A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae

Optimized vectors for genetic engineering of Aureobasidium pullulans

Aureobasidium pullulans is a polyextremotolerant black yeast that exhibits impressive morphological plasticity. Consequently, it shows promise as a model system for investigating mechanisms of cell adaptation to different environments and the regulation of cell shape. Here, we build upon the current toolkit for working with A. pullulans and design and test 25 vectors with seven different codon-optimized fluorophores and three selection cassettes. This includes vectors that allow for dual expression of green fluorescent protein and mCherry-tagged proteins at the URA3 locus and vectors that enable homology-based deletion or C-terminal tagging of endogenous genes without the need for cloning. This versatile vector series for working with A. pullulans will enable a broad range of experiments in this emerging model system.

Genetic suppression interactions are highly conserved across genetically diverse yeast isolates

Genetic suppression occurs when the phenotypic defects caused by a deleterious mutation are rescued by another mutation. Suppression interactions are of particular interest for genetic diseases, as they identify ways to reduce disease severity, thereby potentially highlighting avenues for therapeutic intervention. To what extent suppression interactions are influenced by the genetic background in which they operate remains largely unknown. However, a high degree of suppression conservation would be crucial for developing therapeutic strategies that target suppressors. To gain an understanding of the effect of the genetic context on suppression, we isolated spontaneous suppressor mutations of temperature-sensitive alleles of SEC17, TAO3, and GLN1 in 3 genetically diverse natural isolates of the budding yeast Saccharomyces cerevisiae. After identifying and validating the genomic variants responsible for suppression, we introduced the suppressors in all 3 genetic backgrounds, as well as in a laboratory strain, to assess their specificity. Ten out of 11 tested suppression interactions were conserved in the 4 yeast strains, although the extent to which a suppressor could rescue the temperature-sensitive mutant varied across genetic backgrounds. These results suggest that suppression mechanisms are highly conserved across genetic contexts, a finding that is potentially reassuring for the development of therapeutics that mimic genetic suppressors.

Vacuoles provide the source membrane for TORC1-containing signaling endosomes

Organelle biogenesis is fundamental to eukaryotic cell biology. Yeast signaling endosomes were recently identified as a signaling platform for the evolutionarily conserved Target of Rapamycin Complex 1 (TORC1) kinase complex. Despite the importance of signaling endosomes for TORC1-mediated control of cellular metabolism, how this organelle is generated has been a mystery. Here, we developed a system to induce synchronized de novo formation of signaling endosomes, enabling real-time monitoring of their biogenesis. Using this system, we identify vacuoles as a membrane source for newly formed signaling endosomes. Membrane supply from vacuoles is mediated by the CROP membrane-cutting complex, consisting of Atg18 PROPPIN and retromer subunits. The formation of signaling endosomes requires TORC1 activity, suggestive of a tightly regulated process. This study unveiled the first mechanistic principles and molecular participants of signaling endosome biogenesis.

Acetic acid-induced stress granules function as scaffolding complexes for Hog1 activation by Pbs2

Stress-activated protein kinases (SAPKs) respond to a wide variety of stressors. In most cases, the pathways through which specific stress signals are transmitted to the SAPK are not known. We show that the yeast SAPK Hog1 is activated by acetic acid through an intracellular mechanism that does not involve stimulation of the high osmolarity glycerol (HOG) signaling pathway beyond its basal level. Rather, acetic acid treatment drives the formation of stress granules, which function as a scaffold to bring Hog1 together with Pbs2, its immediately upstream activating kinase, in a stable assembly that leverages the basal activity of Pbs2 to phosphorylate Hog1. Deletion analysis of stress granule components revealed that the assembly is critical for both the acetic acid-induced activation of Hog1 and its association with Pbs2. Activated Hog1 remains associated with stress granules, which may have implications for its targeting.

Yeast Hsp78 plays an essential role in adapting to severe ethanol stress via mild ethanol stress pretreatment in mitochondrial protein quality control

Severe ethanol stress (10 % v/v) causes the denaturation and aggregation of certain mitochondrial proteins, such as aconitase (Aco1), forming the deposits of unfolded mitochondrial proteins (DUMPs) in the budding yeast Saccharomyces cerevisiae. Pre-exposing yeast cells to mild stress often induces adaptation to subsequent severe stress. However, whether pre-exposing yeast cells to mild ethanol stress mitigates mitochondrial protein aggregation remains unclear. Therefore, in this study, we examined the effects of pre-exposing yeast cells to mild ethanol stress on the yeast mitochondrial protein quality control (mtPQC) system under severe ethanol stress. Pretreatment with 6 % (v/v) ethanol significantly mitigated the formation of DUMPs and Aco1 aggregates under subsequent 10 % ethanol stress in wild-type cells but not in hsp78∆ and mdj1∆ cells. Pretreatment with 6 % ethanol increased the protein levels of mtPQC-related factors, Hsp78, Mdj1, and Hsp10; however, hsp78∆ cells showed significantly lower levels of Ssc1 (mtHsp70) and its co-chaperone Mdj1 than wild-type cells. Moreover, intracellular reactive oxygen species levels and the frequency of respiration-deficient mutants under 10 % ethanol stress were reduced after pretreatment with 6 % ethanol in wild-type cells but not in hsp78∆ cells. Overall, this study demonstrated that pre-exposing yeast cells to mild ethanol stress mitigated ethanol-induced mitochondrial damage by activating the mtPQC system, including HSP78 expression, providing novel insights into the effects of ethanol stress on mitochondria and the corresponding responses in yeast.

Interface integrity in septin protofilaments is maintained by an arginine residue conserved from yeast to man

The septins are conserved, filament-forming, guanine nucleotide binding cytoskeletal proteins. They assemble into palindromic protofilaments which polymerize further into higher-ordered structures that participate in essential intracellular processes such as cytokinesis or polarity establishment. Septins belong structurally to the P-Loop NTPases but, unlike their relatives Ras or Rho, do not mediate signals to effectors through GTP binding and hydrolysis. Biochemical approaches addressing how and why septins utilize nucleotides are hampered by the lack of nucleotide-free complexes. Using molecular dynamics simulations, we determined structural alterations and intersubunit binding free energies in human and yeast septin dimer structures and in their in silico generated apo forms. An interchain salt bridge network around the septin unique β-meander, conserved across all kingdoms of septin containing species, is destabilized upon nucleotide removal, concomitant with disruption of the entire G-interface. Within this network, we confirmed a conserved arginine residue, which coordinates the guanine base of the nucleotide, as the central interaction hub. The essential role of this arginine for interface integrity was experimentally confirmed to be conserved in septins from yeast to human.

Snf1 and yeast GSK3-β activates Tda1 to suppress glucose starvation signaling

In budding yeast, the presence of glucose, a preferred energy source, suppresses the expression of respiration-related genes through a process known as glucose repression. Conversely, under glucose starvation conditions, Snf1 phosphorylates and activates downstream factors, relieving this repression and allowing cells to adapt. Recently, the Tda1 protein kinase has been implicated in these glucose starvation responses, although its function remains largely uncharacterized. In this study, we demonstrate that Snf1 and yeast glycogen synthase kinase 3-beta (GSK3-β) independently phosphorylate and activate Tda1, which in turn phosphorylates Hxk2 at Ser15. The Ser483 and Thr484 residues of Tda1 are critical for its activation by Snf1, while the Ser509 residue is crucial for its activation by yeast GSK3-β. Importantly, under glucose starvation conditions, the TDA1 deletion mutant shows increased expression of respiration-related genes and a faster growth rate compared to wild-type cells, which is opposite to what is observed in SNF1 and yeast GSK3-β deletion mutants. These findings suggest that Tda1 is activated by Snf1 and yeast GSK3-β, and functions as a suppressor of the glucose starvation signaling.

