Global Regulatory Functions of Oaf1p and Pip2p (Oaf2p), Transcription Factors That Regulate Genes Encoding Peroxisomal Proteins in Saccharomyces cerevisiae

ABSTRACT Two transcription factors, Oaf1p and Pip2p (Oaf2p), are key components in the pathway by which several Saccharomyces cerevisiae genes encoding peroxisomal proteins are activated in the presence of a fatty acid such as oleate. By searching the S. cerevisiae genomic database for the consensus sequence that acts as a target for these transcription factors, we identified 40 genes that contain a putative Oaf1p-Pip2p binding site in their promoter region. Quantitative Northern analysis confirmed that the expression of 22 of the genes identified is induced by oleate and that either one or both of these transcription factors are required for the activation. In addition to known peroxisomal proteins, the regulated genes encode novel peroxisomal proteins, a mitochondrial protein, and proteins of unknown location and function. We demonstrate that Oaf1p regulates certain genes in the absence of Pip2p and that both of these transcription factors play a role in maintaining the glucose-repressed state of one gene. Furthermore, we provide evidence that the defined consensus binding site is not required for the regulation of certain oleate-responsive genes.

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Genes encoding components of the olfactory signal transduction cascade contain a DNA binding site that may direct neuronal expression.

Molecular and Cellular Biology ◽

10.1128/mcb.13.9.5805 ◽

1993 ◽

Vol 13 (9) ◽

pp. 5805-5813 ◽

Cited By ~ 52

Author(s):

M M Wang ◽

R Y Tsai ◽

K A Schrader ◽

R R Reed

Keyword(s):

Signal Transduction ◽

Dna Binding ◽

Binding Site ◽

Binding Sites ◽

Consensus Sequence ◽

Initiation Site ◽

Olfactory Neuron ◽

Promoter Regions ◽

Transcriptional Initiation ◽

Genes Encoding

Genes which mediate odorant signal transduction are expressed at high levels in neurons of the olfactory epithelium. The molecular mechanism governing the restricted expression of these genes likely involves tissue-specific DNA binding proteins which coordinately activate transcription through sequence-specific interactions with olfactory promoter regions. We have identified binding sites for the olfactory neuron-specific transcription factor, Olf-1, in the sequences surrounding the transcriptional initiation site of five olfactory neuron-specific genes. The Olf-1 binding sites described define the consensus sequence YTCCCYRGGGAR. In addition, we have identified a second binding site, the U site, in the olfactory cyclic nucleotide gated channel and type III cyclase promoters, which binds factors present in all tissue examined. These experiments support a model in which expression of Olf-1 in the sensory neurons coordinately activates a set of olfactory neuron-specific genes. Furthermore, expression of a subset of these genes may be modulated by additional binding factors.

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Regulatory Mechanisms Controlling Expression of the DAN/TIR Mannoprotein Genes During Anaerobic Remodeling of the Cell Wall in Saccharomyces cerevisiae

Genetics ◽

10.1093/genetics/157.3.1169 ◽

2001 ◽

Vol 157 (3) ◽

pp. 1169-1177

Author(s):

Natalia E Abramova ◽

Brian D Cohen ◽

Odeniel Sertil ◽

Rachna Kapoor ◽

Kelvin J A Davies ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Consensus Sequence ◽

