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1.
PLoS Genet ; 19(8): e1010848, 2023 08.
Article in English | MEDLINE | ID: mdl-37585488

ABSTRACT

N-terminal ends of polypeptides are critical for the selective co-translational recruitment of N-terminal modification enzymes. However, it is unknown whether specific N-terminal signatures differentially regulate protein fate according to their cellular functions. In this work, we developed an in-silico approach to detect functional preferences in cellular N-terminomes, and identified in S. cerevisiae more than 200 Gene Ontology terms with specific N-terminal signatures. In particular, we discovered that Mitochondrial Targeting Sequences (MTS) show a strong and specific over-representation at position 2 of hydrophobic residues known to define potential substrates of the N-terminal acetyltransferase NatC. We validated mitochondrial precursors as co-translational targets of NatC by selective purification of translating ribosomes, and found that their N-terminal signature is conserved in Saccharomycotina yeasts. Finally, systematic mutagenesis of the position 2 in a prototypal yeast mitochondrial protein confirmed its critical role in mitochondrial protein import. Our work highlights the hydrophobicity of MTS N-terminal residues and their targeting by NatC as important features for the definition of the mitochondrial proteome, providing a molecular explanation for mitochondrial defects observed in yeast or human NatC-depleted cells. Functional mapping of N-terminal residues thus has the potential to support the discovery of novel mechanisms of protein regulation or targeting.


Subject(s)
Proteome , Saccharomyces cerevisiae , Humans , Saccharomyces cerevisiae/genetics , Amino Acid Sequence , Proteome/metabolism , Protein Transport , Fungal Proteins/metabolism , Mitochondrial Proteins/metabolism
2.
Front Cell Infect Microbiol ; 11: 731988, 2021.
Article in English | MEDLINE | ID: mdl-34900750

ABSTRACT

The CCAAT-binding complex (CBC) is a conserved heterotrimeric transcription factor which, in fungi, requires additional regulatory subunits to act on transcription. In the pathogenic yeast Candida glabrata, CBC has a dual role. Together with the Hap4 regulatory subunit, it activates the expression of genes involved in respiration upon growth with non-fermentable carbon sources, while its association with the Yap5 regulatory subunit is required for the activation of iron tolerance genes in response to iron excess. In the present work, we investigated further the interplay between CBC, Hap4 and Yap5. We showed that Yap5 regulation requires a specific Yap Response Element in the promoter of its target gene GRX4 and that the presence of Yap5 considerably strengthens the binding of CBC to the promoters of iron tolerance genes. Chromatin immunoprecipitation (ChIP) and transcriptome experiments showed that Hap4 can also bind these promoters but has no impact on the expression of those genes when Yap5 is present. In the absence of Yap5 however, GRX4 is constitutively regulated by Hap4, similarly to the genes involved in respiration. Our results suggest that the distinction between the two types of CBC targets in C. glabrata is mainly due to the dependency of Yap5 for very specific DNA sequences and to the competition between Hap4 and Yap5 at the promoter of the iron tolerance genes.


Subject(s)
Candida glabrata , Saccharomyces cerevisiae Proteins , Basic-Leucine Zipper Transcription Factors/genetics , Candida glabrata/genetics , Gene Expression Regulation, Fungal , Homeostasis , Humans , Iron/metabolism , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/genetics
3.
Mol Cell ; 81(11): 2417-2427.e5, 2021 06 03.
Article in English | MEDLINE | ID: mdl-33838103

ABSTRACT

mRNA translation is coupled to multiprotein complex assembly in the cytoplasm or to protein delivery into intracellular compartments. Here, by combining systematic RNA immunoprecipitation and single-molecule RNA imaging in yeast, we have provided a complete depiction of the co-translational events involved in the biogenesis of a large multiprotein assembly, the nuclear pore complex (NPC). We report that binary interactions between NPC subunits can be established during translation, in the cytoplasm. Strikingly, the nucleoporins Nup1/Nup2, together with a number of nuclear proteins, are instead translated at nuclear pores, through a mechanism involving interactions between their nascent N-termini and nuclear transport receptors. Uncoupling this co-translational recruitment further triggers the formation of cytoplasmic foci of unassembled polypeptides. Altogether, our data reveal that distinct, spatially segregated modes of co-translational interactions foster the ordered assembly of NPC subunits and that localized translation can ensure the proper delivery of proteins to the pore and the nucleus.