TRS85 and LEM3 suppressor mutations rescue stress hypersensitivities caused by lack of structural diversity of complex sphingolipids in budding yeast

The budding yeast Saccharomyces cerevisiae can synthesise 15 subtypes of complex sphingolipids, and this structural diversity is thought to be the molecular basis that enables the range of biological functions of complex sphingolipids. Through analyses of yeast mutants with various deletion combinations of complex-sphingolipid-metabolising enzyme genes (CSG1, CSH1, IPT1, SUR2 and SCS7), it was previously shown that less structural diversity of complex sphingolipids leads to increased sensitivity to multiple environmental stresses, with impaired plasma-membrane and cell-wall integrity. In this study, we screened for suppressor mutations that can alleviate the stress hypersensitivities of csg1Δ csh1Δ sur2Δ scs7Δ (ccssΔ) cells. Mutations of trafficking protein particle complex III-specific subunit 85 (TRS85; encodes a component of the TRAPPIII complex, involved in membrane trafficking) and phospholipid-transporting ATPase Dnf2 (DNF2; encodes the plasma-membrane glycerophospholipid flippase) were identified as suppressor mutations. Loss of Trs85 or phospholipid-transporting ATPase accessory subunit Lem3 (LEM3; encodes a regulatory subunit of Dnf2) differed in the type of stress being conferred resistance to ccss∆ cells. Furthermore, it was also found that impaired plasma-membrane and cell-wall integrities in ccssΔ cells were suppressed by trs85∆ but not lem3∆. Moreover, ccss∆ cells exhibited abnormal localisation of yeGFP-Snc1 in endosomes, which is suppressed by trs85∆ but not lem3∆. Overexpression of GTP-binding protein Ypt1, which is regulated by TRAPPIII and involved in vesicular trafficking, exacerbated plasma-membrane integrity abnormalities and stress sensitivities in ccss∆ cells. Thus, it was suggested that TRS85 and LEM3 deletion confer stress tolerances to ccssΔ cells through distinct mechanisms. These findings will provide insights into the physiological significance of the structural diversity of complex sphingolipids.

Design, Construction, and Validation of a Yeast-Displayed Chemically Expanded Antibody Library

In vitro display technologies, exemplified by phage and yeast display, have emerged as powerful platforms for antibody discovery and engineering. However, the identification of antibodies that disrupt target functions beyond binding remains a challenge. In particular, there are very few strategies that support identification and engineering of either protein-based irreversible binders or inhibitory enzyme binders. Expanding the range of chemistries in antibody libraries has the potential to lead to efficient discovery of function-disrupting antibodies. In this work, we describe a yeast display-based platform for the discovery of chemically diversified antibodies. We constructed a billion-member antibody library, called the "Clickable CDR-H3 Library", that supports the presentation of a range of chemistries within antibody variable domains via noncanonical amino acid (ncAA) incorporation and subsequent bioorthogonal click chemistry conjugations. Use of a polyspecific orthogonal translation system enables introduction of chemical groups with various properties, including photoreactive, proximity-reactive, and click chemistry-enabled functional groups for library screening. We established conjugation conditions that facilitate modification of the full library, demonstrating the feasibility of sorting the full billion-member library in "protein-small molecule hybrid" format in future work. Here, we conducted initial library screens after introducing O-(2-bromoethyl)tyrosine (OBeY), a weakly electrophilic ncAA capable of undergoing proximity-induced crosslinking to a target. Enrichments against donkey IgG and protein tyrosine phosphatase 1B (PTP1B) each led to the identification of several OBeY-substituted clones that bind to the targets of interest. Flow cytometry analysis on the yeast surface confirmed higher retention of binding for OBeY-substituted clones compared to clones substituted with ncAAs lacking electrophilic side chains after denaturation. However, subsequent crosslinking experiments in solution with ncAA-substituted clones yielded inconclusive results, suggesting that weakly reactive OBeY side chain is not sufficient to drive robust crosslinking in the clones isolated here. Nonetheless, this work establishes a multimodal, chemically expanded antibody library and demonstrates the feasibility of conducting discovery campaigns in chemically expanded format. This versatile platform offers new opportunities for identifying and characterizing antibodies with properties beyond what is accessible with the canonical amino acids, potentially enabling discovery of new classes of reagents, diagnostics, and even therapeutic leads.

Humanized Saccharomyces cerevisiae provides a facile and effective tool to identify damaging human variants that cause exosomopathies

The RNA exosome is an evolutionarily conserved, multiprotein complex that is the major RNase in 3' processing and degradation of a wide range of RNAs in eukaryotes. Single amino acid changes in RNA exosome subunits cause rare genetic diseases collectively called exosomopathies. However, distinguishing disease-causing variants from nonpathogenic ones remains challenging, and the mechanism by which these variants cause disease is largely unknown. Previous studies have employed a budding yeast model of RNA exosome-linked diseases that relies on mutating the orthologous yeast genes. Here, we develop a humanized yeast model of exosomopathies that allows us to unambiguously assess damaging effects of the exact patient variant in budding yeast. Individual replacement of the yeast subunits with corresponding mammalian orthologs identified 6 out of 9 noncatalytic core subunits of the budding yeast RNA exosome that can be replaced by a mammalian subunit, with 3 of the replacements supporting close to normal growth. Further analysis of the disease-associated variants utilizing the hybrid yeast/mammalian RNA exosome revealed functional defects caused by both previously characterized and uncharacterized variants of EXOSC2, EXOSC4, EXOSC7, and EXOSC9. Analysis of the protein levels of these variants indicates that a subset of the patient-derived variants causes reduced protein levels, while other variants are defective but are expressed as well as the reference allele, suggesting a more direct contribution of these residues to RNA exosome function. This humanized yeast model of exosomopathies provides a convenient and sensitive genetic tool to help distinguish damaging RNA exosome variants from benign variants. This disease model can be further exploited to uncover the underpinning mechanism of RNA exosome defects.

Vps41 functions as a molecular ruler for HOPS tethering complex-mediated membrane fusion

Fusion at the lysosome (or the yeast vacuole) requires the conserved hexameric HOPS tethering complex. In the yeast Saccharomyces cerevisiae, HOPS binds to the vacuolar Rab7-like GTPase Ypt7 via its subunits Vps41 and Vps39 and supports fusion by promoting SNARE assembly. In contrast to its sister complex CORVET, the Ypt7-interacting domain of Vps41 in the HOPS complex is connected to the core by a long, extended α-solenoid domain. Here, we show that this solenoid acts as a molecular ruler to position the Ypt7-interacting region of Vps41 relative to the core of HOPS to support function. Mutant complexes with a shortened or extended α-solenoid region in Vps41 still tethered membranes, but failed to efficiently support their fusion. In vivo, Vps41 mutants grew poorly and showed defects in vacuolar morphology, endolysosomal sorting and autophagy. Importantly, when a length-compensating linker was inserted instead of the shortened α-solenoid domain, these defects were rescued. This suggests that the Rab-specific Vps41 subunit requires the exact length of the α-solenoid domain but not the α-solenoid architecture for functionality, suggesting a revised model of how HOPS supports fusion.

Molecular basis for the assembly of the Vps5-Vps17 SNX-BAR proteins with Retromer

Retromer mediates endosomal retrieval of transmembrane proteins in all eukaryotes and was first discovered in yeast in complex with the Vps5 and Vps17 sorting nexins (SNXs). Cryoelectron tomography (cryoET) studies of Retromer-Vps5 revealed a pseudo-helical coat on membrane tubules where dimers of the Vps26 subunit bind Vps5 membrane-proximal domains. However, the Vps29 subunit is also required for Vps5-Vps17 association despite being far from the membrane. Here, we show that Vps5 binds both Vps29 and Vps35 subunits through its unstructured N-terminal domain. A Pro-Leu (PL) motif in Vps5 binds Vps29 and is required for association with Retromer on membrane tubules in vitro, and for the proper recycling of the Vps10 cargo in Saccharomyces cerevisiae. CryoET of Retromer tubules with Vps5-Vps17 heterodimers show a similar architecture to the coat with Vps5-Vps5 homodimers, however, the spatial relationship between Retromer units is highly restricted, likely due to more limited orientations for docking. These results provide mechanistic insights into how Retromer and SNX-BAR association has evolved across species.

Vulnerable Nucleotide Pools and Genomic Instability in Yeast Strains with Deletion of the ADE12 Gene Encoding for Adenylosuccinate Synthetase

Adenylosuccinate synthetase (AdSS), encoded by the ADE12 gene in yeast Saccharomyces cerevisiae, plays a critical role in purine biosynthesis, catalyzing the conversion of inosine 5'-monophosphate (IMP) and aspartic acid to adenylosuccinate, a substrate for the following adenosine 5'-monophosphate (AMP) synthesis step. Mutants lacking AdSS activity exhibit a range of pleiotropic phenotypes: slow growth, poor spore germination, accumulation, and secretion of inosine and hypoxanthine. We report new phenotypes of ade12 mutants and explain their molecular mechanisms. A GC-MS analysis showed that ade12 mutants have highly altered metabolite profiles: the accumulation of IMP leads to an impaired cellular energy metabolism, resulting in a dysregulation of key processes-the metabolism of nucleotides, carbohydrates, and amino acids. These metabolic perturbations explain the cell division arrest observed in ade12 yeast strains. A slowed replication in ade12 mutants, because of the insufficient availability of energy, nucleotides, and proteins, leads to the error-prone DNA polymerase ζ-dependent elevation of spontaneous mutagenesis, connecting multiple roles of AdSS in metabolism with genome stability control.

