Yeast Protein Research Articles

Subtleties in Clathrin heavy chain binding boxes provide selectivity among adaptor proteins of budding yeast

Clathrin forms a triskelion, or three-legged, network that regulates cellular processes by facilitating cargo internalization and trafficking in eukaryotes. Its N-terminal domain is crucial for interacting with adaptor proteins, which link clathrin to the membrane and engage with specific cargo. The N-terminal domain contains up to four adaptor-binding sites, though their role in preferential occupancy by adaptor proteins remains unclear. In this study, we examine the binding hierarchy of adaptors for clathrin, using integrative biophysical and structural approaches, along with in vivo functional experiments. We find that yeast epsin Ent5 has the highest affinity for clathrin, highlighting its key role in cellular trafficking. Epsins Ent1 and Ent2, crucial for endocytosis but thought to have redundant functions, show distinct binding patterns. Ent1 exhibits stronger interactions with clathrin than Ent2, suggesting a functional divergence toward actin binding. These results offer molecular insights into adaptor protein selectivity, suggesting they competitively bind clathrin while also targeting three different clathrin sites.

Substituting imported soybean meal with locally produced novel yeast protein in concentrates for Norwegian Red dairy cows: implications for rumen microbiota and fatty acid composition.

This research paper addresses the hypothesis that substituting soybean meal with locally produced yeast protein from Cyberlindnera jadinii in barley-based concentrates for Norwegian Red (NR) dairy cows does not have adverse effects on milk fatty acid (FA) composition, rumen microbiota and sensory quality of milk. As soybeans also represent valuable protein sources for human consumption, alternative protein sources need to be investigated for animal feed. A total of 48 NR dairy cows were allocated into three feeding treatments, with the same basal diet of grass silage, but different concentrates. The concentrates were all based on barley, but 7% of the barley in the barley-concentrate (BAR; negative control) was replaced by either soybean meal (SBM; conventional control) or yeast microbial protein (YEA). The experiment lasted for a total of 10 weeks, including 2 weeks of adaptation with the soybean meal concentrate. Analysis of the feed revealed some differences in the FA composition of the YEA concentrate compared to the SBM and BAR concentrates. In milk, only two FAs (C17:1n-8cis9 and an unidentified isomer of C18:3) were significantly different between the YEA- and SBM-group, while six FAs differed between the BAR- and SBM-group. However, the amount of these FAs was low compared to the entire FA profile (<0.7 g/100 g). The experimental diets did not affect rumen microbiota nor the milk sensory quality. This study shows that C. jadinii can replace soybean meal as a protein source in concentrates (7% inclusion) for NR dairy cows fed a diet composed of grass silage and concentrates without any effects on rumen microbiota, and without compromising the FA composition or sensory quality of milk.

Regulation of tapioca starch 3D printability by yeast protein: Rheological, textural evaluation, and machine learning prediction

This article investigated the effects of yeast protein (YP) on gel rheology, texture, and 3D printability of tapioca starch and the feasibility of Principal component analysis (PCA) and support vector machine (SVM) algorithms for classification and prediction of printability. The results indicated that increasing YP content enhanced the viscosity, storage and loss moduli, and hardness, thereby improving extrudability and supportability of 3D printing. The addition of 15% YP exhibited the best 3D printing performance, but excessively high YP addition hindered ink extrusion. PCA analysis based on rheological and texture indices categorized the ink's 3D printing performance into four classes: poor support and low printing accuracy; good support but low printing accuracy; good support and high printing accuracy; and non-smooth extrusion. Furthermore, SVM algorithm used texture data to predict printability classification, with the highest prediction accuracy (91.67%) achieved at polynomial kernel among four different kernel functions. These results confirm that YP can serve as a potential ink for 3D printing and underscore SVM's efficacy in predicting ink's 3D printing performance.