Ectopic Expression ◽

Constitutive Expression ◽

Anaerobic Growth ◽

Zinc Cluster ◽

Sterol Transport ◽

Genes Encoding ◽

Altered Regulation ◽

Repression Domain

Abstract The DAN/TIR genes of Saccharomyces cerevisiae encode homologous mannoproteins, some of which are essential for anaerobic growth. Expression of these genes is induced during anaerobiosis and in some cases during cold shock. We show that several heme-responsive mechanisms combine to regulate DAN/TIR gene expression. The first mechanism employs two repression factors, Mox1 and Mox2, and an activation factor, Mox4 (for mannoprotein regulation by oxygen). The genes encoding these proteins were identified by selecting for recessive mutants with altered regulation of a dan1::ura3 fusion. MOX4 is identical to UPC2, encoding a binucleate zinc cluster protein controlling expression of an anaerobic sterol transport system. Mox4/Upc2 is required for expression of all the DAN/TIR genes. It appears to act through a consensus sequence termed the AR1 site, as does Mox2. The noninducible mox4Δ allele was epistatic to the constitutive mox1 and mox2 mutations, suggesting that Mox1 and Mox2 modulate activation by Mox4 in a heme-dependent fashion. Mutations in a putative repression domain in Mox4 caused constitutive expression of the DAN/TIR genes, indicating a role for this domain in heme repression. MOX4 expression is induced both in anaerobic and cold-shocked cells, so heme may also regulate DAN/TIR expression through inhibition of expression of MOX4. Indeed, ectopic expression of MOX4 in aerobic cells resulted in partially constitutive expression of DAN1. Heme also regulates expression of some of the DAN/TIR genes through the Rox7 repressor, which also controls expression of the hypoxic gene ANB1. In addition Rox1, another heme-responsive repressor, and the global repressors Tup1 and Ssn6 are also required for full aerobic repression of these genes.

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A synthetic silencer mediates SIR-dependent functions in Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.11.11.5648-5659.1991 ◽

1991 ◽

Vol 11 (11) ◽

pp. 5648-5659

Author(s):

F J McNally ◽

J Rine

Keyword(s):

Saccharomyces Cerevisiae ◽

Binding Site ◽

Binding Sites ◽

Consensus Sequence ◽

Protein A ◽

Replication Initiation ◽

Yeast Saccharomyces Cerevisiae ◽

Autonomously Replicating Sequence ◽

Functional Components

Copies of the mating-type genes are present at three loci on chromosome III of the yeast Saccharomyces cerevisiae. The genes at the MAT locus are transcribed, whereas the identical genes at the silent loci, HML and HMR, are not transcribed. Several genes, including the four SIR genes, and two sites, HMR-E and HMR-I, are required for repression of transcription at the HMR locus. Three elements have been implicated in the function of the HMR-E silencer: a binding site for the RAP1 protein, a binding site for the ABF1 protein, and an 11-bp consensus sequence common to nearly all autonomously replicating sequence (ARS) elements (putative origins of DNA replication). RAP1 and ABF1 binding sites of different sequence than those found at HMR-E were joined with an 11-bp ARS consensus sequence to form a synthetic silencer. The synthetic silencer was able to repress transcription of the HMRa1 gene, confirming that binding sites for RAP1 and ABF1 and the 11-bp ARS consensus sequence were the functional components of the silencer in vivo. Mutations in the ABF1 binding site or in the ARS consensus sequence of the synthetic silencer caused nearly complete derepression of transcription at HMR. The ARS consensus sequence mutation also eliminated the ARS activity of the synthetic silencer. These data suggested that replication initiation at the HMR-E silencer was required for establishment of the repressed state at the HMR locus.

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Role of the IE62 Consensus Binding Site in Transactivation by the Varicella-Zoster Virus IE62 Protein

Journal of Virology ◽

10.1128/jvi.02522-09 ◽

2010 ◽

Vol 84 (8) ◽

pp. 3767-3779 ◽

Cited By ~ 13

Author(s):

Kris White ◽

Hua Peng ◽

John Hay ◽

William T. Ruyechan

Keyword(s):