Subject(s)
Nuclear Pore Complex Proteins/genetics , Protein Biosynthesis , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/genetics , Active Transport, Cell Nucleus , Cytoplasm/genetics , Cytoplasm/metabolism , Gene Expression Regulation, Fungal , Karyopherins/genetics , Karyopherins/metabolism , Nuclear Pore/genetics , Nuclear Pore/metabolism , Nuclear Pore Complex Proteins/classification , Nuclear Pore Complex Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/classification , Saccharomyces cerevisiae Proteins/metabolism
4.
Microb Cell ; 6(6): 267-285, 2019 May 28.
Article in English | MEDLINE | ID: mdl-31172012

ABSTRACT

Yeast adaptation to stress has been extensively studied. It involves large reprogramming of genome expression operated by many, more or less specific, transcription factors. Here, we review our current knowledge on the function of the eight Yap transcription factors (Yap1 to Yap8) in Saccharomyces cerevisiae, which were shown to be involved in various stress responses. More precisely, Yap1 is activated under oxidative stress, Yap2/Cad1 under cadmium, Yap4/Cin5 and Yap6 under osmotic shock, Yap5 under iron overload and Yap8/Arr1 by arsenic compounds. Yap3 and Yap7 seem to be involved in hydroquinone and nitrosative stresses, respectively. The data presented in this article illustrate how much knowledge on the function of these Yap transcription factors is advanced. The evolution of the Yap family and its roles in various pathogenic and non-pathogenic fungal species is discussed in the last section.

5.
Microbiology (Reading) ; 165(10): 1041-1060, 2019 10.
Article in English | MEDLINE | ID: mdl-31050635

ABSTRACT

Iron is an essential element to most microorganisms, yet an excess of iron is toxic. Hence, living cells have to maintain a tight balance between iron uptake and iron consumption and storage. The control of intracellular iron concentrations is particularly challenging for pathogens because mammalian organisms have evolved sophisticated high-affinity systems to sequester iron from microbes and because iron availability fluctuates among the different host niches. In this review, we present the current understanding of iron homeostasis and its regulation in the fungal pathogen Candida glabrata. This yeast is an emerging pathogen which has become the second leading cause of candidemia, a life-threatening invasive mycosis. C. glabrata is relatively poorly studied compared to the closely related model yeast Saccharomyces cerevisiae or to the pathogenic yeast Candida albicans. Still, several research groups have started to identify the actors of C. glabrata iron homeostasis and its transcriptional and post-transcriptional regulation. These studies have revealed interesting particularities of C. glabrata and have shed new light on the evolution of fungal iron homeostasis.


Subject(s)
Candida glabrata/physiology , Gene Expression Regulation, Fungal , Homeostasis/genetics , Iron/metabolism , Candida glabrata/genetics , Candida glabrata/growth & development , Candida glabrata/metabolism , Candidiasis/microbiology , Evolution, Molecular , Fungal Proteins/genetics , Fungal Proteins/metabolism , Humans , Iron Deficiencies , Transcription Factors/genetics , Transcription Factors/metabolism , Transcriptome
6.
Front Microbiol ; 9: 2689, 2018.
Article in English | MEDLINE | ID: mdl-30505294

ABSTRACT

In this work, we used comparative transcriptomics to identify regulatory outliers (ROs) in the human pathogen Candida glabrata. ROs are genes that have very different expression patterns compared to their orthologs in other species. From comparative transcriptome analyses of the response of eight yeast species to toxic doses of selenite, a pleiotropic stress inducer, we identified 38 ROs in C. glabrata. Using transcriptome analyses of C. glabrata response to five different stresses, we pointed out five ROs which were more particularly responsive to iron starvation, a process which is very important for C. glabrata virulence. Global chromatin Immunoprecipitation and gene profiling analyses showed that four of these genes are actually new targets of the iron starvation responsive Aft2 transcription factor in C. glabrata. Two of them (HBS1 and DOM34b) are required for C. glabrata optimal growth in iron limited conditions. In S. cerevisiae, the orthologs of these two genes are involved in ribosome rescue by the NO GO decay (NGD) pathway. Hence, our results suggest a specific contribution of NGD co-factors to the C. glabrata adaptation to iron starvation.