Yeast protein‐derived γ‐glutamyl peptides prepared by transpeptidation reaction exhibit a pronounced taste‐enhancing effect

AbstractA high‐salt diet can induce hypertension, so salt reduction can prevent hypertension. γ‐Glutamyl peptides (GGPs) have obvious taste‐enhancing effects, while their contents in natural foods are relatively low. Yeast protein rich in Glu/Gln is a good precursor for the preparation of GGPs. In this study, yeast protein‐derived GGPs were prepared through hydrolysis and transpeptidation reactions, followed by sensory evaluation and E‐tongue analysis. Peptide sequences were identified by LC−MS/MS and screened for molecular docking. The optimal reaction conditions were hydrolysis for 4 h, enzyme concentration of 16 U/g, and transpeptidation for 4 h. GGPs could increase salt and umami intensity by 60.78% and 40.93% based on sensory evaluation, 22.52%, and 16.40% according to E‐tongue analysis. Fifteen γ‐glutamyl peptides with different peptide lengths were selected for molecular docking. Molecular docking confirmed their binding to calcium‐sensing receptors (CaSr) through hydrogen bonds and hydrophobic interaction, while interaction between CaSR receptor and γ‐glutamyl di‐, tri‐, and oligo‐peptides varied in binding energy. The stimulation received by CaSR lasted a longer time and varied in intensity. It was further proved that the flavor of mixed peptides has a layered sense and can give people a rich taste experience. Overall, yeast protein‐derived GGPs can enhance salt and umami taste, which can reduce salt usage without compromising taste.

Evaluation of the nutritional quality of yeast protein in comparison to animal and plant proteins using growing rats and INFOGEST model

Yeast, identified as a microorganism, boasts a considerable protein content, positioning yeast protein as a highly promising alternative in the quest for sustainable protein sources. The primary aim of this study is to evaluate the protein quality of yeast protein and compare it with animal proteins (whey concentrate/isolate proteins) and plant proteins (soy, wheat, pea proteins). Notably, yeast protein exhibits the highest ratio of indispensable/dispensable amino acids (IAAs/DAAs, 0.91). However, in both in vivo and in vitro digestion experiments, yeast protein demonstrated lower true protein digestibility (TPD) and true ileal digestibility (TID) compared to other proteins. Despite this, the yeast protein's amino acid score (AAS, 1.37 for >3 years), protein digestibility-corrected amino acid score (PDCAAS, 100 % for >3 years), and digestibility-corrected amino acid score (DIAAS, 82.42 % for >3 years) of yeast protein surpassed those of plant proteins, yet remained lower than animal proteins primarily due to its lower digestibility.

Overexpression of CBK1 or deletion of SSD1 confers fludioxonil resistance in yeast by suppressing Hog1 activation

Group III hybrid histidine kinases (HHK3) are known molecular targets of the widely used fungicidal agent fludioxonil which indirectly converts these kinases to a phosphatase form that causes constitutive activation of Hog1 MAPK. To better understand the fungicidal effect of fludioxonil we have screened S. cerevisiae haploid deletion collection for fludioxonil resistant mutant and identified Ssd1 as a critical factor for this. Deletion of SSD1 not only promoted resistance to fludioxonil but also abrogated Hog1 activation and other cellular damages caused by fludioxonil. Our results showed that fludioxonil perturbed the localization of Cbk1 kinase, an essential protein in yeast, at the bud neck triggering the accumulation of Ssd1 in P-bodies. As a result, localized synthesis of Ssd1 bound mRNA encoding cell wall proteins at the polarized growth site was impaired which created a sustained cell wall stress causing constitutive activation of Hog1. Our data, for the first time, clearly indicated the role of Cbk1 upstream of Hog1 and provided a novel paradigm in the mechanism of action of fludioxonil.

Yeast Proteins: Proteomics, Extraction, Modification, Functional Characterization, and Structure: A Review.

Proteins are essential for human tissues and organs, and they require adequate intake for normal physiological functions. With a growing global population, protein demand rises annually. Traditional animal and plant protein sources rely heavily on land and water, making it difficult to meet the increasing demand. The high protein content of yeast and the complete range of amino acids in yeast proteins make it a high-quality source of supplemental protein. Screening of high-protein yeast strains using proteomics is essential to increase the value of yeast protein resources and to promote the yeast protein industry. However, current yeast extraction methods are mainly alkaline solubilization and acid precipitation; therefore, it is necessary to develop more efficient and environmentally friendly techniques. In addition, the functional properties of yeast proteins limit their application in the food industry. To improve these properties, methods must be selected to modify the secondary and tertiary structures of yeast proteins. This paper explores how proteomic analysis can be used to identify nutrient-rich yeast strains, compares the process of preparing yeast proteins, and investigates how modification methods affect the function and structure of yeast proteins. It provides a theoretical basis for solving the problem of inadequate protein intake in China and explores future prospects.

Identification of Novel Umami Peptides from Yeast Protein through Enzymatic, Sensory, and In Silico Approaches.