An auxin-inducible degron system for conditional mutation in the fungal meningitis pathogen Cryptococcus neoformans

Cryptococcus neoformans is the top-ranked W.H.O. fungal priority pathogen, but tools for generating conditional mutations are limited. Auxin-inducible degron systems permit rapid and effective cellular depletion of a tagged protein of interest upon adding a small molecule. These tools are invaluable, particularly for studying essential genes, which may play important roles in pathogen biology. AID2 is one such system that improves on previous strategies. This system achieves greater sensitivity and specificity through an auxin derivative, 5-Ph-IAA, alongside an OsTIR1F74G mutant. We adapted the AID2 system for C. neoformans by codon optimizing OsTIR1F74G and tested its use in multiple scenarios. We demonstrate that the C. neoformans optimized AID2 system enables effective degradation of proteins, including essential proteins, and can be used to help discriminate essential from non-essential genes. This tool enables the study of unexplored parts of the C. neoformans genome.

Dynamic conformations of the P. furiosus MR-DNA complex link Mre11 nuclease activity to DNA-stimulated Rad50 ATP hydrolysis

The MRE11-RAD50-NBS1/Xrs2 (MRN/X) protein complex has essential roles in the repair of damaged DNA. The current understanding of the conformational landscape of the core MR complex comes from various structural studies. However, given the heterogeneous nature of these structures, we suspect that several conformational states may still be unaccounted for. Here, we use methyl-based NMR experiments on P. furiosus MR to determine an ensemble of distinct conformations of MR bound to DNA, consistent with the highly dynamic nature of the MR-DNA complex. Interrogation of these structures via in vitro activity assays on MR mutants reveal an unexpected, striking correlation between the nuclease activity of Mre11 and the magnitude of DNA-stimulated ATP hydrolysis by Rad50. Together, the structures and activity data support a model for MR activity where DNA-stimulated ATP hydrolysis unlocks Rad50 to provide access to the Mre11 active sites and further demonstrate how a heterogeneous ensemble of conformations can be used to coordinate various functions to direct biological outcomes. By elucidating the dynamic conformations of the DNA-bound MR complex, this work lays the foundation for future studies aimed at further characterizing this landscape and dissecting its role in the molecular mechanism of DNA repair and genome stability.

Autophagy-related protein Atg11 is essential for microtubule-mediated chromosome segregation

Emerging studies hint at the roles of autophagy-related proteins in various cellular processes. To understand if autophagy-related proteins influence genome stability, we sought to examine a cohort of 35 autophagy mutants in Saccharomyces cerevisiae. We observe cells lacking Atg11 show poor mitotic stability of minichromosomes. Single-molecule tracking assays and live cell microscopy reveal that Atg11 molecules dynamically localize to the spindle pole bodies (SPBs) in a microtubule (MT)-dependent manner. Loss of Atg11 leads to a delayed cell cycle progression. Such cells accumulate at metaphase at an elevated temperature that is relieved when the spindle assembly checkpoint (SAC) is inactivated. Indeed, atg11∆ cells have stabilized securin levels, that prevent anaphase onset. Ipl1-mediated activation of SAC also confirms that atg11∆ mutants are defective in chromosome biorientation. Atg11 functions in the Kar9-dependent spindle positioning pathway. Stabilized Clb4 levels in atg11∆ cells suggest that Atg11 maintains Kar9 asymmetry by facilitating proper dynamic instability of astral microtubules (aMTs). Loss of Spc72 asymmetry contributes to non-random SPB inheritance in atg11∆ cells. Overall, this study uncovers an essential non-canonical role of Atg11 in the MT-mediated process of chromosome segregation.

A Yeast-Based Assay for Inhibitors of l-Lactate Transport Utilizing Fluorescent Biosensors

Inhibitors of ʟ-lactate transport are in development as a novel mode of action in antitumor therapy and malaria. Previously, we used radiolabeled ʟ-lactate to assay transport via the human monocarboxylate transporter 1, MCT1, and the structurally unrelated malaria parasite's transporter, PfFNT. We encountered a sensitivity limit at IC50 around 100 nM possibly resulting from the required high cell number per sample. Here, we describe a sensitive background-free high-throughput assay in yeast based on fluorescent iLACCO biosensors. We used iLACCO for co-expression and fusions with the transporter protein. Uptake of ʟ-lactate produced strong intensiometric fluorescent responses that could be monitored in cell suspensions using a fluorometer and in individual cells by fluorescence microscopy. The signal decreased dose-dependently in the presence of specific MCT1 and PfFNT inhibitors. Re-evaluation of 36 PfFNT inhibitors yielded IC50 values below 100 nM now matching previous data on Ki compound affinity to isolated transporter protein.

Identification of INOSITOL PHOSPHORYLCERAMIDE SYNTHASE 2 (IPCS2) as a new rate-limiting component in Arabidopsis pathogen entry control

INOSITOL PHOSPHORYLCERAMIDE SYNTHASE 2 (IPCS2) is involved in the biosynthesis of complex sphingolipids at the trans-Golgi network (TGN). Here, we demonstrate a role of IPCS2 in penetration resistance against non-adapted powdery mildew fungi. A novel ipcs2W205* mutant was recovered from a forward genetic screen for Arabidopsis plants with enhanced epidermal cell entry success of the non-adapted barley fungus Blumeria graminis f. sp. hordei (Bgh). A yeast complementation assay and a sphingolipidomic approach revealed that the ipcs2W205* mutant represents a knock-out and lacks IPCS2-specific enzymatic activity. Further mutant analyses suggested that IPCS2-derived glycosyl inositol phosphorylceramides (GIPCs) are required for cell entry control of non-adapted fungal intruders. Confocal laser scanning microscopy (CLSM) studies indicated that upon pathogen attack, IPCS2 remains at the TGN to produce GIPCs, while focal accumulation of the defense cargo PENETRATION 3 (PEN3) at Bgh penetration sites was reduced in the ipcs2W205* mutant background. Thus, we propose a model in which sorting events at the TGN are facilitated by complex sphingolipids, regulating polar secretion of PEN3 to host-pathogen contact sites to terminate fungal ingress.

The Whi2-Psr1-Psr2 complex selectively regulates TORC1 and autophagy under low leucine conditions but not nitrogen depletion

Amino acids and ammonia serve as sources of nitrogen for cell growth and were previously thought to have similar effects on yeast. Consistent with this idea, depletion of either of these two nitrogen sources inhibits the target of rapamycin complex 1 (TORC1), leading to induction of macroautophagy/autophagy and inhibition of cell growth. In this study, we show that Whi2 and the haloacid dehalogenase (HAD)-type phosphatases Psr1 and Psr2 distinguish between these two nitrogen sources in Saccharomyces cerevisiae, as the Whi2-Psr1-Psr2 complex inhibits TORC1 in response to low leucine but not in the absence of nitrogen. In contrast, a parallel pathway controlled by Npr2 and Npr3, components of the Seh1-associated complex inhibiting TORC1 (SEACIT), suppress TORC1 under both low leucine- and nitrogen-depletion conditions. Co-immunoprecipitations with mutants of Whi2, Psr1, Psr2 and fragments of Tor1 support the model that Whi2 recruits Psr1 and Psr2 to TORC1. In accordance, the interaction between Whi2 and Tor1 appears to increase under low leucine but decreases under nitrogen-depletion conditions. Although the targets of Psr1 and Psr2 phosphatases are not known, mutation of their active sites abolishes their inhibitory effects on TORC1. Consistent with the conservation of HAD phosphatases across species, human HAD phosphatases CTDSP1 (CTD small phosphatase 1), CTDSP2, and CTDSPL can functionally replace Psr1 and Psr2 in yeast, restoring TORC1 inhibition and autophagy activation in response to low leucine conditions.