7.
Nat Commun ; 9(1): 1665, 2018 04 25.
Article in English | MEDLINE | ID: mdl-29695777

ABSTRACT

While the activity of multiprotein complexes is crucial for cellular metabolism, little is known about the mechanisms that collectively control the expression of their components. Here, we investigate the regulations targeting the biogenesis of the nuclear pore complex (NPC), the macromolecular assembly mediating nucleocytoplasmic exchanges. Systematic analysis of RNA-binding proteins interactomes, together with in vivo and in vitro assays, reveal that a subset of NPC mRNAs are specifically bound by Hek2, a yeast hnRNP K-like protein. Hek2-dependent translational repression and protein turnover are further shown to finely tune the levels of NPC subunits. Strikingly, mutations or physiological perturbations altering pore integrity decrease the levels of the NPC-associated SUMO protease Ulp1, and trigger the accumulation of sumoylated versions of Hek2 unable to bind NPC mRNAs. Our results support the existence of a quality control mechanism involving Ulp1 as a sensor of NPC integrity and Hek2 as a repressor of NPC biogenesis.


Subject(s)
Cysteine Endopeptidases/metabolism , Feedback, Physiological , Nuclear Pore/metabolism , Ribonucleoproteins/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/physiology , Computational Biology , Datasets as Topic , Protein Binding/physiology , RNA, Messenger/metabolism , Sumoylation/physiology
8.
Sci Rep ; 7(1): 3531, 2017 06 14.
Article in English | MEDLINE | ID: mdl-28615656

ABSTRACT

The CCAAT-binding complex (CBC) is a heterotrimeric transcription factor which is widely conserved in eukaryotes. In the model yeast S. cerevisiae, CBC positively controls the expression of respiratory pathway genes. This role involves interactions with the regulatory subunit Hap4. In many pathogenic fungi, CBC interacts with the HapX regulatory subunit to control iron homeostasis. HapX is a bZIP protein which only shares with Hap4 the Hap4Like domain (Hap4L) required for its interaction with CBC. Here, we show that CBC has a dual role in the pathogenic yeast C. glabrata. It is required, along with Hap4, for the constitutive expression of respiratory genes and it is also essential for the iron stress response, which is mediated by the Yap5 bZIP transcription factor. Interestingly, Yap5 contains a vestigial Hap4L domain. The mutagenesis of this domain severely reduced Yap5 binding to its targets and compromised its interaction with Hap5. Hence, Yap5, like HapX in other species, acts as a CBC regulatory subunit in the regulation of iron stress response. This work reveals new aspects of iron homeostasis in C. glabrata and of the evolution of the role of CBC and Hap4L-bZIP proteins in this process.


Subject(s)
CCAAT-Binding Factor/metabolism , Candida glabrata/genetics , Candida glabrata/metabolism , Fungal Proteins/metabolism , Gene Expression Regulation, Fungal , Homeostasis , Iron/metabolism , Gene Regulatory Networks
9.
Biochim Biophys Acta Gene Regul Mech ; 1860(4): 472-481, 2017 Apr.
Article in English | MEDLINE | ID: mdl-28188921

ABSTRACT

Response to arsenic stress in Saccharomyces cerevisiae is orchestrated by the regulatory protein Yap8, which mediates transcriptional activation of ACR2 and ACR3. This study contributes to the state of art knowledge of the molecular mechanisms underlying yeast stress response to arsenate as it provides the genetic and biochemical evidences that Yap8, through cysteine residues 132, 137, and 274, is the sensor of presence of arsenate in the cytosol. Moreover, it is here reported for the first time the essential role of the Mediator complex in the transcriptional activation of ACR2 by Yap8. Based on our data, we propose an order-of-function map to recapitulate the sequence of events taking place in cells injured with arsenate. Modification of the sulfhydryl state of these cysteines converts Yap8 in its activated form, triggering the recruitment of the Mediator complex to the ACR2/ACR3 promoter, through the interaction with the tail subunit Med2. The Mediator complex then transfers the regulatory signals conveyed by Yap8 to the core transcriptional machinery, which culminates with TBP occupancy, ACR2 upregulation and cell adaptation to arsenate stress. Additional co-factors are required for the transcriptional activation of ACR2 by Yap8, particularly the nucleosome remodeling activity of SWI/SNF and SAGA complexes.


