Anton Khmelinskii
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View article: Bidirectional control of a metabolic transition by the GID ubiquitin ligase
Bidirectional control of a metabolic transition by the GID ubiquitin ligase Open
Summary The GID/CTLH ubiquitin ligase is a multisubunit E3 conserved across eukaryotes. GID/CTLH has been implicated in a variety of processes, including metabolic regulation, cell proliferation, embryonic development and cell differentiat…
Genome-wide conditional degron libraries for functional genomics Open
Functional genomics with libraries of knockout alleles is limited to non-essential genes and convoluted by the potential accumulation of suppressor mutations in knockout backgrounds, which can lead to erroneous functional annotations. To a…
Genome-wide conditional degron libraries for functional genomics Open
The yeast knockout library, comprised of strains carrying precise deletions of individual open reading frames (ORFs), has been a vital resource to understand gene function. However, accumulation of suppressor mutations in knockout strains …
Multiple quality control mechanisms monitor yeast chitin synthase folding in the endoplasmic reticulum Open
The chitin synthase Chs3 is a multipass membrane protein whose trafficking is tightly controlled. Accordingly, its exit from the endoplasmic reticulum (ER) depends on several complementary mechanisms that ensure its correct folding. Despit…
Orphan quality control by an SCF ubiquitin ligase directed to pervasive C-degrons Open
Summary Selective protein degradation typically involves substrate recognition via short linear motifs known as degrons. Various degrons can be found at protein termini from bacteria to mammals. While N-degrons have been extensively studie…
input datasets Open
The folder contains input datasets for the code @ https://github.com/Khmelinskii-Lab/Das1_C-degrons related to the publication:Orphan quality control by an SCF ubiquitin ligase directed to pervasive C-degronsKa-Yiu Edwin Kong1,*,#, Susmith…
SWR1 chromatin remodeling complex prevents mitotic slippage during spindle position checkpoint arrest Open
Caydasi et al. identified the SWR1 chromatin-remodeling complex (SWR1-C) among novel factors that are essential for the integrity of the spindle position checkpoint (SPOC). They show that cells lacking SWR1-C activate the SPOC upon spindle…
Genetic requirements for repair of lesions caused by single genomic ribonucleotides in S phase Open
Single ribonucleoside monophosphates (rNMPs) are transiently present in eukaryotic genomes. The RNase H2-dependent ribonucleotide excision repair (RER) pathway ensures error-free genomic rNMP removal. In pathological conditions, genomic rN…
High-Throughput Analysis of Protein Turnover with Tandem Fluorescent Protein Timers Open
Tandem fluorescent protein timers (tFTs) are versatile reporters of protein dynamics. A tFT consists of two fluorescent proteins with different maturation kinetics and provides a ratiometric readout of protein age, which can be exploited t…
Up-regulation of ubiquitin–proteasome activity upon loss of NatA-dependent N-terminal acetylation Open
N-terminal acetylation is a prominent protein modification, and inactivation of N-terminal acetyltransferases (NATs) cause protein homeostasis stress. Using multiplexed protein stability profiling with linear ubiquitin fusions as reporters…
View article: Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase
Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase Open
Selective protein degradation by the ubiquitin-proteasome system (UPS) is involved in all cellular processes. However, the substrates and specificity of most UPS components are not well understood. Here we systematically characterized the …
Quality control of mislocalized and orphan proteins Open
A healthy and functional proteome is essential to cell physiology. However, this is constantly being challenged as most steps of protein metabolism are error-prone and changes in the physico-chemical environment can affect protein structur…
View article: Exploring whole-genome duplicate gene retention with complex genetic interaction analysis
Exploring whole-genome duplicate gene retention with complex genetic interaction analysis Open