Artificial induction of the UPR by Tet-off system-dependent expression of Hac1 and its application in Saccharomyces cerevisiae cells

In response to endoplasmic reticulum (ER) stress, yeast Saccharomyces cerevisiae cells produce Hac1, which is a transcription factor responsible for the unfolded protein response (UPR). When Hac1 is unregulatedly expressed from a constitutive promoter, the ER is artificially enforced and enlarged, even without ER stress stimuli. However, such cells are unsuitable for applicative bioproduction because they grow quite slowly and quickly lose their high-UPR phenotype upon their long-term storage. To avoid this problem, we constructed S. cerevisiae plasmids for Hac1 expression under the control of the inducible Tet-off promoter. Yeast cells carrying these plasmids did not exhibit a considerable UPR and grew rapidly when the Tet-off promoter was repressed by doxycycline. In contrast, under the Tet-off inducing condition, these plasmids caused UPR induction, growth retardation, and ER expansion, depending on the copy number of the plasmid. Moreover, as expected, lipidic molecule production was increased under these conditions.

Automated plasmid design for marker-free genome editing in budding yeast

Scarless genome editing in budding yeast with elimination of the selection marker has many advantages. Some markers such as URA3 and TRP1 can be recycled through counterselection. This permits seamless genome modification with pop-in/pop-out, in which a DNA construct first integrates in the genome and, subsequently, homologous regions recombine and excise undesired sequences. Popular approaches for creating such constructs use oligonucleotides and PCR. However, the use of oligonucleotides has many practical disadvantages. With the rapid reduction in price, synthesizing custom DNA sequences in specific plasmid backbones has become an appealing alternative. For designing plasmids for seamless pop-in/pop-out gene tagging or deletion, there are a number of factors to consider. To create only the shortest DNA sequences necessary, avoid errors in manual design, specify the amount of homology desired, and customize restriction sites, we created the computational tool PIPOline. Using it, we tested the ratios of homology that improve pop-out efficiency when targeting the genes HTB2 or WHI5. We supply optimal pop-in/pop-out plasmid sequences for tagging or deleting almost all S288C budding yeast open reading frames. Finally, we demonstrate how the histone variant Htb2 marked with a red fluorescent protein can be used as a cell-cycle stage marker, alternative to superfolder GFP, reducing light toxicity. We expect PIPOline to streamline genome editing in budding yeast.

A Plasmid System That Utilises Phosphoribosylanthranilate Isomerase to Select Against Cells Expressing Truncated Proteins

We have generated a vector that enables the removal of plasmids coding for truncated proteins. This vector expresses a protein of interest in the yeast Saccharomyces cerevisiae from a galactose-inducible promoter. The gene of interest is fused in-frame to a downstream sequence coding for phosphoribosylanthranilate isomerase (PRAI), which catalyses the third step in tryptophan biosynthesis. As a consequence, only the full-length protein of interest renders the host cell tryptophan prototrophic, allowing for selection against cells expressing truncated proteins. Our proof-of-principle study demonstrates that PRAI is functional when fused C-terminally to a protein, robustly rendering cells tryptophan prototrophic. The N-terminal GST tag and C-terminal myc tag allow for tag-mediated protein purification, co-precipitation studies, determination of relative expression levels, as well as validation of full-length expression of the protein via Western blotting.

The Sole Essential Low Molecular Weight Tropomyosin Isoform of Caenorhabditis elegans Is Essential for Pharyngeal Muscle Function

Tropomyosin is an actin-binding protein that plays roles ranging from regulating muscle contraction to controlling cytokinesis and cell migration. The simple nematode Caenorhabditis elegans provides a useful model for studying the core functions of tropomyosin in an animal, having a relatively simple anatomy and a single tropomyosin gene, lev-11, that produces seven isoforms. Three higher molecular weight isoforms regulate the contraction of body wall and other muscles, but comparatively less is known of the functions of four lower molecular weight isoforms (LEV-11C, E, T, U). We demonstrate here that C. elegans can survive with a single low molecular weight isoform, LEV-11E. Mutants disrupted for LEV-11E die as young larvae, whereas mutants lacking all other short isoforms are viable, with no overt phenotype. Vertebrate low molecular weight tropomyosins are often considered "nonmuscle" isoforms, but we find LEV-11E localizes to sarcomeric thin filaments in pharyngeal muscle and co-precipitates from worm extracts with the formin FHOD-1, which is also associated with thin filaments in pharyngeal muscle. Pharyngeal sarcomere organization is grossly normal in larvae lacking LEV-11E, indicating that the tropomyosin is not required to stabilize thin filaments, but pharyngeal pumping is absent, suggesting LEV-11E regulates actomyosin activity similar to higher molecular weight sarcomeric tropomyosin isoforms.

Discovery of the antifungal compound ilicicolin K through genetic activation of the ilicicolin biosynthetic pathway in Trichoderma reesei

BACKGROUND

Given the global rise in antimicrobial resistance, the discovery of novel antimicrobial agents and production processes thereof are of utmost importance. To this end we have activated the gene cluster encoding for the biosynthesis of the potent antifungal compound ilicicolin H in the fungus Trichoderma reesei. While the biosynthetic gene cluster (BGC) is silent under standard cultivation conditions, we achieved BGC activation by genetically overexpressing the transcription factor TriliR.

RESULTS

Successful activation was confirmed by RT-qPCR, proteomic and metabolomic analyses. Metabolomic profiling upon BGC expression revealed high-yield production of ilicicolin H. To elucidate the enzymatically highly diverse functionality of this BGC, we employed a combination of overexpression and deletions of individual genes in the BGC. While we hardly observed any of the previously reported side- or shunt products associated with heterologous ilicicolin H expression, we discovered that Trichoderma reesei produces a novel member of the ilicicolin family using a metabolomic molecular networking approach. This new compound, ilicicolin K, is expressed in substantial amounts in the genetically engineered Trichoderma reesei. Ilicicolin K differs from ilicicolin H in its structure by a second hydroxylation of the tyrosine derived phenol and an additional ring formed by an intramolecular ether bridge of the hydroxyl group at the pyridone towards the tyrosine moiety of the molecule. Bioactivity tests of ilicicolin K revealed a strong antifungal activity against Saccharomyces cerevisiae and a moderate activity against the human pathogen Candida auris, an emerging multi-drug resistant fungus.

CONCLUSIONS

By activating a silent BGC in T. reesei, we obtained a high-yielding strain for the production of the antifungal compounds ilicicolin H and the novel ilicicolin K. These two compounds share some structural properties and are thus highly likely to act on the fungal cytochrome bc1 complex, a component of the mitochondrial repository chain. However, they possess different bioactive properties, which might suggest that ilicicolin K may overcome certain limitations of ilicicolin H.

Mining yeast diversity unveils novel targets for improved heterologous laccase production in Saccharomyces cerevisiae

The budding yeast Saccharomyces cerevisiae is a widely utilized host cell for recombinant protein production due to its well studied and annotated genome, its ability to secrete large and post-translationally modified proteins, fast growth and cost-effective culturing. However, recombinant protein yields from S. cerevisiae often fall behind that of other host systems. To address this, we developed a high-throughput screen of wild, industrial and laboratory S. cerevisiae isolates to identify strains with a natural propensity for greater recombinant protein production, specifically focussing on laccase multicopper oxidases from the fungi Trametes trogii and Myceliophthora thermophila. Using this method, we identified 20 non-laboratory strains with higher capacity to produce active laccase. Interestingly, lower levels of laccase mRNA were measured in most cases, indicating that the drivers of elevated protein production capacity lie beyond the regulation of recombinant gene expression. We characterized the identified strains using complementary genomic and proteomic approaches to reveal several potential pathways driving the improved expression phenotype. Gene ontology analysis suggests broad changes in cellular metabolism, specifically in genes/proteins involved in carbohydrate catabolism, thiamine biosynthesis, transmembrane transport and vacuolar degradation. Targeted deletions of the hexose transporter HXT11 and the Coat protein complex II interacting paralogs PRM8 and 9, involved in ER to Golgi transport, resulted in significantly improved laccase production from the S288C laboratory strain. Whereas the deletion of the Hsp110 SSE1 gene, guided by our proteomic analysis, also led to higher laccase activity, we did not observe major changes of the protein homeostasis network within the strains with higher laccase activity. This study opens new avenues to leverage the vast diversity of Saccharomyces cerevisiae for recombinant protein production, as well as offers new strategies and insights to enhance recombinant protein yields of current strains.

