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1.
Life Sci Alliance ; 3(12)2020 12.
Article in English | MEDLINE | ID: mdl-33037058

ABSTRACT

The yeast galactose switch operated by the Gal4p-Gal80p-Gal3p regulatory module is a textbook model of transcription regulation in eukaryotes. The Gal80 protein inhibits Gal4p-mediated transcription activation by binding to the transcription activation domain. In Saccharomyces cerevisiae, inhibition is relieved by formation of an alternative Gal80-Gal3 complex. In yeasts lacking a Gal3p ortholog, such as Kluyveromyces lactis, the Gal1 protein (KlGal1p) combines regulatory and enzymatic activity. The data presented here reveal a yet unknown role of the KlGal80 N terminus in the mechanism of Gal4p activation. The N terminus contains an NLS, which is responsible for nuclear accumulation of KlGal80p and KlGal1p and for KlGal80p-mediated galactokinase inhibition. Herein, we present a model where the N terminus of KlGal80p reaches the catalytic center of KlGal1p causing enzyme inhibition in the nucleus and stabilization of the KlGal1-KlGal80p complex. We corroborate this model by genetic analyses and structural modelling and provide a rationale for the divergent evolution of the mechanism activating Gal4p.


Subject(s)
DNA-Binding Proteins/metabolism , Repressor Proteins/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Transcription Factors/metabolism , Cell Nucleus/metabolism , Galactokinase/genetics , Galactose/metabolism , Kluyveromyces/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Transcriptional Activation
2.
Curr Genet ; 66(4): 823-833, 2020 Aug.
Article in English | MEDLINE | ID: mdl-32236652

ABSTRACT

Kti12 (Kluyveromyces lactis toxin insensitive 12) is an evolutionary highly conserved ATPase, crucial for the tRNA-modification activity of the eukaryotic Elongator complex. The protein consists of an N-terminal ATPase and a C-terminal tRNA-binding domain, which are connected by a flexible linker. The precise role of the linker region and its involvement in the communication between the two domains and their activities remain elusive. Here, we analyzed all available Kti12 protein sequences and report the discovery of a subset of Kti12 proteins with abnormally long linker regions. These Kti12 proteins are characterized by a co-occurring lysine to leucine substitution in their Walker A motif, previously thought to be invariable. We show that the K14L substitution lowers the affinity to ATP, but does not affect the catalytic activity of Kti12 at high ATP concentrations. We compare the activity of mutated variants of Kti12 in vitro with complementation assays in vivo in yeast. Ultimately, we compared Kti12 to other known p-loop ATPase family members known to carry a similar deviant Walker A motif. Our data establish Kti12 of Eurotiomycetes as an example of eukaryotic ATPase harboring a significantly deviating but still functional Walker A motif.


Subject(s)
Fungal Proteins/chemistry , Fungal Proteins/metabolism , Saccharomyces cerevisiae/metabolism , AAA Domain , Adaptor Proteins, Signal Transducing/chemistry , Adaptor Proteins, Signal Transducing/genetics , Adaptor Proteins, Signal Transducing/metabolism , Amino Acid Substitution , Animals , Catalytic Domain , Evolution, Molecular , Fungal Proteins/genetics , Killer Factors, Yeast/pharmacology , Kluyveromyces/metabolism , Lysine/chemistry , Machine Learning , Models, Molecular , Mutation , Protein Conformation , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism
3.
Sci Adv ; 5(7): eaaw2326, 2019 07.
Article in English | MEDLINE | ID: mdl-31309145

ABSTRACT

The highly conserved Elongator complex modifies transfer RNAs (tRNAs) in their wobble base position, thereby regulating protein synthesis and ensuring proteome stability. The precise mechanisms of tRNA recognition and its modification reaction remain elusive. Here, we show cryo-electron microscopy structures of the catalytic subcomplex of Elongator and its tRNA-bound state at resolutions of 3.3 and 4.4 Å. The structures resolve details of the catalytic site, including the substrate tRNA, the iron-sulfur cluster, and a SAM molecule, which are all validated by mutational analyses in vitro and in vivo. tRNA binding induces conformational rearrangements, which precisely position the targeted anticodon base in the active site. Our results provide the molecular basis for substrate recognition of Elongator, essential to understand its cellular function and role in neurodegenerative diseases and cancer.