Subject(s)
Arsenate Reductases/genetics , Arsenates/toxicity , Basic-Leucine Zipper Transcription Factors/metabolism , Mediator Complex/metabolism , Multiprotein Complexes/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Transcriptional Activation/genetics , Arsenate Reductases/metabolism , Basic-Leucine Zipper Transcription Factors/chemistry , Cysteine/metabolism , Promoter Regions, Genetic , Protein Binding , Protein Subunits/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/genetics , Stress, Physiological/drug effects
10.
Nucleic Acids Res ; 44(18): 8826-8841, 2016 Oct 14.
Article in English | MEDLINE | ID: mdl-27580715

ABSTRACT

The discovery of novel specific ribosome-associated factors challenges the assumption that translation relies on standardized molecular machinery. In this work, we demonstrate that Tma108, an uncharacterized translation machinery-associated factor in yeast, defines a subpopulation of cellular ribosomes specifically involved in the translation of less than 200 mRNAs encoding proteins with ATP or Zinc binding domains. Using ribonucleoparticle dissociation experiments we established that Tma108 directly interacts with the nascent protein chain. Additionally, we have shown that translation of the first 35 amino acids of Asn1, one of the Tma108 targets, is necessary and sufficient to recruit Tma108, suggesting that it is loaded early during translation. Comparative genomic analyses, molecular modeling and directed mutagenesis point to Tma108 as an original M1 metallopeptidase, which uses its putative catalytic peptide-binding pocket to bind the N-terminus of its targets. The involvement of Tma108 in co-translational regulation is attested by a drastic change in the subcellular localization of ATP2 mRNA upon Tma108 inactivation. Tma108 is a unique example of a nascent chain-associated factor with high selectivity and its study illustrates the existence of other specific translation-associated factors besides RNA binding proteins.


Subject(s)
Aminopeptidases/metabolism , Protein Biosynthesis , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Adenosine Triphosphate/metabolism , Aminopeptidases/chemistry , In Situ Hybridization, Fluorescence , Mitochondria/genetics , Mitochondria/metabolism , Peptide Chain Elongation, Translational , Protein Binding , Proton-Translocating ATPases/genetics , RNA Transport , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA-Binding Proteins/chemistry , RNA-Binding Proteins/metabolism , Ribosomes/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/genetics , Zinc/metabolism
11.
Front Microbiol ; 7: 645, 2016.
Article in English | MEDLINE | ID: mdl-27242683

ABSTRACT

The yeast Candida glabrata has become the second cause of systemic candidemia in humans. However, relatively few genome-wide studies have been conducted in this organism and our knowledge of its transcriptional regulatory network is quite limited. In the present work, we combined genome-wide chromatin immunoprecipitation (ChIP-seq), transcriptome analyses, and DNA binding motif predictions to describe the regulatory interactions of the seven Yap (Yeast AP1) transcription factors of C. glabrata. We described a transcriptional network containing 255 regulatory interactions and 309 potential target genes. We predicted with high confidence the preferred DNA binding sites for 5 of the 7 CgYaps and showed a strong conservation of the Yap DNA binding properties between S. cerevisiae and C. glabrata. We provided reliable functional annotation for 3 of the 7 Yaps and identified for Yap1 and Yap5 a core regulon which is conserved in S. cerevisiae, C. glabrata, and C. albicans. We uncovered new roles for CgYap7 in the regulation of iron-sulfur cluster biogenesis, for CgYap1 in the regulation of heme biosynthesis and for CgYap5 in the repression of GRX4 in response to iron starvation. These transcription factors define an interconnected transcriptional network at the cross-roads between redox homeostasis, oxygen consumption, and iron metabolism.

12.
Mol Microbiol ; 96(5): 951-72, 2015 Jun.
Article in English | MEDLINE | ID: mdl-25732006

ABSTRACT

Flavohemoglobins are the main detoxifiers of nitric oxide (NO) in bacteria and fungi and are induced in response to nitrosative stress. In fungi, the flavohemoglobin encoding gene YHB1 is positively regulated by transcription factors which are activated upon NO exposure. In this study, we show that in the model yeast Saccharomyces cerevisiae and in the human pathogen Candida glabrata, the transcription factor Yap7 constitutively represses YHB1 by binding its promoter. Consequently, YAP7 deletion conferred high NO resistance to the cells. Co-immunoprecipitation experiments and mutant analyses indicated that Yap7 represses YHB1 by recruiting the transcriptional repressor Tup1. In S. cerevisiae, YHB1 repression also involves interaction of Yap7 with the Hap2/3/5 complex through a conserved Hap4-like-bZIP domain, but this interaction has been lost in C. glabrata. The evolutionary origin of this regulation was investigated by functional analyses of Yap7 and of its paralogue Yap5 in different yeast species. These analyses indicated that the negative regulation of YHB1 by Yap7 arose by neofunctionalization after the whole genome duplication which led to the C. glabrata and S. cerevisiae extant species. This work describes a new aspect of the regulation of fungal nitric oxidase and provides detailed insights into its functioning and evolution.