TAP-MS analysis of FACT interactions and regulation by a ubiquitin ligase, San1

An evolutionarily conserved heterodimeric FACT (Facilitates chromatin transcription) regulates transcription, DNA repair, replication and other cellular processes via its interactions with other proteins. FACT is recently found to be regulated via ubiquitylation and 26S proteasomal degradation, alteration of which is associated with aberrant transcription and genome integrity. However, there has not been a systematic study to analyze FACT interactions proteome-wide in the presence and absence of its UPS (Ubiquitin-proteasome system) regulation, which could reveal new FACT interactors with mechanistic and functional implications. Here, we have adopted a proteome-wide approach via TAP (Tandem affinity purification)-mediated pull-down of FACT and its interactors from the soluble and insoluble cellular fractions followed by MS (Mass-spectrometry) analysis. We find distinct interactors of FACT in the soluble and insoluble fractions in addition to a common set in both. While a set of all these interactors overlaps with previously known FACT partners, many are new, which are involved in different cellular processes such as transcription, DNA repair and chromatin regulation. Further, an intrinsically disordered ubiquitin ligase, San1, that ubiquitylates the Spt16 component of FACT for proteasomal degradation to regulate chromatin, transcription and genome integrity is found to influence the interactions of FACT with a set of proteins including epigenetic, transcription and DNA repair factors. Collectively, our results unveil proteome-wide FACT interactions and regulation by a ubiquitin ligase, hence shedding much light on FACT networks with functional and mechanistic implications.

Roles for the canonical polarity machinery in the de novo establishment of polarity in budding yeast spores

The yeast Saccharomyces cerevisiae buds at sites predetermined by cortical landmarks deposited during prior budding. During mating between haploid cells in the lab, external pheromone cues override the cortical landmarks to drive polarization and cell fusion. By contrast, in haploid gametes (called spores) produced by meiosis, a predetermined polarity site drives initial polarized morphogenesis independent of mating partner location. Spore membranes are made de novo so existing cortical landmarks were unknown, as were the mechanisms by which the spore polarity site is made and how it works. We find that the landmark canonically required for distal budding, Bud8, stably marks the spore polarity site along with Bud5, a GEF for the GTPase Rsr1 that canonically links cortical landmarks to the conserved Cdc42 polarity machinery. Cdc42 and other GTPase regulators arrive at the site during its biogenesis, after spore membrane closure but apparently at the site where membrane synthesis began, and then these factors leave, pointing to the presence of discrete phases of maturation. Filamentous actin may be required for initial establishment of the site, but thereafter Bud8 accumulates independent of actin filaments. These results suggest a distinct polarization mechanism that may provide insights into gamete polarization in other organisms.

Synthetic Osmolytes for Enhanced RNA Thermotolerance and Extended Plasmid Storage at Room Temperature

Stable formulations for RNA and plasmid DNA are a matter of paramount significance in several fields, ranging from medicine to biotechnology. We have investigated the potential of 15 compounds derived from natural osmolytes to enhance the thermostability and protection of both RNA and plasmid DNA. Our findings demonstrated that several compounds exhibit remarkable effects, enhancing the long-term storage of plasmid DNA at room temperature and the resilience of RNA to high-temperature stress, surpassing the performance of commercial osmolytes. Importantly, we found that one of the compounds enhanced the detection efficacy of a cost-effective RT-PCR test for COVID-19 that we had previously developed. This work offers new possibilities for expanding the capabilities of molecular diagnostic assays and nucleic acid storage methods.

The PKA Signaling Pathway Regulates the Association of the Autophagy Initiation Complex With the Lipidation Machinery

A key step in autophagy is the conjugation by the E3-like Atg12-Atg5-Atg16 complex of the ubiquitin-like protein Atg8 to phosphatidylethanolamine on the autophagosomal membrane, a process known as lipidation. Previous work in yeast showed that recruitment of the E3-like complex to the preautophagosomal structure is mediated by the interaction of Atg16 with the phosphatidylinositol 3-phosphate-binding protein Atg21, and by the association of Atg12 with the scaffold protein of the Atg1 kinase complex, Atg17. Here, we conducted a reverse two-hybrid screen to identify residues in Atg17 and Atg12 critical for Atg17-Atg12 binding, and used these data to generate a docking model of Atg12-Atg5-Atg16 with the Atg17 complex. In this model, a conserved alpha-helix in the N-terminal region of Atg12 binds to the convex side of crescent-shaped Atg17 and appears to form a four-helix bundle with the three helices of Atg17, similar to that described for the binding of Atg31 to Atg17. We further showed that, in agreement with previous work, Atg17-Atg12 and Atg21-Atg16 binding act cooperatively to mediate the recruitment of the E3-like complex, although our results show that alternative mechanisms are involved in this process. Finally, we found that phosphorylation of Atg12 by PKA prevents its interaction with Atg17, thus adding a new regulatory layer in the control of autophagy by the PKA signaling pathway.

Prion-like Properties of Short Isoforms of Human Chromatin Modifier PHC3

The formation of self-perpetuating protein aggregates such as amyloids is associated with various diseases and provides a basis for transmissible (infectious or heritable) protein isoforms (prions). Many human proteins involved in the regulation of transcription contain potentially amyloidogenic regions. Here, it is shown that short N-terminal isoforms of the human protein PHC3, a component of the chromatin-modifying complex PRC1 (Polycomb repressive complex 1), can form prion-like aggregates in yeast assays, exhibit amyloid properties in the E. coli-based C-DAG assay, and produce detergent-resistant aggregates when ectopically expressed in cultured human cells. Moreover, aggregates of short isoforms can sequester the full-length PHC3 protein, causing its accumulation in the cytosol instead of the nucleus. The introduction of an aggregating short PHC3 isoform alters the transcriptional profile of cultured human cells. It is proposed that the aggregation of short isoforms is involved in the feedback downregulation of PRC1 activity, leading to more open chromatin configuration.

Accurate phenotype-to-genotype mapping of high-diversity yeast libraries by heat-shock-electroporation (HEEL)

High-throughput DNA transformation techniques are invaluable when generating high-diversity mutant libraries, a cornerstone of successful protein engineering. However, transformation efficiencies have a direct correlation with the probability of introducing multiple DNA molecules into each cell, although reliable library screenings require cells that contain a single unique genotype. Thus, transformation methods that yield a high multiplicity of transformations are unsuitable for high-diversity library screenings. Here, we describe an innovative yeast library transformation method that is both simple and highly efficient. Our dual heat-shock and electroporation approach (HEEL) creates high-quality DNA libraries by increasing the fraction of mono-transformed yeast cells from 20% to over 70% of all transformed cells, thus allowing for near-perfect phenotype-to-genotype associations. HEEL also allows more than 107 yeast cells per reaction to be transformed with a circular plasmid molecule, which corresponds to an almost 100-fold improvement compared with current yeast transformation methods. To further refine our library screening approach, we integrated an automated yeast genotyping workflow with a dual-barcode design that employs both a single nucleotide polymorphism and a high-diversity region. This design allows for robust identification and quantification of unique genotypes within a heterogeneous population using standard Sanger sequencing. Our findings demonstrate that the longstanding trade-off between the size and quality of transformed yeast libraries can be overcome. By employing the HEEL method, large DNA libraries can be transformed into yeast with high-efficiency, while maintaining high library quality, essential for successful mutant screenings. This advancement holds significant promise for the fields of molecular biology and protein engineering.IMPORTANCEWith the recent expansion of artificial intelligence in the field of synthetic biology, there has never been a greater need for high-quality data and reliable measurements of phenotype-to-genotype relationships. However, one major obstacle to creating accurate computer-based models is the current abundance of low-quality phenotypic measurements originating from numerous high-throughput but low-resolution assays. Rather than increasing the quantity of measurements, new studies should aim to generate as accurate measurements as possible. The HEEL methodology presented here aims to address this issue by minimizing the problem of multi-plasmid uptake during high-throughput yeast DNA transformations, which leads to the creation of heterogeneous cellular genotypes. HEEL should enable highly accurate phenotype-to-genotype measurements going forward, which could be used to construct better computer-based models.