Subject(s)
Multiprotein Complexes/metabolism , Peptide Elongation Factors/metabolism , RNA, Transfer/genetics , Anticodon/chemistry , Binding Sites , Catalytic Domain , Histone Acetyltransferases/chemistry , Histone Acetyltransferases/genetics , Histone Acetyltransferases/metabolism , Models, Molecular , Molecular Conformation , Multiprotein Complexes/chemistry , Peptide Elongation Factors/chemistry , Peptide Elongation Factors/genetics , Protein Binding , RNA, Transfer/chemistry , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism
4.
Nucleic Acids Res ; 47(9): 4814-4830, 2019 05 21.
Article in English | MEDLINE | ID: mdl-30916349

ABSTRACT

Posttranscriptional RNA modifications occur in all domains of life. Modifications of anticodon bases are of particular importance for ribosomal decoding and proteome homeostasis. The Elongator complex modifies uridines in the wobble position and is highly conserved in eukaryotes. Despite recent insights into Elongator's architecture, the structure and function of its regulatory factor Kti12 have remained elusive. Here, we present the crystal structure of Kti12's nucleotide hydrolase domain trapped in a transition state of ATP hydrolysis. The structure reveals striking similarities to an O-phosphoseryl-tRNA kinase involved in the selenocysteine pathway. Both proteins employ similar mechanisms of tRNA binding and show tRNASec-dependent ATPase activity. In addition, we demonstrate that Kti12 binds directly to Elongator and that ATP hydrolysis is crucial for Elongator to maintain proper tRNA anticodon modification levels in vivo. In summary, our data reveal a hitherto uncharacterized link between two translational control pathways that regulate selenocysteine incorporation and affect ribosomal tRNA selection via specific tRNA modifications.


Subject(s)
Adaptor Proteins, Signal Transducing/genetics , Adenosine Triphosphatases/genetics , RNA Processing, Post-Transcriptional/genetics , Saccharomyces cerevisiae Proteins/genetics , Adaptor Proteins, Signal Transducing/chemistry , Adenosine Triphosphatases/chemistry , Anticodon/genetics , Carrier Proteins/chemistry , Carrier Proteins/genetics , Chaetomium/chemistry , Chaetomium/enzymology , Crystallography, X-Ray , Protein Conformation , RNA, Transfer/genetics , Ribosomes/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/chemistry , Uridine/genetics
5.
Toxins (Basel) ; 9(9)2017 09 05.
Article in English | MEDLINE | ID: mdl-28872616

ABSTRACT

Saccharomyces cerevisiae cells are killed by zymocin, a tRNase ribotoxin complex from Kluyveromyces lactis, which cleaves anticodons and inhibits protein synthesis. Zymocin's action requires specific chemical modification of uridine bases in the anticodon wobble position (U34) by the Elongator complex (Elp1-Elp6). Hence, loss of anticodon modification in mutants lacking Elongator or related KTI (K. lactis Toxin Insensitive) genes protects against tRNA cleavage and confers resistance to the toxin. Here, we show that zymocin can be used as a tool to genetically analyse KTI12, a gene previously shown to code for an Elongator partner protein. From a kti12 mutant pool of zymocin survivors, we identify motifs in Kti12 that are functionally directly coupled to Elongator activity. In addition, shared requirement of U34 modifications for nonsense and missense tRNA suppression (SUP4; SOE1) strongly suggests that Kti12 and Elongator cooperate to assure proper tRNA functioning. We show that the Kti12 motifs are conserved in plant ortholog DRL1/ELO4 from Arabidopsis thaliana and seem to be involved in binding of cofactors (e.g., nucleotides, calmodulin). Elongator interaction defects triggered by mutations in these motifs correlate with phenotypes typical for loss of U34 modification. Thus, tRNA modification by Elongator appears to require physical contact with Kti12, and our preliminary data suggest that metabolic signals may affect proper communication between them.


Subject(s)
Adaptor Proteins, Signal Transducing/genetics , Arabidopsis Proteins/genetics , Killer Factors, Yeast/pharmacology , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/drug effects , Adaptor Proteins, Signal Transducing/metabolism , Arabidopsis Proteins/metabolism , RNA, Transfer/genetics , RNA, Transfer/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/metabolism
6.
EMBO Rep ; 18(2): 264-279, 2017 02.
Article in English | MEDLINE | ID: mdl-27974378

ABSTRACT

The highly conserved eukaryotic Elongator complex performs specific chemical modifications on wobble base uridines of tRNAs, which are essential for proteome stability and homeostasis. The complex is formed by six individual subunits (Elp1-6) that are all equally important for its tRNA modification activity. However, its overall architecture and the detailed reaction mechanism remain elusive. Here, we report the structures of the fully assembled yeast Elongator and the Elp123 sub-complex solved by an integrative structure determination approach showing that two copies of the Elp1, Elp2, and Elp3 subunits form a two-lobed scaffold, which binds Elp456 asymmetrically. Our topological models are consistent with previous studies on individual subunits and further validated by complementary biochemical analyses. Our study provides a structural framework on how the tRNA modification activity is carried out by Elongator.