This study aimed to rapidly develop novel umami peptides using yeast protein as an alternative protein source. Yeast protein hydrolysates exhibiting pronounced umami intensity were produced using flavorzyme under optimum conditions determined via a sensory-guided response surface methodology. Six out of 2138 peptides predicted to possess umami taste by composite machine learning and assessed as nontoxic, nonallergenic, water-soluble, and stable using integrated bioinformatics were screened as potential umami peptides. Sensory evaluation results revealed these peptides exhibited multiple taste attributes (detection threshold: 0.37 ± 0.10-1.1 ± 0.30 mmol/L), including umami. In light of the molecular docking outcomes, it is inferred that hydrogen bond, hydrophobic, and electrostatic interactions enhanced the theoretically stable binding of peptides to T1R1/T1R3, with their contributions gradually diminishing. Hydrophilic amino acids within T1R1/T1R3, especially Ser, may play a particularly pivotal role in binding with umami peptides. Future research will involve establishing heterologous cell models expressing T1R1 and T1R3 to delve into the cellular physiology of umami peptides. Peptide sequences (FADL, LPDP, and LDIGGDF) also had synergistic saltiness-enhancing effects; to overcome the limitation of not investigating the saltiness enhancement mechanism, comprehensive experiments at the molecular and cellular levels will also be conducted. This study offers a rapid umami peptide development framework and lays the groundwork for exploring yeast protein taste compounds.

Protein Arginine Methylation of the Translation Initiation Factor eIF1A Increases Usage of a Near-cognate Start Codon.

Protein arginine methylation has emerged as a key post-translational modification responsible for many facets of eukaryotic gene expression. To better understand the extent of this modification in cellular pathways, we carried out bioorthogonal methylation profiling in Saccharomyces cerevisiae to comprehensively identify the in vivo substrates of the major yeast protein arginine methyltransferase Hmt1. Gene ontology analysis of candidate substrates revealed an enrichment of proteins involved in the process of translation. We verified one such factor, eIF1A, by in vitro methylation. Three sites on eIF1A were found to be responsible for its methylation: R13, R14, and R62, with varied capacity by which each site contributed to the overall methylation capacity in vitro. To determine the role of methylation in eIF1A function, we used a battery of arginine-to-alanine substitution mutants to evaluate translation fidelity in these mutants. Our data show that substitution mutants at R13 and R14 in the N-terminal tail improved the fidelity of start codon recognition in an initiation fidelity assay. Overall, our data suggest that Hmt1-mediated methylation of eIF1A fine-tunes the fidelity of start codon recognition for proper translation initiation.

Assessment of the potential risks in SD rats gavaged with genetically modified yeast containing the cp4-epsps gene.

Despite the absence of definitive evidence indicating that the cp4-epsps gene and its resultant recombinant proteins have significant harmful effects on either human or animal health, the safety assessment of genetically modified (GM) crops expressing the CP4-EPSPS proteins has been controversial. This study endeavor was aimed at evaluating the potential risks posed by the CP4-EPSPS protein in transgenic crops, thereby contributing to the advancement of risk assessment methodologies in the context of genetically engineered crops. To ascertain the appropriate daily dosages for oral gavage administration, the expression levels of the CP4-EPSPS protein in a recombinant yeast were quantified. Subsequently, physiological and biochemical analysis, metabolomics, and metagenomic analysis were conducted based on a 90-day Sprague-Dawley (SD) rats feeding experiment, respectively, thereby enhancing the depth and precision of our risk assessment framework. The results from the physiological and biochemical analysis, organ pathological, blood metabolism, gut microbiota, and correlation analysis of metabolites and gut microbiota revealed several biomarkers for further risk assessment. These biomarkers include clinical biochemical indexes such as total bilirubin (TBIL), direct bilirubin (DBIL), creatine kinase (CK), and lactate dehydrogenase (LDH); metabolites like Methionine, 2-Oxovaleric acid, and LysoPC (16:0); and gut microbiota including Blautia wexlerae, Holdemanella biformis, Dorea sp. CAG 317, Coriobacteriaceae and Erysipelotrichaceae. In conclusion, the risk can be significantly reduced by directly consuming inactivated recombinant CP4-EPSPS. Therefore, in everyday life, the risk associated with consuming GM foods containing recombinant CP4-EPSPS is substantially reduced after heat treatment.