Subject(s)
Candida glabrata/genetics , Dioxygenases/genetics , Gene Duplication , Genome, Fungal , Hemeproteins/genetics , Repressor Proteins/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/genetics , Basic-Leucine Zipper Transcription Factors/genetics , Basic-Leucine Zipper Transcription Factors/physiology , Dioxygenases/metabolism , Fungal Proteins/genetics , Fungal Proteins/metabolism , Gene Deletion , Gene Expression Regulation, Fungal , Hemeproteins/metabolism , Humans , Mutation , Nitric Oxide/metabolism , Nuclear Proteins/genetics , Repressor Proteins/metabolism , Saccharomyces cerevisiae Proteins/metabolism
13.
Eukaryot Cell ; 14(5): 442-53, 2015 May.
Article in English | MEDLINE | ID: mdl-25724885

ABSTRACT

ATP-binding cassette transporters Pdr5 and Yor1 from Saccharomyces cerevisiae control the asymmetric distribution of phospholipids across the plasma membrane as well as serving as ATP-dependent drug efflux pumps. Mutant strains lacking these transporter proteins were found to exhibit very different resistance phenotypes to two inhibitors of sphingolipid biosynthesis that act either late (aureobasidin A [AbA]) or early (myriocin [Myr]) in the pathway leading to production of these important plasma membrane lipids. These pdr5Δ yor1 strains were highly AbA resistant but extremely sensitive to Myr. We provide evidence that these phenotypic changes are likely due to modulation of the plasma membrane flippase complexes, Dnf1/Lem3 and Dnf2/Lem3. Flippases act to move phospholipids from the outer to the inner leaflet of the plasma membrane. Genetic analyses indicate that lem3Δ mutant strains are highly AbA sensitive and Myr resistant. These phenotypes are fully epistatic to those seen in pdr5Δ yor1 strains. Direct analysis of AbA-induced signaling demonstrated that loss of Pdr5 and Yor1 inhibited the AbA-triggered phosphorylation of the AGC kinase Ypk1 and its substrate Orm1. Microarray experiments found that a pdr5Δ yor1 strain induced a Pdr1-dependent induction of the entire Pdr regulon. Our data support the view that Pdr5/Yor1 negatively regulate flippase function and activity of the nuclear Pdr1 transcription factor. Together, these data argue that the interaction of the ABC transporters Pdr5 and Yor1 with the Lem3-dependent flippases regulates permeability of AbA via control of plasma membrane protein function as seen for the high-affinity tryptophan permease Tat2.


Subject(s)
ATP-Binding Cassette Transporters/metabolism , Cell Membrane Permeability/physiology , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Transcription Factors/metabolism , Gene Expression Regulation, Fungal , Trans-Activators/metabolism
14.
PLoS One ; 9(11): e111589, 2014.
Article in English | MEDLINE | ID: mdl-25365506

ABSTRACT

Previous experiments revealed that DHH1, a RNA helicase involved in the regulation of mRNA stability and translation, complemented the phenotype of a Saccharomyces cerevisiae mutant affected in the expression of genes coding for monocarboxylic-acids transporters, JEN1 and ADY2 (Paiva S, Althoff S, Casal M, Leao C. FEMS Microbiol Lett, 1999, 170:301-306). In wild type cells, JEN1 expression had been shown to be undetectable in the presence of glucose or formic acid, and induced in the presence of lactate. In this work, we show that JEN1 mRNA accumulates in a dhh1 mutant, when formic acid was used as sole carbon source. Dhh1 interacts with the decapping activator Dcp1 and with the deadenylase complex. This led to the hypothesis that JEN1 expression is post-transcriptionally regulated by Dhh1 in formic acid. Analyses of JEN1 mRNAs decay in wild-type and dhh1 mutant strains confirmed this hypothesis. In these conditions, the stabilized JEN1 mRNA was associated to polysomes but no Jen1 protein could be detected, either by measurable lactate carrier activity, Jen1-GFP fluorescence detection or western blots. These results revealed the complexity of the expression regulation of JEN1 in S. cerevisiae and evidenced the importance of DHH1 in this process. Additionally, microarray analyses of dhh1 mutant indicated that Dhh1 plays a large role in metabolic adaptation, suggesting that carbon source changes triggers a complex interplay between transcriptional and post-transcriptional effects.