Dna Binding ◽

Varicella Zoster Virus ◽

Binding Site ◽

Consensus Sequence ◽

Binding Domain ◽

Dna Binding Domain ◽

Consensus Binding Site ◽

Mobility Shift ◽

Varicella Zoster ◽

Mobility Shift Assay

ABSTRACT The varicella-zoster virus (VZV) IE62 protein is the major transcriptional activator. IE62 is capable of associating with DNA both nonspecifically and in a sequence-specific manner via a consensus binding site (5′-ATCGT-3′). However, the function of the consensus site is poorly understood, since IE62 efficiently transactivates promoter elements lacking this sequence. In the work presented here, sequence analysis of the VZV genome revealed the presence of 245 IE62 consensus sites throughout the genome. Some 54 sites were found to be present within putative VZV promoters. Electrophoretic mobility shift assay (EMSA) experiments using an IE62 fragment containing the IE62 DNA-binding domain and duplex oligonucleotides that did or did not contain the IE62 consensus binding sequence yielded KD (equilibrium dissociation constant) values in the nanomolar range. Further, the IE62 DNA binding domain was shown to have a 5-fold-increased affinity for its consensus site compared to nonconsensus sequences. The effect of consensus site presence and position on IE62-mediated activation of native VZV and model promoters was examined using site-specific mutagenesis and transfection and superinfection reporter assays. In all promoters examined, the consensus sequence functioned as a distance-dependent repressive element. Protein recruitment assays utilizing the VZV gI promoter indicated that the presence of the consensus site increased the recruitment of IE62 but not Sp1. These data suggest a model where the IE62 consensus site functions to down-modulate IE62 activation, and interaction of IE62 with this sequence may result in loss or decrease of the ability of IE62 to recruit cellular factors needed for full promoter activation.

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PBX1 and MEIS1 up-regulate SOX3 gene expression by direct interaction with a consensus binding site within the basal promoter region

Biochemical Journal ◽

10.1042/bj20090694 ◽

2009 ◽

Vol 425 (1) ◽

pp. 107-116 ◽

Cited By ~ 20

Author(s):

Marija Mojsin ◽

Milena Stevanovic

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Binding Site ◽

Integration Site ◽

Direct Interaction ◽

Cell Leukaemia ◽

Upstream Stimulatory Factor ◽

Consensus Binding Site ◽

Functional Link ◽

Sox3 Gene

Sox3/SOX3 [SRY (sex determining region Y)-box 3] is considered to be one of the earliest neural markers in vertebrates, playing a role in specifying neuronal fate. We have previously reported characterization of the SOX3 promoter and demonstrated that the general transcription factors NF-Y (nuclear factor-Y), Sp1 (specificity protein 1) and USF (upstream stimulatory factor) are involved in transcriptional regulation of SOX3 promoter activity. In the present study we provide the first evidence that the TALE (three-amino-acid loop extension) transcription factors PBX1 (pre-B-cell leukaemia homeobox 1) and MEIS1 (myeloid ecotropic viral integration site 1 homologue) participate in regulating human SOX3 gene expression in NT2/D1 cells by direct interaction with the consensus PBX/MEIS-binding site, which is conserved in all mammalian orthologue promoters analysed. PBX1 is present in the protein complex formed at this site with nuclear proteins from uninduced cells, whereas both PBX1 and MEIS1 proteins were detected in the complex created with extract from RA (retinoic acid)-induced NT2/D1 cells. By functional analysis we also showed that mutations of the PBX1/MEIS1-binding sites resulted in profound reduction of SOX3 promoter responsiveness to RA. Finally, we demonstrated that overexpressed PBX1 and MEIS1 increased endogenous SOX3 protein expression in both uninduced and RA-induced NT2/D1 cells. With the results of the present study, for the first time, we have established a functional link between the TALE proteins, PBX1 and MEIS1, and expression of the human SOX3 gene. This link is of particular interest since both TALE family members and members of the SOX superfamily are recognized as important developmental regulators.