Subject(s)
Fungal Proteins/chemistry , Models, Molecular , Multiprotein Complexes/chemistry , Fungal Proteins/genetics , Fungal Proteins/metabolism , Multiprotein Complexes/metabolism , Multiprotein Complexes/ultrastructure , Mutation , Protein Binding , Protein Conformation , Protein Multimerization , Protein Subunits/chemistry , Protein Subunits/metabolism , Protein Transport , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/metabolism , Structure-Activity Relationship
7.
Nat Struct Mol Biol ; 23(9): 794-802, 2016 09.
Article in English | MEDLINE | ID: mdl-27455459

ABSTRACT

During translation elongation, decoding is based on the recognition of codons by corresponding tRNA anticodon triplets. Molecular mechanisms that regulate global protein synthesis via specific base modifications in tRNA anticodons are receiving increasing attention. The conserved eukaryotic Elongator complex specifically modifies uridines located in the wobble base position of tRNAs. Mutations in Elongator subunits are associated with certain neurodegenerative diseases and cancer. Here we present the crystal structure of D. mccartyi Elp3 (DmcElp3) at 2.15-Å resolution. Our results reveal an unexpected arrangement of Elp3 lysine acetyltransferase (KAT) and radical S-adenosyl methionine (SAM) domains, which share a large interface and form a composite active site and tRNA-binding pocket, with an iron-sulfur cluster located in the dimerization interface of two DmcElp3 molecules. Structure-guided mutagenesis studies of yeast Elp3 confirmed the relevance of our findings for eukaryotic Elp3s and should aid in understanding the cellular functions and pathophysiological roles of Elongator.


Subject(s)
Bacterial Proteins/chemistry , Histone Acetyltransferases/chemistry , RNA, Transfer/chemistry , Catalytic Domain , Chloroflexi/enzymology , Crystallography, X-Ray , Protein Binding , Protein Conformation, alpha-Helical , Protein Multimerization , RNA, Bacterial/chemistry , Substrate Specificity
8.
PLoS One ; 10(10): e0139464, 2015.
Article in English | MEDLINE | ID: mdl-26440109

ABSTRACT

Cellular responses to starvation are of ancient origin since nutrient limitation has always been a common challenge to the stability of living systems. Hence, signaling molecules involved in sensing or transducing information about limiting metabolites are highly conserved, whereas transcription factors and the genes they regulate have diverged. In eukaryotes the AMP-activated protein kinase (AMPK) functions as a central regulator of cellular energy homeostasis. The yeast AMPK ortholog SNF1 controls the transcriptional network that counteracts carbon starvation conditions by regulating a set of transcription factors. Among those Cat8 and Sip4 have overlapping DNA-binding specificity for so-called carbon source responsive elements and induce target genes upon SNF1 activation. To analyze the evolution of the Cat8-Sip4 controlled transcriptional network we have compared the response to carbon limitation of Saccharomyces cerevisiae to that of Kluyveromyces lactis. In high glucose, S. cerevisiae displays tumor cell-like aerobic fermentation and repression of respiration (Crabtree-positive) while K. lactis has a respiratory-fermentative life-style, respiration being regulated by oxygen availability (Crabtree-negative), which is typical for many yeasts and for differentiated higher cells. We demonstrate divergent evolution of the Cat8-Sip4 network and present evidence that a role of Sip4 in controlling anabolic metabolism has been lost in the Saccharomyces lineage. We find that in K. lactis, but not in S. cerevisiae, the Sip4 protein plays an essential role in C2 carbon assimilation including induction of the glyoxylate cycle and the carnitine shuttle genes. Induction of KlSIP4 gene expression by KlCat8 is essential under these growth conditions and a primary function of KlCat8. Both KlCat8 and KlSip4 are involved in the regulation of lactose metabolism in K. lactis. In chromatin-immunoprecipitation experiments we demonstrate binding of both, KlSip4 and KlCat8, to selected CSREs and provide evidence that KlSip4 counteracts KlCat8-mediated transcription activation by competing for binding to some but not all CSREs. The finding that the hierarchical relationship of these transcription factors differs between K. lactis and S. cerevisiae and that the sets of target genes have diverged contributes to explaining the phenotypic differences in metabolic life-style.