A mechanistic investigation into combined influences of NaCl and extrusion temperature on fibrous structures of high-moisture textured yeast protein

NaCl and extrusion temperature have an important influence on the qualities of high-moisture textured proteins, but the influence mechanism is still unclear. Therefore, this study prepared high-moisture textured yeast protein (HMTYP) with different NaCl contents (0%–4%) under different extrusion temperatures (170 °C, 180 °C) and characterized their physicochemical properties. The results showed that the HMTYP containing 1% and 2% NaCl prepared at 180 °C contained a strong fibrous structure. The possible mechanism was as follows: YP could not be sufficiently melted at 170 °C after adding NaCl, causing a decrease in the structural strength; however, at 180 °C, YP still reached a fully molten state even though 1%–2% NaCl was added. After YP sufficiently melted, NaCl enhanced the cross-linking and aggregation of proteins during cooling, which improved the textural properties of HMTYP. Accordingly, NaCl and extrusion temperature could combine to adjust the fibrous structure and texture of HMTYP.

A biallelic variant of the RNA exosome gene, EXOSC4, associated with neurodevelopmental defects impairs RNA exosome function and translation

The RNA exosome is an evolutionarily conserved complex required for both precise RNA processing and decay. Pathogenic variants in EXOSC genes, which encode structural subunits of this complex, are linked to several autosomal recessive disorders. Here, we describe a missense allele of the EXOSC4 gene that causes a collection of clinical features in two affected siblings. This missense variant (NM_019037.3: exon3:c.560T>C) changes a leucine residue within a conserved region of EXOSC4 to proline (p.Leu187Pro). The two affected individuals show prenatal growth restriction, failure to thrive, global developmental delay, intracerebral and basal ganglia calcifications, and kidney failure. Homozygosity for the damaging variant was identified by exome sequencing with Sanger sequencing to confirm segregation. To explore the functional consequences of this amino acid change, we modeled EXOSC4-L187P in the corresponding budding yeast protein, Rrp41 (Rrp41-L187P). Cells that express Rrp41-L187P as the sole copy of the essential Rrp41 protein show growth defects. Steady-state levels of both Rrp41-L187P and EXOSC4-L187P are decreased compared to controls, and EXOSC4-L187P shows decreased copurification with other RNA exosome subunits. RNA exosome target transcripts accumulate in rrp41-L187P cells, including the 7S precursor of 5.8S rRNA. Polysome profiles show a decrease in actively translating ribosomes in rrp41-L187P cells as compared to control cells with the incorporation of 7S pre-rRNA into polysomes. This work adds EXOSC4 to the structural subunits of the RNA exosome that have been linked to human disease and defines foundational molecular defects that could contribute to the adverse phenotypes caused by EXOSC pathogenic variants.

Carp growth, body composition, lipidomics, and flesh quality in response to replacing dietary fish meal with a complex protein source

Alternatives to fish meal (FM) in fish feed are urgently required in aquaculture. We therefore examined the effect of replacing FM with a complex protein source (CPS) comprising soybean meal, peanut meal, corn protein meal, feather meal, and yeast protein, on carp (Cyprinus carpio) growth, body composition, lipidomics, and flesh quality. Lipidomics analysis was conducted to reveal the impact of dietary changes on fish lipid composition and metabolism, which is closely related to flesh quality and nutritional value. Over an eight-week growth trial, fish meal was replaced with CPS at 0 % (FM only), 20 %, 40 %, 60 %, 80 %, or 100 %. Weight gain and other growth parameters did not differ significantly among the treatments. Lipid deposition (LD) was positively correlated, and protein deposition negatively correlated, with CPS levels. LD and fillet ether extract were significantly elevated at 100 % CPS, whereas superoxidase dismutase expression, claudin-1 expression, and lipase activity were significantly reduced. The n-3 PUFA level and n-3/n-6 PUFA ratio were significantly lower following CPS feeding, reducing flesh quality. These findings indicate that CPS successfully replaced 60–80 % of dietary FM in carp diets, while the 100 % replacement group provided insights into the comprehensive effects of total substitution. Future studies will further optimize formulations based on these results to resemble practical production more closely. CPS with nutrient supplementation may therefore present a viable and safe partial replacement for dietary FM.

Advanced Protocol for Molecular Characterization of Viral Genome in Fission Yeast (Schizosaccharomyces pombe).