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The Saccharomyces cerevisiae ADR1 gene is a positive regulator of transcription of genes encoding peroxisomal proteins

Molecular and Cellular Biology ◽

10.1128/mcb.11.2.699-704.1991 ◽

1991 ◽

Vol 11 (2) ◽

pp. 699-704 ◽

Cited By ~ 1

Author(s):

M Simon ◽

G Adam ◽

W Rapatz ◽

W Spevak ◽

H Ruis

Keyword(s):

Saccharomyces Cerevisiae ◽

Glucose Repression ◽

Northern Hybridization ◽

Multicopy Plasmid ◽

Beta Oxidation ◽

Positive Regulator ◽

Ethanol Medium ◽

Genes Encoding ◽

Multiple Copies ◽

Regulatory Functions

Expression of the CTA1 gene of Saccharomyces cerevisiae, encoding catalase A, the peroxisomal catalase of this yeast, is sensitive to glucose repression. A DNA fragment cloned as a multicopy plasmid suppressing the glucose repression of CTA1 transcription was demonstrated to contain the ADR1 gene. Multiple copies of ADR1 increased catalase A formation not only on 10% glucose, but also on ethanol medium and in the presence of oleic acid, an inducer of peroxisome proliferation. Compared with wild-type cells, adr1 null mutants produced by disruption of the gene exhibit reduced CTA1 expression. This demonstrates that ADR1 is a true positive regulator of CTA1. Further experiments showed that it acts directly on CTA1. Alcohol dehydrogenase II, which is under ADR1 control, was excluded as a mediator of the effect on CTA1; deletion of bases -123 to -168 of CTA1 reduces expression and eliminates the response to the ADR1 multicopy plasmid without eliminating fatty acid induction; and gel retardation experiments demonstrated that ADR1 binds to a CTA1 upstream fragment (-156 to -184) with limited similarity to the ADR1 binding site of ADH2. Northern hybridization experiments further demonstrated that expression of two genes encoding enzymes of peroxisomal beta-oxidation (beta-ketothiolase, trifunctional enzyme) and of a gene involved in peroxisome assembly (PAS1) is also negatively affected by the adr1 null mutation. These findings demonstrate that the ADR1 protein has much broader regulatory functions than previously recognized.

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A synthetic silencer mediates SIR-dependent functions in Saccharomyces cerevisiae.

Molecular and Cellular Biology ◽

10.1128/mcb.11.11.5648 ◽

1991 ◽

Vol 11 (11) ◽

pp. 5648-5659 ◽

Cited By ~ 53

Author(s):

F J McNally ◽

J Rine

Keyword(s):

Saccharomyces Cerevisiae ◽

Binding Site ◽

Binding Sites ◽

Consensus Sequence ◽

Protein A ◽

Replication Initiation ◽

Yeast Saccharomyces Cerevisiae ◽

Autonomously Replicating Sequence ◽

Functional Components

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Frataxin, a molecule of mystery: trading stability for function in its iron-binding site

Biochemical Journal ◽

10.1042/bj20091959 ◽

2010 ◽

Vol 426 (2) ◽

pp. e1-e3 ◽

Cited By ~ 16

Author(s):

Darius J. R. Lane ◽

Des R. Richardson

Keyword(s):

Binding Site ◽

Protein Interactions ◽

Mitochondrial Protein ◽

Iron Binding ◽

Protein Protein Interactions ◽

Iron Sulfur Cluster ◽

Downstream Effects ◽

Biochemical Journal ◽

And Function ◽

The Relationship

What are the structural implications for iron binding by frataxin, the mitochondrial protein whose decreased expression results in Friedreich's ataxia? Though frataxin has been shown to be essential for proper handling of iron within mitochondria (e.g. for iron–sulfur cluster and haem biosynthesis), its exact molecular function remains unclear. In this issue of the Biochemical Journal, Correia and colleagues investigate the relationship between structure and function at the putative iron-binding site of Yfh1 (yeast frataxin). Using a host of Yfh1 combination point mutants, the authors observe that the presence of a semi-conserved pocket of negative charge within the ‘acidic ridge’ region (thought to be responsible for iron binding) only mildly enhances Yfh1's ability to bind iron, though it does significantly increase the protein's structural flexibility. The general emerging view is that frataxin's keystone role in mitochondrial iron metabolism depends on iron binding. This appears to have downstream effects on protein–protein interactions that are crucial for frataxin function. The current results reveal a somewhat delicate relationship between iron binding and structural plasticity that may help unravel the enigma of frataxin's metabolic roles.