Subject(s)
Basic-Leucine Zipper Transcription Factors/genetics , Gene Expression Regulation, Fungal , Gene Regulatory Networks , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/genetics , Transcriptional Activation
9.
Structure ; 23(1): 149-160, 2015 Jan 06.
Article in English | MEDLINE | ID: mdl-25543256

ABSTRACT

The small, highly conserved Kti11 alias Dph3 protein encoded by the Kluyveromyces lactis killer toxin insensitive gene KTI11/DPH3 is involved in the diphthamide modification of eukaryotic elongation factor 2 and, together with Kti13, in Elongator-dependent tRNA wobble base modifications, thereby affecting the speed and accuracy of protein biosynthesis through two distinct mechanisms. We have solved the crystal structures of Saccharomyces cerevisiae Kti13 and the Kti11/Kti13 heterodimer at 2.4 and 2.9 Å resolution, respectively, and validated interacting residues through mutational analysis in vitro and in vivo. We show that metal coordination by Kti11 and its heterodimerization with Kti13 are essential for both translational control mechanisms. Our structural and functional analyses identify Kti13 as an additional component of the diphthamide modification pathway and provide insight into the molecular mechanisms that allow the Kti11/Kti13 heterodimer to coregulate two consecutive steps in ribosomal protein synthesis.


Subject(s)
Peptide Elongation Factor 2/metabolism , RNA, Transfer/metabolism , Repressor Proteins/chemistry , Repressor Proteins/physiology , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/physiology , Models, Molecular , Organisms, Genetically Modified , Peptide Elongation Factor 2/chemistry , Protein Biosynthesis/genetics , Protein Multimerization , Protein Structure, Quaternary , RNA Processing, Post-Transcriptional/genetics , RNA, Transfer/chemistry , Repressor Proteins/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/metabolism
10.
Biol Chem ; 395(7-8): 855-69, 2014 Jul.
Article in English | MEDLINE | ID: mdl-25003388

ABSTRACT

Abstract Many transcription factors contribute to cellular homeostasis by integrating multiple signals. Signaling via the yeast Gal80 protein, a negative regulator of the prototypic transcription activator Gal4, is primarily regulated by galactose. ScGal80 from Saccharomyces cerevisiae has been reported to bind NAD(P). Here, we show that the ability to bind these ligands is conserved in KlGal80, a Gal80 homolog from the distantly related yeast Kluyveromyces lactis. However, the homologs apparently have diverged with respect to response to the dinucleotide. Strikingly, ScGal80 binds NAD(P) and NAD(P)H with more than 50-fold higher affinity than KlGal80. In contrast to ScGal80, where NAD is neutral, NAD and NADP have a negative effect in KlGal80 on its interaction with a KlGal4-peptide in vitro. Swapping a loop in the NAD(P) binding Rossmann-fold of ScGal80 into KlGal80 increases the affinity for NAD(P) and has a significant impact on KlGal4 regulation in vivo. Apparently, dinucleotide binding allows coupling of the metabolic state of the cell to regulation of the GAL/LAC genes. The particular sequences involved in binding determine how exactly the metabolic state is sensed and integrated by Gal80 to regulate Gal4.


Subject(s)
Coenzymes/metabolism , Fungal Proteins/metabolism , Oxidoreductases/metabolism , Coenzymes/genetics , Fungal Proteins/genetics , Galactose/metabolism , Ligands , NAD/metabolism , Oxidoreductases/genetics
11.
Mol Cell Proteomics ; 13(3): 860-75, 2014 Mar.
Article in English | MEDLINE | ID: mdl-24434903

ABSTRACT

The analysis of glucose signaling in the Crabtree-positive eukaryotic model organism Saccharomyces cerevisiae has disclosed a dual role of its hexokinase ScHxk2, which acts as a glycolytic enzyme and key signal transducer adapting central metabolism to glucose availability. In order to identify evolutionarily conserved characteristics of hexokinase structure and function, the cellular response of the Crabtree-negative yeast Kluyveromyces lactis to rag5 null mutation and concomitant deficiency of its unique hexokinase KlHxk1 was analyzed by means of difference gel electrophoresis. In total, 2,851 fluorescent spots containing different protein species were detected in the master gel representing all of the K. lactis proteins that were solubilized from glucose-grown KlHxk1 wild-type and mutant cells. Mass spectrometric peptide analysis identified 45 individual hexokinase-dependent proteins related to carbohydrate, short-chain fatty acid and tricarboxylic acid metabolism as well as to amino acid and protein turnover, but also to general stress response and chromatin remodeling, which occurred as a consequence of KlHxk1 deficiency at a minimum 3-fold enhanced or reduced level in the mutant proteome. In addition, three proteins exhibiting homology to 2-methylcitrate cycle enzymes of S. cerevisiae were detected at increased concentrations, suggesting a stimulation of pyruvate formation from amino acids and/or fatty acids. Experimental validation of the difference gel electrophoresis approach by post-lysis dimethyl labeling largely confirmed the abundance changes detected in the mutant proteome via the former method. Taking into consideration the high proportion of identified hexokinase-dependent proteins exhibiting increased proteomic levels, KlHxk1 is likely to have a repressive function in a multitude of metabolic pathways. The proteomic alterations detected in the mutant classify KlHxk1 as a multifunctional enzyme and support the view of evolutionary conservation of dual-role hexokinases even in organisms that are less specialized than S. cerevisiae in terms of glucose utilization.