The fate of genes after duplication Gene duplication within an organism is a relatively common event during evolution. However, we cannot predict the fate of the duplicated genes: Will they be lost, evolve, or overlap in function within an…
View article: Ubc13–Mms2 cooperates with a family of RING E3 proteins in budding yeast membrane protein sorting
Ubc13–Mms2 cooperates with a family of RING E3 proteins in budding yeast membrane protein sorting Open
Polyubiquitin chains linked via lysine (K) 63 play an important role in endocytosis and membrane trafficking. Their primary source is the ubiquitin protein ligase (E3) Rsp5/NEDD4, which acts as a key regulator of membrane protein sorting. …
Mechanisms of up-regulation of Ubiquitin-Proteasome activity in the absence of NatA dependent N-terminal acetylation Open
N-terminal acetylation is a prominent protein modification and inactivation of N-terminal acetyltransferases (NATs) cause protein homeostasis stress. Using multiplexed protein stability (MPS) profiling with linear ubiquitin fusions as repo…
SWR1 Chromatin Remodeling Complex Prevents Mitotic Slippage during Spindle Position Checkpoint Arrest Open
Faithful chromosome segregation in budding yeast requires correct positioning of the mitotic spindle along the mother to daughter cell polarity axis. When the anaphase spindle is not correctly positioned, a surveillance mechanism, named as…
Cooperation of mitochondrial and ER factors in quality control of tail-anchored proteins Open
Tail-anchored (TA) proteins insert post-translationally into the endoplasmic reticulum (ER), the outer mitochondrial membrane (OMM) and peroxisomes. Whereas the GET pathway controls ER-targeting, no dedicated factors are known for OMM inse…
Author response: Cooperation of mitochondrial and ER factors in quality control of tail-anchored proteins Open
Article Figures and data Abstract Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Tail-anchored (TA) proteins insert post-tr…
View article: The ubiquitin-conjugating enzyme Ubc13-Mms2 cooperates with a family of FYVE-type-RING ubiquitin protein ligases in K63-polyubiquitylation at internal membranes
The ubiquitin-conjugating enzyme Ubc13-Mms2 cooperates with a family of FYVE-type-RING ubiquitin protein ligases in K63-polyubiquitylation at internal membranes Open
The heterodimeric ubiquitin-conjugating enzyme (E2), Ubc13-Mms2, catalyses K63-specific polyubiquitylation in genome maintenance and inflammatory signalling. In budding yeast, the only ubiquitin protein ligase (E3) known to cooperate with …
Determinants of the cytosolic turnover of mitochondrial intermembrane space proteins Open
The present study confirms the involvement of ubiquitin-proteasome system in the quality control of mitochondrial IMS proteins in the cytosol. Notably, ubiquitination of IMS proteins prohibits their import into mitochondria. Therefore, ubi…
A genome-wide resource for high-throughput genomic tagging of yeast ORFs Open
Here we describe a C-SWAT library for high-throughput tagging of Saccharomyces cerevisiae ORFs. It consists of 5661 strains with an acceptor module inserted after each ORF, which can be efficiently replaced with tags or regulatory elements…
Upregulation of SPS100 gene expression by an antisense RNA via a switch of mRNA isoforms with different stabilities Open
Pervasive transcription of genomes generates multiple classes of non-coding RNAs. One of these classes are stable long non-coding RNAs which overlap coding genes in antisense direction (asRNAs). The function of such asRNAs is not fully und…
Mapping degradation signals and pathways in a eukaryotic N-terminome [data set] Open
Data accompanying the paper "Mapping degradation signals and pathways in a eukaryotic N-terminome".
Temporal and compartment-specific signals coordinate mitotic exit with spindle position Open
The spatiotemporal control of mitotic exit is crucial for faithful chromosome segregation during mitosis. In budding yeast, the mitotic exit network (MEN) drives cells out of mitosis, whereas the spindle position checkpoint (SPOC) blocks M…
Protein Abundance Control by Non-coding Antisense Transcription Open
Stable unannotated transcripts (SUTs), some of which overlap protein-coding genes in antisense direction, are a class of non-coding RNAs. While case studies have reported important regulatory roles for several of such RNAs, their general i…