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Context-Dependent Modulation of Replication Activity of Saccharomyces cerevisiae Autonomously Replicating Sequences by Transcription Factors

Molecular and Cellular Biology ◽

10.1128/mcb.19.11.7428 ◽

1999 ◽

Vol 19 (11) ◽

pp. 7428-7435 ◽

Cited By ~ 10

Author(s):

Hidetsugu Kohzaki ◽

Yoshiaki Ito ◽

Yota Murakami

Keyword(s):

Saccharomyces Cerevisiae ◽

Transcription Factor ◽

Transcription Factors ◽

Binding Site ◽

Selectable Marker ◽

Marker Gene ◽

Selectable Marker Gene ◽

Autonomously Replicating Sequence ◽

Replication Activity

ABSTRACT Evidence for transcription factor involvement in the initiation of DNA replication at certain replication origins in Saccharomyces cerevisiae mainly comes from an indirect assay which measures the mitotic stability of plasmids containing an autonomously replicating sequence (ARS), a selectable marker gene, and a centromere. In order to eliminate the effect of transcription factor binding to the selectable marker gene or centromere in such assays, we have adapted theDpnI assay to directly measure ARS replication activity in vivo by using ARS plasmids devoid of extraneous transcription elements. Using this assay, we found that the B3 element of ARS1, which serves as a binding site for the transcription factor Abf1p, does not stimulate ARS activity on plasmids lacking a centromere and a selectable marker gene. We also found with such plasmids that exogenous expression of the strong transcriptional activators Gal4 and Gal4-VP16 inhibited the replication activity of ARS1 when B3 was replaced by the Gal4 binding site, although these activators had previously been shown to stimulate replication activity in the stability assay. Moreover, a chromosomally inactive ARS, ARS301, which was active by itself on a plasmid, was inactivated by placing an Abf1p binding site in its vicinity. These results indicate that the sequences surrounding the ARS as well as properties of the ARS element itself determine its response to transcription factors.

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Small mitochondrial protein NERCLIN regulates cardiolipin homeostasis and mitochondrial ultrastructure

10.1101/2021.01.03.424667 ◽

2021 ◽

Author(s):

Svetlana Konovalova ◽

Rubén Torregrosa-Muñumer ◽

Pooja Manjunath ◽

Sundar Baral ◽

Xiaonan Liu ◽

...

Keyword(s):

Lipid Analysis ◽

Mitochondrial Dynamics ◽

Mitochondrial Protein ◽

Membrane Lipid ◽

Negative Regulator ◽

Mitochondrial Ultrastructure ◽

Inner Mitochondrial Membrane ◽

The Matrix ◽

And Function ◽

Regulatory Functions

ABSTRACTCardiolipin (CL) is an essential phospholipid for mitochondrial structure and function. Here we present a small mitochondrial protein, NERCLIN, as a negative regulator of CL homeostasis and mitochondrial ultrastructure. Primate-specific NERCLIN is expressed ubiquitously from GRPEL2 locus on a tightly regulated low level, but induced by heat stress. NERCLIN overexpression severely disrupts mitochondrial cristae structure and induces mitochondrial fragmentation. Proximity labeling suggested interactions of NERCLIN with CL synthesis and prohibitin complexes on the matrix side of the inner mitochondrial membrane. Lipid analysis indicated that NERCLIN regulates mitochondrial CL content. The regulation may occur directly through interaction with PTPMT1, a proximal partner on the CL synthesis pathway, as its product phosphatidylglycerol was also reduced by NERCLIN. We propose that NERCLIN contributes to stress-induced adaptation of mitochondrial dynamics and turnover by regulating the mitochondrial CL content. Our findings add NERCLIN to the group of recently identified small mitochondrial proteins with important regulatory functions.

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