Subject(s)
Fungal Proteins/metabolism , Glucose/pharmacology , Hexokinase/deficiency , Kluyveromyces/drug effects , Kluyveromyces/enzymology , Proteome/metabolism , Proteomics , Carbon/pharmacology , Electrophoresis, Gel, Two-Dimensional , Gene Ontology , Hexokinase/metabolism , Kluyveromyces/growth & development , Metabolic Networks and Pathways/drug effects , Mutation/genetics , Phosphorylation/drug effects , Phosphoserine/metabolism
12.
PLoS One ; 7(9): e42870, 2012.
Article in English | MEDLINE | ID: mdl-23024743

ABSTRACT

Here we report on vaccination approaches against infectious bursal disease (IBD) of poultry that were performed with complete yeast of the species Kluyveromyces lactis (K. lactis). Employing a genetic system that enables the rapid production of stably transfected recombinant K. lactis, we generated yeast strains that expressed defined quantities of the virus capsid forming protein VP2 of infectious bursal disease virus (IBDV). Both, subcutaneous as well as oral vaccination regiments with the heat-inactivated but otherwise untreated yeast induced IBDV-neutralizing antibodies in mice and chickens. A full protection against a subsequent IBDV infection was achieved by subcutaneous inoculation of only milligram amounts of yeast per chicken. Oral vaccination also generated protection: while mortality was observed in control animals after virus challenge, none of the vaccinees died and ca. one-tenth were protected as indicated by the absence of lesions in the bursa of Fabricius. Recombinant K. lactis was thus indicated as a potent tool for the induction of a protective immune response by different applications. Subcutaneously applied K. lactis that expresses the IBDV VP2 was shown to function as an efficacious anti-IBD subunit vaccine.


Subject(s)
Birnaviridae Infections/veterinary , Chickens/virology , Infectious bursal disease virus/immunology , Kluyveromyces/genetics , Poultry Diseases/prevention & control , Viral Structural Proteins/immunology , Viral Vaccines/immunology , Administration, Oral , Animals , Birnaviridae Infections/immunology , Birnaviridae Infections/prevention & control , Chickens/immunology , Female , Gene Expression , Gene Order , Gene Targeting , Infectious bursal disease virus/genetics , Injections, Subcutaneous , Mice , Poultry Diseases/immunology , Vaccines, Inactivated/administration & dosage , Vaccines, Inactivated/immunology , Viral Structural Proteins/genetics , Viral Vaccines/administration & dosage
13.
Microb Cell Fact ; 11: 112, 2012 Aug 20.
Article in English | MEDLINE | ID: mdl-22905717

ABSTRACT

BACKGROUND: The Crabtree-negative yeast species Kluyveromyces lactis has been established as an attractive microbial expression system for recombinant proteins at industrial scale. Its LAC genes allow for utilization of the inexpensive sugar lactose as a sole source of carbon and energy. Lactose efficiently induces the LAC4 promoter, which can be used to drive regulated expression of heterologous genes. So far, strain manipulation of K. lactis by homologous recombination was hampered by the high rate of non-homologous end-joining. RESULTS: Selection for growth on lactose was applied to target the insertion of heterologous genes downstream of the LAC4 promoter into the K. lactis genome and found to yield high numbers of positive transformants. Concurrent reconstitution of the ß-galactosidase gene indicated the desired integration event of the expression cassette, and ß-galactosidase activity measurements were used to monitor gene expression for strain improvement and fermentation optimization. The system was particularly improved by usage of a cell lysis resistant strain, VAK367-D4, which allowed for protein accumulation in long-term fermentation. Further optimization was achieved by increased gene dosage of KlGAL4 encoding the activator of lactose and galactose metabolic genes that led to elevated transcription rates. Pilot experiments were performed with strains expressing a single-chain antibody fragment (scFvox) and a viral envelope protein (BVDV-E2), respectively. scFvox was shown to be secreted into the culture medium in an active, epitope-binding form indicating correct processing and protein folding; the E2 protein could be expressed intracellularly. Further data on the influence of protein toxicity on batch fermentation and potential post-transcriptional bottlenecks in protein accumulation were obtained. CONCLUSIONS: A novel Kluyveromyces lactis host-vector system was developed that places heterologous genes under the control of the chromosomal LAC4 promoter and that allows monitoring of its transcription rates by ß-galactosidase measurement. The procedure is rapid and efficient, and the resulting recombinant strains contain no foreign genes other than the gene of interest. The recombinant strains can be grown non-selectively in rich medium and stably maintained even when the gene product exerts protein toxicity.