Subject(s)
DEAD-box RNA Helicases/genetics , DEAD-box RNA Helicases/metabolism , Gene Expression Regulation, Fungal , Monocarboxylic Acid Transporters/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Adaptation, Physiological , Formates/metabolism , Gene Expression Profiling , Genome-Wide Association Study , Monocarboxylic Acid Transporters/metabolism , Mutation , Polyribosomes/metabolism , RNA Stability , RNA, Messenger/genetics , RNA, Messenger/metabolism , Saccharomyces cerevisiae/growth & development , Symporters/genetics , Symporters/metabolism
15.
PLoS One ; 9(8): e104554, 2014.
Article in English | MEDLINE | ID: mdl-25105295

ABSTRACT

Candida albicans causes superficial to systemic infections in immuno-compromised individuals. The concomitant use of fungistatic drugs and the lack of cidal drugs frequently result in strains that could withstand commonly used antifungals, and display multidrug resistance (MDR). In search of novel fungicidals, in this study, we have explored a plant alkaloid berberine (BER) for its antifungal potential. For this, we screened an in-house transcription factor (TF) mutant library of C. albicans strains towards their susceptibility to BER. Our screen of TF mutant strains identified a heat shock factor (HSF1), which has a central role in thermal adaptation, to be most responsive to BER treatment. Interestingly, HSF1 mutant was not only highly susceptible to BER but also displayed collateral susceptibility towards drugs targeting cell wall (CW) and ergosterol biosynthesis. Notably, BER treatment alone could affect the CW integrity as was evident from the growth retardation of MAP kinase and calcineurin pathway null mutant strains and transmission electron microscopy. However, unlike BER, HSF1 effect on CW appeared to be independent of MAP kinase and Calcineurin pathway genes. Additionally, unlike hsf1 null strain, BER treatment of Candida cells resulted in dysfunctional mitochondria, which was evident from its slow growth in non-fermentative carbon source and poor labeling with mitochondrial membrane potential sensitive probe. This phenotype was reinforced with an enhanced ROS levels coinciding with the up-regulated oxidative stress genes in BER-treated cells. Together, our study not only describes the molecular mechanism of BER fungicidal activity but also unravels a new role of evolutionary conserved HSF1, in MDR of Candida.


Subject(s)
Antifungal Agents/pharmacology , Berberine/pharmacology , Candida albicans/drug effects , Candidiasis/drug therapy , Candida albicans/genetics , Candida albicans/growth & development , Candida albicans/metabolism , Candidiasis/microbiology , Drug Resistance, Fungal , Drug Resistance, Multiple , Fungal Proteins/genetics , Heat-Shock Proteins/genetics , Humans , Mutation , Reactive Oxygen Species/metabolism , Transcription Factors/genetics
16.
Yeast ; 31(10): 375-91, 2014 Oct.
Article in English | MEDLINE | ID: mdl-25041923

ABSTRACT

Peak calling is a critical step in ChIPseq data analysis. Choosing the correct algorithm as well as optimized parameters for a specific biological system is an essential task. In this article, we present an original peak-calling method (bPeaks) specifically designed to detect transcription factor (TF) binding sites in small eukaryotic genomes, such as in yeasts. As TF interactions with DNA are strong and generate high binding signals, bPeaks uses simple parameters to compare the sequences (reads) obtained from the immunoprecipitation (IP) with those from the control DNA (input). Because yeasts have small genomes (<20 Mb), our program has the advantage of using ChIPseq information at the single nucleotide level and can explore, in a reasonable computational time, results obtained with different sets of parameter values. Graphical outputs and text files are provided to rapidly assess the relevance of the detected peaks. Taking advantage of the simple promoter structure in yeasts, additional functions were implemented in bPeaks to automatically assign the peaks to promoter regions and retrieve peak coordinates on the DNA sequence for further predictions of regulatory motifs, enriched in the list of peaks. Applications of the bPeaks program to three different ChIPseq datasets from Saccharomyces cerevisiae, Candida albicans and Candida glabrata are presented. Each time, bPeaks allowed us to correctly predict the DNA binding sequence of the studied TF and provided relevant lists of peaks. The bioinformatics tool bPeaks is freely distributed to academic users. Supplementary data, together with detailed tutorials, are available online: http://bpeaks.gene-networks.net.


