-dependence of the codon in bulk 40S recycling.

Jensen M. teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering

Synthetic biology dictates the data-driven engineering of biocatalysis, cellular functions, and organism behavior. Integral to synthetic biology is the aspiration to efficiently find, access, interoperate, and reuse high-quality data on genotype-phenotype relationships of native and engineered biosystems under FAIR principles, and from this facilitate forward-engineering strategies. However, biology is complex at the regulatory level, and noisy at the operational level, thus necessitating systematic and diligent data handling at all levels of the design, build, and test phases in order to maximize learning in the iterative design-build-test-learn engineering cycle. To enable user-friendly simulation, organization, and guidance for the engineering of biosystems, we have developed an open-source python-based computer-aided design and analysis platform operating under a literate programming user-interface hosted on Github. The platform is called teemi and is fully compliant with FAIR principles. In this study we apply teemi for i) designing and simulating bioengineering, ii) integrating and analyzing multivariate datasets, and iii) machine-learning for predictive engineering of metabolic pathway designs for production of a key precursor to medicinal alkaloids in yeast. The teemi platform is publicly available at PyPi and GitHub.

Engineering Saccharomyces cerevisiae for fast vitamin-independent aerobic growth

Chemically defined media for cultivation of Saccharomyces cerevisiae strains are commonly supplemented with a mixture of multiple Class-B vitamins, whose omission leads to strongly reduced growth rates. Fast growth without vitamin supplementation is interesting for industrial applications, as it reduces costs and complexity of medium preparation and may decrease susceptibility to contamination by auxotrophic microbes. In this study, suboptimal growth rates of S. cerevisiae CEN.PK113-7D in the absence of pantothenic acid, para-aminobenzoic acid (pABA), pyridoxine, inositol and/or biotin were corrected by single or combined overexpression of ScFMS1, ScABZ1/ScABZ2, ScSNZ1/ScSNO1, ScINO1 and Cyberlindnera fabianii BIO1, respectively. Several strategies were explored to improve growth of S. cerevisiae CEN.PK113-7D in thiamine-free medium. Overexpression of ScTHI4 and/or ScTHI5 enabled thiamine-independent growth at 83% of the maximum specific growth rate of the reference strain in vitamin-supplemented medium. Combined overexpression of seven native S. cerevisiae genes and CfBIO1 enabled a maximum specific growth rate of 0.33 ± 0.01 h-1 in vitamin-free synthetic medium. This growth rate was only 17 % lower than that of a congenic reference strain in vitamin-supplemented medium. Physiological parameters of the engineered vitamin-independent strain in aerobic glucose-limited chemostat cultures (dilution rate 0.10 h-1) grown on vitamin-free synthetic medium were similar to those of similar cultures of the parental strain grown on vitamin-supplemented medium. Transcriptome analysis revealed only few differences in gene expression between these cultures, which primarily involved genes with roles in Class-B vitamin metabolism. These results pave the way for development of fast-growing vitamin-independent industrial strains of S. cerevisiae.