Subject(s)
Kluyveromyces/metabolism , Lactase/genetics , Recombinant Proteins/biosynthesis , Biomass , Diarrhea Viruses, Bovine Viral/metabolism , Plasmids/genetics , Plasmids/metabolism , Promoter Regions, Genetic , Recombinant Proteins/genetics , Single-Chain Antibodies/genetics , Single-Chain Antibodies/metabolism , Viral Envelope Proteins/genetics , Viral Envelope Proteins/metabolism , beta-Galactosidase/genetics
14.
Methods Mol Biol ; 734: 259-77, 2011.
Article in English | MEDLINE | ID: mdl-21468994

ABSTRACT

The budding yeast Kluyveromyces lactis has diverged from the Saccharomyces lineage before the whole-genome duplication and its genome sequence reveals lower redundancy of many genes. Moreover, it shows lower preference for fermentative carbon metabolism and a broader substrate spectrum making it a particularly rewarding system for comparative and evolutionary studies of carbon-regulated genetic networks. The lactose/galactose regulon of K. lactis, which is regulated by the prototypic transcription activator Gal4 exemplifies important aspects of network evolution when compared with the model GAL regulon of Saccharomyces cerevisiae. Differences in physiology relate to different subcellular compartmentation of regulatory components and, importantly, to quantitative differences in protein-protein interactions rather than major differences in network architecture. Here, we introduce genetic and biochemical tools to study K. lactis in general and the lactose/galactose regulon in particular. We present methods to quantify relevant protein-protein interactions in that network and to visualize such differences in simple plate assays allowing for genetic approaches in further studies.


Subject(s)
Evolution, Molecular , Galactose/genetics , Gene Regulatory Networks/genetics , Genetic Techniques , Kluyveromyces/genetics , Lactose/genetics , Regulon/genetics , Biological Assay , Fungal Proteins/isolation & purification , Galactokinase/antagonists & inhibitors , Galactokinase/metabolism , Gene Expression Regulation, Fungal , Kluyveromyces/cytology , Kluyveromyces/growth & development , Kluyveromyces/metabolism , Models, Genetic , Protein Binding , Saccharomyces cerevisiae/genetics , Selection, Genetic , Transformation, Genetic
15.
FEMS Yeast Res ; 11(3): 243-51, 2011 May.
Article in English | MEDLINE | ID: mdl-21205157

ABSTRACT

Kluyveromyces lactis Lac12 permease mediates lactose and low-affinity galactose transports. In this study we investigated the effects of carbon sources on internalization of Lac12 using a LAC12-GFP fusion construct. When galactose- or lactose-grown cells are shifted to a fresh sugar medium, Lac12-GFP is removed from the plasma membrane and is localized intracellularly. Surprisingly, either galactose or lactose in the new media caused the internalization, and cells responded differently to these two sugars. Our results reveal that this process is dependent on sugar species and also sugar concentration. Lac12-GFP internalization causes reduction of [C(14) ]lactose uptake rates and also occurs in a Klsnf1 mutant strain; it is therefore independent of KlSnf1 activity. We suggest that glucose-6-phosphate is the intracellular signal, as internalization was induced by 2-deoxyglucose, and inhibition of phosphoglucomutase by lithium prevented galactose- but not lactose- or glucose-induced internalization. Lac12-GFP internalization was not triggered by 6-deoxyglucose, and was irreversible in the absence of protein synthesis.


Subject(s)
Catabolite Repression , Galactose/metabolism , Glucose-6-Phosphate/metabolism , Kluyveromyces/metabolism , Lactose/metabolism , Monosaccharide Transport Proteins/metabolism , Carbon Isotopes/analysis , Cell Membrane/enzymology , Deoxyglucose/metabolism , Deoxyglucose/pharmacology , Fungal Proteins/genetics , Fungal Proteins/metabolism , Galactose/pharmacology , Glucose/metabolism , Glucose/pharmacology , Glucose-6-Phosphate/pharmacology , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Intracellular Space/enzymology , Kluyveromyces/enzymology , Kluyveromyces/genetics , Lactose/pharmacology , Lithium/pharmacology , Microscopy, Fluorescence , Monosaccharide Transport Proteins/genetics , Phenotype , Phosphoglucomutase/antagonists & inhibitors , Phosphoglucomutase/metabolism , Protein Serine-Threonine Kinases/metabolism , Protein Transport , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Signal Transduction , Time Factors
16.
Mol Microbiol ; 76(5): 1082-94, 2010 Jun 01.
Article in English | MEDLINE | ID: mdl-20398216