Dbi1 is an oxidoreductase and an assembly chaperone for mitochondrial inner membrane proteins

Import and assembly of mitochondrial proteins into multimeric complexes are essential for cellular function. Yet, many steps of these processes and the proteins involved remain unknown. Here, we identify a novel pathway for disulfide bond formation and assembly of mitochondrial inner membrane (IM) proteins. Dbi1, a previously uncharacterized IM protein, interacts with an unassembled pool of Tim17, the central subunit of the presequence translocase of the IM, and is upregulated in cells with increased levels of unassembled Tim17. In the absence of Dbi1, the conformation of the presequence translocase is affected and stability of Tim17 is reduced. Furthermore, Dbi1, through its conserved CxxC motif, is involved in the formation of the disulfide bond in Tim17 in a manner independent of the disulfide relay system, the major oxidation-driven protein import pathway into mitochondria. The substrate spectrum of Dbi1 is not limited to Tim17 but includes at least two more IM proteins, Tim22 and Cox20. We conclude that Dbi1 is a novel oxidoreductase in mitochondria which introduces disulfide bonds into IM proteins and chaperones their assembly into multimeric protein complexes.

A protein interaction map of the myosin Myo2 reveals a role for Alo1 in mitochondrial inheritance in yeast

Budding yeast cells multiply by asymmetric cell division. During this process, the cell organelles are transported by myosin motors along the actin cytoskeleton into the growing bud, and, at the same time, some organelles must be retained in the mother cell. The ordered partitioning of organelles depends on highly regulated binding of motor proteins to cargo membranes. To search for novel components involved in this process, we performed a protein fragment complementation screen using the cargo-binding domain of Myo2, the major organelle transporter in yeast, as bait and a genome-wide strain collection expressing yeast proteins as prey. One robust hit was Alo1, a poorly characterized D-arabinono-1,4-lactone oxidase located in the mitochondrial outer membrane. We found that mutants lacking Alo1 exhibited defects in mitochondrial morphology and inheritance. During oxidative stress, dysfunctional mitochondria are immobilized in the mother in wild-type cells. Intriguingly, overexpression of ALO1 restored bud-directed transport of mitochondria under these conditions. We propose that Alo1 supports the recruitment of Myo2 to mitochondria and its activity is particularly important under oxidative stress.

Functional constraints of wtf killer meiotic drivers

Killer meiotic drivers are selfish DNA loci that sabotage the gametes that do not inherit them from a driver+/driver- heterozygote. These drivers often employ toxic proteins that target essential cellular functions to cause the destruction of driver- gametes. Identifying the mechanisms of drivers can expand our understanding of infertility and reveal novel insights about the cellular functions targeted by drivers. In this work, we explore the molecular mechanisms underlying the wtf family of killer meiotic drivers found in fission yeasts. Each wtf killer acts using a toxic Wtfpoison protein that can be neutralized by a corresponding Wtfantidote protein. The wtf genes are rapidly evolving and extremely diverse. Here we found that self-assembly of Wtfpoison proteins is broadly conserved and associated with toxicity across the gene family, despite minimal amino acid conservation. In addition, we found the toxicity of Wtfpoison assemblies can be modulated by protein tags designed to increase or decrease the extent of the Wtfpoison assembly, implicating assembly size in toxicity. We also identified a conserved, critical role for the specific co-assembly of the Wtfpoison and Wtfantidote proteins in promoting effective neutralization of Wtfpoison toxicity. Finally, we engineered wtf alleles that encode toxic Wtfpoison proteins that are not effectively neutralized by their corresponding Wtfantidote proteins. The possibility of such self-destructive alleles reveals functional constraints on wtf evolution and suggests similar alleles could be cryptic contributors to infertility in fission yeast populations. As rapidly evolving killer meiotic drivers are widespread in eukaryotes, analogous self-killing drive alleles could contribute to sporadic infertility in many lineages.

The Saccharomyces cerevisiae ∑1278b strain is sensitive to NaCl because of mutations in its ENA1 gene

Most laboratory strains of the yeast Saccharomyces cerevisiae are incapable of invading agar, to form large colonies (mats), and to develop filament-like structures (pseudohyphae). A prominent strain that manifests these morphologies is ∑1278b. While induced transcription of the FLO11 gene is critical for executing invasive growth, mat formation, and pseudohyphal growth, downregulation of the 'general stress response' also seems to be required. As this response is weak in ∑1278b cells, we assumed that they may be sensitives to stresses. We report, however, that they are resistant to various stressors, but severely sensitive specifically to NaCl. We found that this sensitivity is a result of mutations in the single ∑1278b's ENA gene, encoding P-type sodium ATPase. Other laboratory strains harbor three to five copies of ENA, suggesting that ∑1278b was selected against Ena activity. Obtaining ∑1278b cells that can grow on NaCl allows checking its effect on colony morphologies. In the presence of NaCl, ∑1278b/ENA1+ cells do not invade agar, and do not form pseudohyphae or mats. Thus, we have found the following: (i) The ∑1278b strain differs from other laboratory strains with respect to sensitivity to NaCl, because it has no active Na+ ATPase exporter. (ii) NaCl is a suppressor of invasiveness, filamentous growth, and mat formation.

Engineering Inorganic Pyrophosphate Metabolism as a Strategy to Generate a Fluoride-Resistant Saccharomyces cerevisiae Strain

Fluorine accounts for 0.3 g/kg of the Earth's crust, being widely distributed in the environment as fluoride. The toxic effects of this anion in humans and other organisms have been known for a long time. Fluoride has been reported to alter several cellular processes although the mechanisms involved are largely unknown. Inorganic pyrophosphatases (PPases) are ubiquitous enzymes that hydrolyze inorganic pyrophosphate (PPi), a metabolite generated from ATP. In Saccharomyces cerevisiae, the enzyme responsible for PPi hydrolysis in the cytosol (IPP1) is strongly inhibited by fluoride in vitro. The essentiality of IPP1 for growth has been previously demonstrated using YPC3, a yeast mutant with conditional expression of the corresponding gene. Here, YPC3 was used to generate cells that tolerate high concentrations of fluoride by (a) the overexpression of IPP1 or its human ortholog, or (b) the substitution of IPP1 by the fluoride-insensitive PPase from Streptococcus mutans. The results obtained suggest that maintaining appropriate levels of PPase activity in the cytosol is essential for the adaptation of S. cerevisiae to high fluoride concentrations. The increase in fluoride tolerance allows YPC3 cells transformed with suitable plasmids to be selected on rich non-selective medium supplemented with this anion.

Functional characterization of human recessive DIS3 variants in premature ovarian insufficiency†

Premature ovarian insufficiency (POI) is characterized by the loss or complete absence of ovarian activity in women under the age of 40. Clinical presentation of POI varies with phenotypic severity ranging from premature loss of menses to complete gonadal dysgenesis. POI is genetically heterogeneous with >100 causative gene variants identified thus far. The etiology of POI varies from syndromic, idiopathic, monogenic to autoimmune causes the condition. Genetic diagnoses are beneficial to those impacted by POI as it allows for improved clinical management and fertility preservation. Identifying novel variants in candidate POI genes, however, is insufficient to make clinical diagnoses. The impact of missense variants can be predicted using bioinformatic algorithms but computational approaches have limitations and can generate false positive and false negative predictions. Functional characterization of missense variants, is therefore imperative, particularly for genes lacking a well-established genotype:phenotype correlation. Here we used whole-exome sequencing (WES) to identify the first case of a homozygous missense variant in DIS3 (c.2320C > T; p.His774Tyr) a critical component of the RNA exosome in a POI patient. This adds to the previously described compound heterozygous patient. We perform the first functional characterization of a human POI-associated DIS3 variant. A slight defect in mitotic growth was caused by the variant in a Saccharomyces cerevisiae model. Transgenic rescue of Dis3 knockdown in Drosophila melanogaster with human DIS3 carrying the patient variant led to aberrant ovarian development and egg chamber degeneration. This supports a potential deleterious impact of the human c.2320C > T; p.His774Tyr variant.

Enhancement of fermentation traits in industrial Baker's yeast for low or high sugar environments

Saccharomyces cerevisiae SPC-SNU 70-1 is a commercial diploid baking yeast strain valued for its excellent bread-making qualities, including superior leavening capabilities and the production of flavor-enhancing volatile organic acids. Despite its benefits, this strain faces challenges in fermenting both lean (low-sugar) and sweet (high-sugar) doughs. To address these issues, we employed the CRISPR/Cas9 genome editing system to modify genes without leaving any genetic scars. For lean doughs, we enhanced the yeast's ability to utilize maltose over glucose by deleting a gene involved in glucose repression. For sweet doughs, we increased glycerol production by overexpressing glycerol biosynthetic genes and optimizing redox balance, thereby improving the tolerence to osmotic stress during fermentation. Additionally, the glycerol-overproducing strain demonstrated enhanced freeze tolerance, and bread made from this strain exhibited improved storage properties. This study demonstrates the feasibility and benefits of using engineered yeast strains, created solely by editing their own genes without introducing foreign genes, to enhance bread making.