Fission yeast, a single-cell eukaryotic organism, shares many fundamental cellular processes with higher eukaryotes, including gene transcription and regulation, cell cycle regulation, vesicular transport and membrane trafficking, and cell death resulting from the cellular stress response. As a result, fission yeast has proven to be a versatile model organism for studying human physiology and diseases such as cell cycle dysregulation and cancer, as well as autophagy and neurodegenerative diseases like Alzheimer's, Parkinson's, and Huntington's diseases. Given that viruses are obligate intracellular parasites that rely on host cellular machinery to replicate and produce, fission yeast could serve as a surrogate to identify viral proteins that affect host cellular processes. This approach could facilitate the study of virus-host interactions and help identify potential viral targets for antiviral therapy. Using fission yeast for functional characterization of viral genomes offers several advantages, including a well-characterized and haploid genome, robustness, cost-effectiveness, ease of maintenance, and rapid doubling time. Therefore, fission yeast emerges as a valuable surrogate system for rapid and comprehensive functional characterization of viral proteins, aiding in the identification of therapeutic antiviral targets or viral proteins that impact highly conserved host cellular functions with significant virologic implications. Importantly, this approach has a proven track record of success in studying various human and plant viruses. In this protocol, we present a streamlined and scalable molecular cloning strategy tailored for genome-wide and comprehensive functional characterization of viral proteins in fission yeast.

Benchmarking and Automating the Biotinylation Proteomics Workflow.

Protein biotinylation has been widely used in biotechnology with various labeling and enrichment strategies. However, different enrichment strategies have not been systematically evaluated due to the lack of a benchmarking model for fair comparison. Most biotinylation proteomics workflows suffer from lengthy experimental steps, non-specific bindings, limited throughput, and experimental variability. To address these challenges, we designed a two-proteome model, where biotinylated yeast proteins were spiked in unlabeled human proteins, allowing us to distinguish true enrichment from non-specific bindings. Using this benchmarking model, we compared common biotinylation proteomics methods and provided practical selection guidelines. We significantly optimized and shortened sample preparation from 3 days to 9 hours, enabling fully-automated 96-well plate sample processing. Next, we applied this optimized and automated workflow for proximity labeling to investigate the intricate interplay between mitochondria and lysosomes in living cells under both healthy state and mitochondrial damage. Our results suggested a time-dependent proteome remodeling and dynamic translocation within mitochondria and between mitochondria and lysosomes upon mitochondrial damage. This newly established benchmarking model and the fully-automated 9-hour workflow can be readily applied to the broad fields of protein biotinylation to study protein interaction and organelle dynamics.

Importance of conserved hydrophobic pocket region in yeast mitoribosomal mL44 protein for mitotranslation and transcript preference

The mitochondrial ribosome (mitoribosome) is responsible for the synthesis of key oxidative phosphorylation subunits encoded by the mitochondrial genome. Defects in mitoribosomal function therefore can have serious consequences for the bioenergetic capacity of the cell. Mutation of the conserved mitoribosomal mL44 protein has been directly linked to childhood cardiomyopathy and progressive neurophysiology issues. To further explore the functional significance of the mL44 protein in supporting mitochondrial protein synthesis we have performed a mutagenesis study of the yeast mL44 homolog, the MrpL3/mL44 protein. We specifically investigated the conserved hydrophobic pocket region of the MrpL3/mL44 protein, where the known disease-related residue in the human mL44 protein (L156R) is located. While our findings identify a number of residues in this region critical for MrpL3/mL44’s ability to support the assembly of translationally active mitoribosomes, the introduction of the disease-related mutation into the equivalent position in the yeast protein (residue A186) was found not have a major impact on function. The human and yeast mL44 proteins share many similarities in sequence and structure, however results presented here indicate that these two proteins have diverged somewhat in evolution. Finally, we observed that mutation of the MrpL3/mL44 does not impact the translation of all mitochondrial encoded proteins equally, suggesting the mitochondrial translation system may exhibit a transcript hierarchy and prioritization.

Application of Turbiscan Lab® to study the mechanism of fining in red wine using a specific yeast protein extract: A comparison with gelatine