Subject(s)
Algorithms , Candida/genetics , Computational Biology/methods , Genome, Fungal/genetics , Saccharomyces cerevisiae/genetics , Transcription Factors/genetics , Binding Sites , Candida albicans/genetics , Fungal Proteins/genetics , Fungal Proteins/metabolism , High-Throughput Nucleotide Sequencing , Oligonucleotide Array Sequence Analysis , Protein Binding , Sequence Analysis, DNA , Transcription Factors/metabolism
17.
Nucleic Acids Res ; 42(8): 5043-58, 2014 Apr.
Article in English | MEDLINE | ID: mdl-24500206

ABSTRACT

Assembly of messenger ribonucleoparticles (mRNPs) is a pivotal step in gene expression, but only a few molecular mechanisms contributing to its regulation have been described. Here, through a comprehensive proteomic survey of mRNP assembly, we demonstrate that the SUMO pathway specifically controls the association of the THO complex with mRNPs. We further show that the THO complex, a key player in the interplay between gene expression, mRNA export and genetic stability, is sumoylated on its Hpr1 subunit and that this modification regulates its association with mRNPs. Altered recruitment of the THO complex onto mRNPs in sumoylation-defective mutants does not affect bulk mRNA export or genetic stability, but impairs the expression of acidic stress-induced genes and, consistently, compromises viability in acidic stress conditions. Importantly, inactivation of the nuclear exosome suppresses the phenotypes of the hpr1 non-sumoylatable mutant, showing that SUMO-dependent mRNP assembly is critical to allow a specific subset of mRNPs to escape degradation. This article thus provides the first example of a SUMO-dependent mRNP-assembly event allowing a refined tuning of gene expression, in particular under specific stress conditions.


Subject(s)
Nuclear Proteins/metabolism , Ribonucleoproteins/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Sumoylation , Cysteine Endopeptidases/genetics , Exosome Multienzyme Ribonuclease Complex/metabolism , Gene Expression , Proteome/metabolism , RNA Transport , RNA, Messenger/metabolism , SUMO-1 Protein/metabolism , Stress, Physiological/genetics , Ubiquitination
18.
Cell Rep ; 5(4): 1082-94, 2013 Nov 27.
Article in English | MEDLINE | ID: mdl-24210826

ABSTRACT

The THO complex is involved in transcription, genome stability, and messenger ribonucleoprotein (mRNP) formation, but its precise molecular function remains enigmatic. Under heat shock conditions, THO mutants accumulate large protein-DNA complexes that alter the chromatin density of target genes (heavy chromatin), defining a specific biochemical facet of THO function and a powerful tool of analysis. Here, we show that heavy chromatin distribution is dictated by gene boundaries and that the gene promoter is necessary and sufficient to convey THO sensitivity in these conditions. Single-molecule fluorescence in situ hybridization measurements show that heavy chromatin formation correlates with an unusually high firing pace of the promoter with more than 20 transcription events per minute. Heavy chromatin formation closely follows the modulation of promoter firing and strongly correlates with polymerase occupancy genome wide. We propose that the THO complex is required for tuning the dynamic of gene-nuclear pore association and mRNP release to the same high pace of transcription initiation.