ABSTRACT

Based on studies in yeast and mammalian cells the Elongator complex has been implicated in functions as diverse as histone acetylation, polarized protein trafficking and tRNA modification. Here we show that Arabidopsis mutants lacking the Elongator subunit AtELP3/ELO3 have a defect in tRNA wobble uridine modification. Moreover, we demonstrate that yeast elp3 and elp1 mutants expressing the respective Arabidopsis Elongator homologues AtELP3/ELO3 and AtELP1/ELO2 assemble integer Elongator complexes indicating a high degree of structural conservation. Surprisingly, in vivo complementation studies based on Elongator-dependent tRNA nonsense suppression and zymocin tRNase toxin assays indicated that while AtELP1 rescued defects of a yeast elp1 mutant, the most conserved Elongator gene AtELP3, failed to complement an elp3 mutant. This lack of complementation is due to incompatibility with yeast ELP1 as coexpression of both plant genes in an elp1 elp3 yeast mutant restored Elongator's tRNA modification function in vivo. Similarly, AtELP1, not ScELP1 also supported partial complementation by yeast-plant Elp3 hybrids suggesting that AtElp1 has less stringent sequence requirements for Elp3 than ScElp1. We conclude that yeast and plant Elongator share tRNA modification roles and propose that this function might be conserved in Elongator from all eukaryotic kingdoms of life.


Subject(s)
Arabidopsis Proteins/metabolism , Histone Acetyltransferases/metabolism , RNA, Transfer/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Uridine/genetics , Acetyltransferases/genetics , Acetyltransferases/metabolism , Animals , Arabidopsis/enzymology , Arabidopsis/genetics , Arabidopsis Proteins/genetics , Genetic Complementation Test , Histone Acetyltransferases/genetics , Membrane Proteins/genetics , Membrane Proteins/metabolism , Molecular Structure , RNA, Transfer/chemistry , RNA, Transfer/genetics , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Saccharomyces cerevisiae/enzymology , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/genetics , Uridine/chemistry , Uridine/metabolism
17.
Mol Microbiol ; 73(5): 869-81, 2009 Sep.
Article in English | MEDLINE | ID: mdl-19656297

ABSTRACT

In yeast, the role for the Elongator complex in tRNA anticodon modification is affected by phosphorylation of Elongator subunit Elp1. Thus, hyperphosphorylation of Elp1 due to inactivation of protein phosphatase Sit4 correlates with Elongator-minus phenotypes including resistance towards zymocin, a tRNase cleaving anticodons of Elongator-dependent tRNAs. Here we show that zymocin resistance of casein kinase hrr25 mutants associates with hypophosphorylation of Elp1 and that nonsense suppression by the Elongator-dependent SUP4 tRNA is abolished in hrr25 or sit4 mutants. Thus changes that perturb the evenly balanced ratio between hyper- and hypophosphorylated Elp1 forms present in wild-type cells lead to Elongator inactivation. Antagonistic roles for Hrr25 and Sit4 in Elongator function are further supported by our data that Sit4 inactivation is capable of restoring both zymocin sensitivity and normal ratios between the two Elp1 forms in hrr25 mutants. Hrr25 binds to Elongator in a fashion dependent on Elongator partner Kti12. Like sit4 mutants, overexpression of Kti12 triggers Elp1 hyperphosphorylation. Intriguingly, this effect of Kti12 is blocked by hrr25 mutations, which also show enhanced binding of Kti12 to Elongator. Collectively, our data suggest that rather than directly targeting Elp1, the Hrr25 kinase indirectly affects Elp1 phosphorylation states through control of Sit4-dependent dephosphorylation of Elp1.


Subject(s)
Casein Kinase I/metabolism , Gene Expression Regulation , Histone Acetyltransferases/metabolism , Peptide Elongation Factors/metabolism , Protein Biosynthesis , Protein Phosphatase 2/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/physiology , Antifungal Agents/pharmacology , Casein Kinase I/genetics , Codon, Nonsense , Drug Resistance, Fungal , Genes, Suppressor , Killer Factors, Yeast/pharmacology , Mutation , Phosphorylation , Protein Phosphatase 2/genetics , Saccharomyces cerevisiae/drug effects , Saccharomyces cerevisiae Proteins/genetics , Suppression, Genetic
18.
FEBS Lett ; 582(5): 549-57, 2008 Mar 05.
Article in English | MEDLINE | ID: mdl-18242190

ABSTRACT

The KlICL1 gene, encoding isocitrate lyase in Kluyveromyces lactis, is essential for ethanol utilization. Deletion analyses identified two functional promoter elements, CSRE-A and CSRE-B. Transcription is activated on ethanol, but not on glucose, glycerol or lactate. Expression depends on the KlCat8p transcription factor and KlSip4p binds to the promoter elements. Glycerol diminishes KlICL1 expression and a single carbon source responsive element (CSRE) sequence is both necessary and sufficient to mediate this regulation. The glycerol effect is less pronounced in Saccharomyces cerevisiae than in K. lactis. Mutants lacking KlGUT2 (which encodes the glycerol 3-phosphate dehydrogenase) still show reduced expression in glycerol, whereas mutants deficient in glycerol kinase (Klgut1) do not. We conclude that a metabolite of glycerol is required for this regulation.