Coordination of cytochrome bc1 complex assembly at MICOS

The boundary and cristae domains of the mitochondrial inner membrane are connected by crista junctions. Most cristae membrane proteins are nuclear-encoded and inserted by the mitochondrial protein import machinery into the inner boundary membrane. Thus, they must overcome the diffusion barrier imposed by crista junctions to reach their final location. Here, we show that respiratory chain complexes and assembly intermediates are physically connected to the mitochondrial contact site and cristae organizing system (MICOS) that is essential for the formation and stability of crista junctions. We identify the inner membrane protein Mar26 (Fmp10) as a determinant in the biogenesis of the cytochrome bc1 complex (complex III). Mar26 couples a Rieske Fe/S protein-containing assembly intermediate to MICOS. Our data indicate that Mar26 maintains an assembly-competent Rip1 pool at crista junctions where complex III maturation likely occurs. MICOS facilitates efficient Rip1 assembly by recruiting complex III assembly intermediates to crista junctions. We propose that MICOS, via interaction with assembly factors such as Mar26, contributes to the spatial and temporal coordination of respiratory chain biogenesis.

Use of the D4H Probe to Track Sterols in Yeast

Cholesterol is a fundamental component of cellular membranes, and its organization, distribution, and recycling are tightly regulated. Cholesterol can form, together with other lipids and proteins, membrane nanodomains, which play important roles in membrane trafficking, the spatiotemporal organization of signal transduction, or the modulation of plasma membrane transporters, among others. Not surprisingly then, the misregulation of cholesterol biosynthetic and transport pathways has been related to numerous diseases, including neurodegenerative and metabolic disorders. Here, we focus on the cholesterol-binding domain 4 (D4) of perfringolysin O (PFO, theta toxin) and its use as a probe to define the dynamics and subcellular localization of yeast sterols using time-lapse live-cell fluorescence microscopy. In combination with drugs that acutely interfere with sterol synthesis, such as terbinafine, the probe can also be used to monitor in real-time the extraction of sterols from specialized endoplasmic reticulum subdomains named ERSES (endoplasmic reticulum sterol exit sites) by the OSBP-related protein Osh2.

The sole essential low molecular weight tropomyosin isoform of Caenorhabditis elegans is essential for pharyngeal muscle function

Tropomyosin is an actin-binding protein that plays roles ranging from regulating muscle contraction to controlling cytokinesis and cell migration. The simple nematode Caenorhabditis elegans provides a useful model for studying the core functions of tropomyosin in an animal, having a relatively simple anatomy, and a single tropomyosin gene, lev-11, that produces seven isoforms. Three higher molecular weight isoforms (LEV-11A, D, O) regulate contraction of body wall and other muscles, but comparatively less is known of the functions of four lower molecular weight isoforms (LEV-11C, E, T, U). We demonstrate here C. elegans can survive with a single low molecular weight isoform, LEV-11E. Mutants disrupted for LEV-11E die as young larvae, whereas mutants disrupted for all other short isoforms are viable with no overt phenotype. Vertebrate low molecular weight tropomyosins are often considered "nonmuscle" isoforms, but we find LEV-11E localizes to sarcomeric thin filaments in pharyngeal muscle, and co-precipitates from worm extracts with the formin FHOD-1, which is also associated with thin filaments in pharyngeal muscle. Pharyngeal sarcomere organization is grossly normal in larvae lacking LEV-11E, indicating the tropomyosin is not required to stabilize thin filaments, but pharyngeal pumping is absent, suggesting LEV-11E regulates actomyosin activity similar to higher molecular weight sarcomeric tropomyosin isoforms.

The interaction networks of small rubber particle proteins in the latex of Taraxacum koksaghyz reveal diverse functions in stress responses and secondary metabolism

The Russian dandelion (Taraxacum koksaghyz) is a promising source of natural rubber (NR). The synthesis of NR takes place on the surface of organelles known as rubber particles, which are found in latex - the cytoplasm of specialized cells known as laticifers. As well as the enzymes directly responsible for NR synthesis, the rubber particles also contain small rubber particle proteins (SRPPs), the most abundant of which are SRPP3, 4 and 5. These three proteins support NR synthesis by maintaining rubber particle stability. We used homology-based searches to identify the whole TkSRPP gene family and qPCR to create their spatial expression profiles. Affinity enrichment-mass spectrometry was applied to identify TkSRPP3/4/5 protein interaction partners in T. koksaghyz latex and selected interaction partners were analyzed using qPCR, confocal laser scanning microscopy and heterologous expression in yeast. We identified 17 SRPP-like sequences in the T. koksaghyz genome, including three apparent pseudogenes, 10 paralogs arranged as an inverted repeat in a cluster with TkSRPP3/4/5, and one separate gene (TkSRPP6). Their sequence diversity and different expression profiles indicated distinct functions and the latex interactomes obtained for TkSRPP3/4/5 suggested that TkSRPP4 is a promiscuous hub protein that binds many partners from different compartments, whereas TkSRPP3 and 5 have more focused interactomes. Two interactors shared by TkSRPP3/4/5 (TkSRPP6 and TkUGT80B1) were chosen for independent validation and detailed characterization. TkUGT80B1 triterpenoid glycosylating activity provided first evidence for triterpenoid saponin synthesis in T. koksaghyz latex. Based on its identified interaction partners, TkSRPP4 appears to play a special role in the endoplasmic reticulum, interacting with lipidmodifying enzymes that may facilitate rubber particle formation. TkSRPP5 appears to be involved in GTPase-dependent signaling and TkSRPP3 may act as part of a kinase signaling cascade, with roles in stress tolerance. TkSRPP interaction with TkUGT80B1 draws a new connection between TkSRPPs and triterpenoid saponin synthesis in T. koksaghyz latex. Our data contribute to the functional differentiation between TkSRPP paralogs and demonstrate unexpected interactions that will help to further elucidate the network of proteins linking TkSRPPs, stress responses and NR biosynthesis within the cellular complexity of latex.

Elucidation of Ubiquitin-Related Functions via an Ubiquitin Overexpression Approach

To identify new ubiquitin-related functions using yeast, we searched for mutants conferring a temperature-sensitivity phenotype that could be rescued through ubiquitin overexpression. Screening of mutants using this overexpression strategy identified SPC2, which encodes a subunit of the endoplasmic reticulum (ER) signal peptidase complex (SPC). Ubiquitin overexpression rescued a high-temperature sensitivity of spc2 deletion mutant, suggesting that ubiquitin could compensate for Spc2 loss-of-function at high temperatures. The double mutant of Spc2 and Hrd1, an ER E3 ubiquitin ligase, showed a synergistic growth defect at higher temperatures. A weak genetic interaction was also observed between spc2Δ and cdc48-3 mutation. The results suggest a close functional relationship between SPC and the ubiquitin-proteasome system in yeast and further provide proof-of-principle for this ubiquitin overexpression approach to identify novel ubiquitin-related genes and associated cellular processes.

RNA degradation triggered by decapping is largely independent of initial deadenylation

RNA stability, important for eukaryotic gene expression, is thought to depend on deadenylation rates, with shortened poly(A) tails triggering decapping and 5' to 3' degradation. In contrast to this view, recent large-scale studies indicate that the most unstable mRNAs have, on average, long poly(A) tails. To clarify the role of deadenylation in mRNA decay, we first modeled mRNA poly(A) tail kinetics and mRNA stability in yeast. Independent of deadenylation rates, differences in mRNA decapping rates alone were sufficient to explain current large-scale results. To test the hypothesis that deadenylation and decapping are uncoupled, we used rapid depletion of decapping and deadenylation enzymes and measured changes in mRNA levels, poly(A) length and stability, both transcriptome-wide and with individual reporters. These experiments revealed that perturbations in poly(A) tail length did not correlate with variations in mRNA stability. Thus, while deadenylation may be critical for specific regulatory mechanisms, our results suggest that for most yeast mRNAs, it is not critical for mRNA decapping and degradation.