Fining of wines using proteins is a standard practice in the winemaking process. Gelatine is a common fining agent used for red wines. However, the consumer demand for wines that are free of animal-derived products has reinforced the search for alternative protein sources such as yeast origin as the latter is originally present in wine. In 2012, the International Organization of Vine and Wine (OIV) authorized yeast protein extract (YPE) as a processing aid for the fining of musts and wines (OIV-Eno 452–2012). The present work aimed at better understanding the fining mechanisms of a specific YPE, to evaluate the part played by interactions in solution with polyphenols, but also at the interfaces with suspended particles. Polyphenols from the soluble phase of red wine were separated from the suspended particles by centrifugation, and these particles were resuspended in a wine model solution. Interactions with YPE were studied with each fraction separately through static multiple light scattering (SMLS) using the Turbiscan Lab® apparatus and optical microscopy. The impact on wine color and astringency was assessed by UV–visible spectrophotometry and BSA assay test. Faster aggregation and sedimentation kinetics were observed with gelatine than with YPE, but the levels of clarification and lees were similar for both fining agents after a couple of hours (4 h maximum). Gelatine resulted in higher tannin and pigment removal, likely to decrease astringency but also derived pigments involved in red wine color stability. Meanwhile, the impact of the YPE was moderate, likely to modulate astringency while preserving wine color and structure. In addition to interacting directly with polyphenols in solutions such as gelatine, YPE exhibited the additional ability to trap particles and promote their sedimentation in the absence of tannins. This double performance of the YPE used in this work, is likely to guarantee an effective fining of red wines as well as for low tannin content matrices such as rosé and white wines.

Integrating Experimental and Computational Analyses of Yeast Protein Profiles for Optimizing the Production of High-Quality Microbial Proteins.

Microbial proteins represent a promising solution to address the escalating global demand for protein, particularly in regions with limited arable land. Yeasts, such as Saccharomyces cerevisiae, are robust and safe protein-producing strains. However, the utilization of non-conventional yeast strains for microbial protein production has been hindered, partly due to a lack of comprehensive understanding of protein production traits. In this study, we conducted experimental analyses focusing on the growth, protein content, and amino acid composition of nine yeast strains, including one S. cerevisiae strain, three Yarrowia lipolytica strains, and five Pichia spp. strains. We identified that, though Y. lipolytica and Pichia spp. strains consumed glucose at a slower rate compared to S. cerevisiae, Pichia spp. strains showed a higher cellular protein content, and Y. lipolytica strains showed a higher glucose-to-biomass/protein yield and methionine content. We further applied computational approaches to explain that metabolism economy was the main underlying factor for the limited amount of scarce/carbon-inefficient amino acids (such as methionine) within yeast cell proteins. We additionally verified that the specialized metabolism was a key reason for the high methionine content in Y. lipolytica strains, and proposed Y. lipolytica strain as a potential producer of high-quality single-cell protein rich in scarce amino acids. Through experimental evaluation, we identified Pichia jadinii CICC 1258 as a potential strain for high-quality protein production under unfavorable pH/temperature conditions. Our work suggests a promising avenue for optimizing microbial protein production, identifying the factors influencing amino acid composition, and paving the way for the use of unconventional yeast strains to meet the growing protein demands.

Effect of yeast protein on reduced‐fat ice cream: Sensory quality, rheological behaviour, thermal properties and fat destabilisation

This study prepared six different ice creams to investigate the effect of yeast protein (YP) on their sensory, rheological, thermal properties and fat destabilisation. Results indicated that YP could improve sensory quality, flow and viscoelastic properties. The thermal property was also positively influenced by YP with a significant decrease in frozen water percentage and an increase in glass transition temperature (P &lt; 0.05). Additionally, the particle size and confocal laser scanning microscopy results illustrated that YP could moderately promote the fat aggregate percentage and size. Overall, YP could serve as a fat replacer to produce reduced‐fat ice cream.

A Single-step Generation of AlissAID-based Conditional Knockdown Strains Using Nanobody that Targets GFP or mCherry in Budding Yeast.

The Auxin-inducible degron (AID) system is a genetic tool that induces rapid target protein depletion in an auxin-dependent manner. Recently, two advanced AID systems-the super-sensitive AID and AID 2-were developed using an improved pair of synthetic auxins and mutated TIR1 proteins. In these AID systems, a nanomolar concentration of synthetic auxins is sufficient as a degradation inducer for target proteins. However, despite these advancements, AID systems still require the fusion of an AID tag to the target protein for degradation, potentially affecting its function and stability. To address this limitation, we developed an affinity linker-based super-sensitive AID (AlissAID) system using a single peptide antibody known as a nanobody. In this system, the degradation of GFP- or mCherry-tagged target proteins is induced in a synthetic auxin (5-Ad-IAA)-dependent manner. Here, we introduce a simple method for generating AlissAID strains targeting GFP or mCherry fusion proteins in budding yeasts. Key features • AlissAID system enables efficient degradation of the GFP or mCherry fusion proteins in a 5-Ad-IAA-depending manner. • Transforming the pAlissAID plasmids into strains with GFP- or mCherry- tagged proteins.