Subject(s)
Carbon/pharmacology , Gene Expression Regulation, Fungal/drug effects , Isocitrate Lyase/genetics , Kluyveromyces/enzymology , Kluyveromyces/genetics , Milk/microbiology , Transcription, Genetic/drug effects , Animals , Base Sequence , Chromatin Immunoprecipitation , Fermentation/drug effects , Glycerol/metabolism , Glycerol/pharmacology , Glycerol Kinase/metabolism , Isocitrate Lyase/biosynthesis , Kluyveromyces/cytology , Kluyveromyces/drug effects , Molecular Sequence Data , Mutation/genetics , Protein Binding/drug effects , RNA, Messenger/genetics , RNA, Messenger/metabolism , Response Elements/genetics , Reverse Transcriptase Polymerase Chain Reaction , Sequence Alignment
19.
FEMS Yeast Res ; 7(5): 683-92, 2007 Aug.
Article in English | MEDLINE | ID: mdl-17573926

ABSTRACT

Recent data suggest that hexokinase KlHxk1 (Rag5) represents the only glucose-phosphorylating enzyme of Kluyveromyces lactis, which also is required for glucose signalling. Long-term growth studies of a K. lactis rag5 mutant, however, reveal slow growth on glucose, but no growth on fructose. Isolation of the permissive glucose-phosphorylating enzyme, mass spectrometric tryptic peptide analysis and determination of basic kinetic data identify a novel glucokinase (KlGlk1) encoded by ORF KLLA0C01,155g. In accordance with the growth characteristics of the rag5 mutant, KlGlk1 phosphorylates glucose, but fails to act on fructose as a sugar substrate. Multiple sequence alignment indicates the presence of at least one glucokinase gene in all sequenced yeast genomes.


Subject(s)
Gene Expression Regulation, Fungal , Glucokinase , Kluyveromyces/enzymology , Amino Acid Sequence , Fructose/metabolism , Fungal Proteins/chemistry , Fungal Proteins/genetics , Fungal Proteins/isolation & purification , Fungal Proteins/metabolism , Glucokinase/chemistry , Glucokinase/genetics , Glucokinase/isolation & purification , Glucokinase/metabolism , Glucose/metabolism , Humans , Kluyveromyces/genetics , Kluyveromyces/growth & development , Molecular Sequence Data , Phosphorylation , Phylogeny , Sequence Alignment , Substrate Specificity
20.
J Biol Chem ; 281(39): 29337-48, 2006 Sep 29.
Article in English | MEDLINE | ID: mdl-16867978

ABSTRACT

The Gal4 protein represents a universally functional transcription activator, which in yeast is regulated by protein-protein interaction of its transcription activation domain with the inhibitor Gal80. Gal80 inhibition is relieved via galactose-mediated Gal80-Gal1-Gal3 interaction. The Gal4-Gal80-Gal1/3 regulatory module is conserved between Saccharomyces cerevisiae and Kluyveromyces lactis. Here we demonstrate that K. lactis Gal80 (KlGal80) is a nuclear protein independent of the Gal4 activity status, whereas KlGal1 is detected throughout the entire cell, which implies that KlGal80 and KlGal1 interact in the nucleus. Consistently KlGal1 accumulates in the nucleus upon KlGAL80 overexpression. Furthermore, we show that the KlGal80-KlGal1 interaction blocks the galactokinase activity of KlGal1 and is incompatible with KlGal80-KlGal4-AD interaction. Thus, we propose that dissociation of KlGal80 from the AD forms the basis of KlGal4 activation in K. lactis. Quantitation of the dissociation constants for the KlGal80 complexes gives a much lower affinity for KlGal1 as compared with Gal4. Mathematical modeling shows that with these affinities a switch based on competition between Gal1 and Gal4 for Gal80 binding is nevertheless efficient provided two monomeric Gal1 molecules interact with dimeric Gal80. Consistent with such a mechanism, analysis of the sedimentation behavior by analytical ultracentrifugation demonstrates the formation of a heterotetrameric KlGal80-KlGal1 complex of 2:2 stoichiometry.


Subject(s)
Galactokinase/metabolism , Galactose/metabolism , Kluyveromyces/metabolism , Repressor Proteins/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Transcription Factors/metabolism , Binding, Competitive , Cell Nucleus/metabolism , Chromatography, Gel , DNA-Binding Proteins , Dimerization , Fungal Proteins/chemistry , Models, Chemical , Models, Theoretical , Peptides/chemistry , Plasmids/metabolism , Saccharomyces cerevisiae/metabolism
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