Significantly reduced, but balanced, rates of mitochondrial fission and fusion are sufficient to maintain the integrity of yeast mitochondrial DNA

Mitochondria exist as dynamic tubular networks and the morphology of these networks impacts organelle function and cell health. Mitochondrial morphology is maintained in part by the opposing activities of mitochondrial fission and fusion. Mitochondrial fission and fusion are also required to maintain mitochondrial DNA (mtDNA) integrity. In Saccharomyces cerevisiae, the simultaneous inhibition of mitochondrial fission and fusion results in increased mtDNA mutation and the consequent loss of respiratory competence. The mechanism by which fission and fusion maintain mtDNA integrity is not fully understood. Previous work demonstrates that mtDNA is spatially linked to mitochondrial fission sites. Here, we extend this finding using live-cell imaging to localize mtDNA to mitochondrial fusion sites. While mtDNA is present at sites of mitochondrial fission and fusion, mitochondrial fission and fusion rates are not altered in cells lacking mtDNA. Using alleles that alter mitochondrial fission and fusion rates, we find that mtDNA integrity can be maintained in cells with significantly reduced, but balanced, rates of fission and fusion. In addition, we find that increasing mtDNA copy number reduces the loss of respiratory competence in double mitochondrial fission-fusion mutants. Our findings add novel insights into the relationship between mitochondrial dynamics and mtDNA integrity.

Novel yeast-based biosensor for environmental monitoring of tebuconazole

Due to increasing demand for high and stable crop production, human populations are highly dependent on pesticide use for growing and storing food. Environmental monitoring of these agrochemicals is therefore of utmost importance, because of their collateral effects on ecosystem and human health. Even though most current-use analytical methods achieve low detection limits, they require procedures that are too complex and costly for routine monitoring. As such, there has been an increased interest in biosensors as alternative or complementary tools to streamline detection and quantification of environmental contaminants. In this work, we developed a biosensor for environmental monitoring of tebuconazole (TEB), a common agrochemical fungicide. For that purpose, we engineered S. cerevisiae cells with a reporter gene downstream of specific promoters that are expressed after exposure to TEB and characterized the sensitivity and specificity of this model system. After optimization, we found that this easy-to-use biosensor consistently detects TEB at concentrations above 5 μg L-1 and does not respond to realistic environmental concentrations of other tested azoles, suggesting it is specific. We propose the use of this system as a complementary tool in environmental monitoring programs, namely, in high throughput scenarios requiring screening of numerous samples. KEY POINTS: • A yeast-based biosensor was developed for environmental monitoring of tebuconazole. •The biosensor offers a rapid and easy method for tebuconazole detection ≥ 5 μg L-1. •The biosensor is specific to tebuconazole at environmentally relevant concentrations.

Functional similarities and differences among subunits of the nascent polypeptide-associated complex (NAC) of Saccharomyces cerevisiae

Protein factors bind ribosomes near the tunnel exit, facilitating protein trafficking and folding. In eukaryotes, the heterodimeric nascent polypeptide-associated complex (NAC) is the most abundant-equimolar to ribosomes. Saccharomyces cerevisiae has a minor β-type subunit (Nacβ2) in addition to abundant Nacβ1, and therefore two NAC heterodimers, α/β1 and α/β12. The additional beta NAC gene arose at the time of the whole genome duplication that occurred in the S. cerevisiae lineage. Nacβ2 has been implicated in regulating the fate of messenger RNA encoding ribosomal protein Rpl4 during translation via its interaction with the Caf130 subunit of the regulatory CCR4-Not complex. We found that Nacβ2 residues just C-terminal to the globular domain are required for its interaction with Caf130 and its negative effect on the growth of cells lacking Acl4, the specialized chaperone for Rpl4. Substitution of these Nacβ2 residues at homologous positions in Nacβ1 results in a chimeric protein that interacts with Caf130 and slows the growth of ∆acl4 cells lacking Nacβ2. Furthermore, alteration of residues in the N-terminus of Nacβ2 or chimeric Nacβ1 previously shown to affect ribosome binding overcomes the growth defect of ∆acl4. Our results are consistent with a model in which Nacβ2's ribosome association per se or its precise positioning is necessary for productive recruitment of CCR4-Not via its interaction with the Caf130 subunit to drive Rpl4 messenger RNA degradation.

Determinants of chemoselectivity in ubiquitination by the J2 family of ubiquitin-conjugating enzymes

Ubiquitin-conjugating enzymes (E2) play a crucial role in the attachment of ubiquitin to proteins. Together with ubiquitin ligases (E3), they catalyze the transfer of ubiquitin (Ub) onto lysines with high chemoselectivity. A subfamily of E2s, including yeast Ubc6 and human Ube2J2, also mediates noncanonical modification of serines, but the structural determinants for this chemical versatility remain unknown. Using a combination of X-ray crystallography, molecular dynamics (MD) simulations, and reconstitution approaches, we have uncovered a two-layered mechanism that underlies this unique reactivity. A rearrangement of the Ubc6/Ube2J2 active site enhances the reactivity of the E2-Ub thioester, facilitating attack by weaker nucleophiles. Moreover, a conserved histidine in Ubc6/Ube2J2 activates a substrate serine by general base catalysis. Binding of RING-type E3 ligases further increases the serine selectivity inherent to Ubc6/Ube2J2, via an allosteric mechanism that requires specific positioning of the ubiquitin tail at the E2 active site. Our results elucidate how subtle structural modifications to the highly conserved E2 fold yield distinct enzymatic activity.

Specificity of Membrane-Associated J-Domain Protein, Caj1, in Amphotericin B Tolerance in Budding Yeast

Hsp70:J-domain protein (JDP) machineries play pivotal roles in maintaining cellular proteostasis and governing various aspects of fungal physiology. While Hsp70 is known for its involvement in conferring tolerance to diverse antifungal drugs, the specific contribution of JDPs remains unclear. In this study, we examined the sensitivity of cytosolic JDP deletion strains of budding yeast to amphotericin B (AmB), a polyene antifungal agent widely utilized in fungal disease treatment due to its ability to disrupt the fungal plasma membrane (PM). Deleting Caj1, a PM-associated class II JDP, heightened susceptibility to AmB, and the protection conferred by Caj1 against AmB necessitated both its N-terminal J-domain and C-terminal lipid binding domain. Moreover, Caj1 deficiency compromised PM integrity as evidenced by increased phosphate efflux and exacerbated AmB sensitivity, particularly at elevated temperatures. Notably, phytosphingosine (PHS) addition as well as overexpression of PMP3, a positive PM integrity regulator, significantly rescued AmB sensitivity of caj1Δ cells. Our results align with the notion that Caj1 associates with the PM and cooperates with Hsp70 to regulate PM proteostasis, thereby influencing PM integrity in budding yeast. Loss of Caj1 function at the PM compromises PM protein quality control, thereby rendering yeast cells more susceptible to AmB.

The CTR hydrophobic residues of Nem1 catalytic subunit are required to form a protein phosphatase complex with Spo7 to activate yeast Pah1 PA phosphatase

The Nem1-Spo7 phosphatase complex plays a key role in lipid metabolism as an activator of Pah1 phosphatidate phosphatase, which produces diacylglycerol for the synthesis of triacylglycerol and membrane phospholipids. For dephosphorylation of Pah1, the Nem1 catalytic subunit requires Spo7 for the recruitment of the protein substrate and interacts with the regulatory subunit through its conserved region (residues 251-446). In this work, we found that the Nem1 C-terminal region (CTR) (residues 414-436), which flanks the haloacid dehalogenase-like catalytic domain (residues 251-413), contains the conserved hydrophobic residues (L414, L415, L417, L418, L421, V430, L434, and L436) that are necessary for the complex formation with Spo7. AlphaFold predicts that some CTR residues of Nem1 interact with Spo7 conserved regions, whereas some residues interact with the haloacid dehalogenase-like domain. By site-directed mutagenesis, Nem1 variants were constructed to lack (Δ(414-446)) or substitute alanines (8A) and arginines (8R) for the hydrophobic residues. When co-expressed with Spo7, the CTR variants of Nem1 did not form a complex with Spo7. In addition, the Nem1 variants were incapable of catalyzing the dephosphorylation of Pah1 in the presence of Spo7. Moreover, the Nem1 variants expressed in nem1Δ cells did not complement the phenotypes characteristic of a defect in the Nem1-Spo7/Pah1 phosphatase cascade function (e.g., lipid synthesis, lipid droplet formation, and phospholipid biosynthetic gene expression). These findings support that Nem1 interacts with Spo7 through its CTR hydrophobic residues to form a phosphatase complex for catalytic activity and physiological functions.