Subject(s)
Chromatin/genetics , DNA-Binding Proteins/genetics , Gene Expression Regulation, Fungal , Nuclear Pore/genetics , Nuclear Proteins/genetics , Promoter Regions, Genetic , Ribonucleoproteins/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/genetics , Transcription Factors/genetics , Heat-Shock Proteins/biosynthesis , Heat-Shock Proteins/genetics , Heat-Shock Response/genetics , Saccharomyces cerevisiae Proteins/biosynthesis , Transcription, Genetic
19.
Biochim Biophys Acta ; 1830(6): 3719-33, 2013 Jun.
Article in English | MEDLINE | ID: mdl-23500070

ABSTRACT

BACKGROUND: Hereditary optic neuropathies (HONs) are a heterogeneous group of disorders that affect retinal ganglion cells (RGCs) and axons that form the optic nerve. Leber's Hereditary Optic Neuropathy and the autosomal dominant optic atrophy related to OPA1 mutations are the most common forms. Nonsyndromic autosomal recessive optic neuropathies are rare and their existence has been long debated. We recently identified the first gene responsible for these conditions, TMEM126A. This gene is highly expressed in retinal cellular compartments enriched in mitochondria and supposed to encode a mitochondrial transmembrane protein of unknown function. METHODS: A specific polyclonal antibody targeting the TMEM126A protein has been generated. Quantitative fluorescent in situ hybridization, cellular fractionation, mitochondrial membrane association study, mitochondrial sub compartmentalization analysis by both proteolysis assays and transmission electron microscopy, and expression analysis of truncated TMEM126A constructs by immunofluorescence confocal microscopy were carried out. RESULTS: TMEM126A mRNAs are strongly enriched in the vicinity of mitochondria and encode an inner mitochondrial membrane associated cristae protein. Moreover, the second transmembrane domain of TMEM126A is required for its mitochondrial localization. CONCLUSIONS: TMEM126A is a mitochondrial located mRNA (MLR) that may be translated in the mitochondrial surface and the protein is subsequently imported to the inner membrane. These data constitute the first step toward a better understanding of the mechanism of action of TMEM126A in RGCs and support the importance of mitochondrial dysfunction in the pathogenesis of HON. GENERAL SIGNIFICANCE: Local translation of nuclearly encoded mitochondrial mRNAs might be a mechanism for rapid onsite supply of mitochondrial membrane proteins.


Subject(s)
Membrane Proteins/biosynthesis , Mitochondrial Membranes/metabolism , Mitochondrial Proteins/biosynthesis , Protein Biosynthesis , Retinal Ganglion Cells/metabolism , Animals , COS Cells , Chlorocebus aethiops , GTP Phosphohydrolases/genetics , GTP Phosphohydrolases/metabolism , Genetic Diseases, Inborn/genetics , Genetic Diseases, Inborn/metabolism , Genetic Diseases, Inborn/pathology , Humans , Membrane Proteins/genetics , Mitochondrial Membranes/pathology , Mitochondrial Proteins/genetics , Mutation , Optic Nerve Diseases/genetics , Optic Nerve Diseases/metabolism , Optic Nerve Diseases/pathology , Protein Structure, Tertiary , RNA, Messenger/genetics , RNA, Messenger/metabolism , Retinal Ganglion Cells/pathology
20.
BMC Genomics ; 13: 396, 2012 Aug 16.
Article in English | MEDLINE | ID: mdl-22897889

ABSTRACT

BACKGROUND: Drug susceptible clinical isolates of Candida albicans frequently become highly tolerant to drugs during chemotherapy, with dreadful consequences to patient health. We used RNA sequencing (RNA-seq) to analyze the transcriptomes of a CDR (Candida Drug Resistance) strain and its isogenic drug sensitive counterpart. RESULTS: RNA-seq unveiled differential expression of 228 genes including a) genes previously identified as involved in CDR, b) genes not previously associated to the CDR phenotype, and c) novel transcripts whose function as a gene is uncharacterized. In particular, we show for the first time that CDR acquisition is correlated with an overexpression of the transcription factor encoding gene CZF1. CZF1 null mutants were susceptible to many drugs, independently of known multidrug resistance mechanisms. We show that CZF1 acts as a repressor of ß-glucan synthesis, thus negatively regulating cell wall integrity. Finally, our RNA-seq data allowed us to identify a new transcribed region, upstream of the TAC1 gene, which encodes the major CDR transcriptional regulator. CONCLUSION: Our results open new perspectives of the role of Czf1 and of our understanding of the transcriptional and post-transcriptional mechanisms that lead to the acquisition of drug resistance in C. albicans, with potential for future improvements of therapeutic strategies.


Subject(s)
Candida albicans/genetics , Drug Resistance, Fungal , Fungal Proteins/genetics , Fungal Proteins/metabolism , Gene Expression Profiling , Sequence Analysis, RNA , Transcription Factors/genetics , Transcription Factors/metabolism , beta-Glucans/metabolism
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