Evolution of a Fungal Regulatory Gene Family: The Zn(II)2Cys6 Binuclear Cluster DNA Binding Motif

Todd, Richard B.; Andrianopoulos, Alex

doi:10.1006/fgbi.1997.0993

Cited by 260 publications

(269 citation statements)

References 158 publications

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“…Although Lys14p conforms to the general properties of the Zn(II) 2 Cys 6 proteins, its target sites differ in several respects from the sites recognized by most other proteins of this class (for a review, see Todd and Andrianopoulos, 1997). First, the UAS LYS contains TCC and GGA triplets instead of the CGG and GCC triplets that are present in the targets of the majority of the zinc cluster proteins.…”

Section: Discussionmentioning

confidence: 93%

“…Recognition can also occur with CGG triplets oriented as direct repeats, as in the case of Hap1p (Zhang and Guarante, 1994;Ha et al, 1996), or as inverted palindromes, as shown recently for Leu3p and Pdr3p . Comparisons of the amino acid sequences of the various C 6 zinc cluster proteins as well as of their DNA targets have appeared recently (Schjerling and Homberg, 1996;Todd and Andrianopoulos, 1997).…”

Section: Introductionmentioning

confidence: 99%

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A nonameric core sequence is required upstream of the LYS genes of Saccharomyces cerevisiae for Lys14p‐mediated activation and apparent repression by lysine

Becker

Feller

Alami

et al. 1998

Molecular Microbiology

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SummaryThe expression of the structural genes for lysine (LYS) biosynthesis is controlled by a pathway-specific regulation mediated by the transcriptional activator Lys14 in the presence of ␣-aminoadipate semialdehyde, an intermediate of the pathway acting as a coinducer. Owing to end product inhibition of the first step of the pathway, excess lysine reduces the production of the co-inducer and causes apparent repression of the LYS genes. Analysis of LYS promoters and insertions within an heterologous reporter gene have allowed the characterization of an upstream activating element (UAS LYS ) able to confer Lys14-and ␣-aminoadipate semialdehyde-dependent activation as well as apparent repression by lysine to another yeast gene. This DNA motif is present as one or several copies in the promoters of at least six LYS genes. The consensus sequence derived from the comparison of the UAS LYS showing the highest activation capacities comprises the nonameric core sequence TCCRNYGGA. The RNY sequence of the 3 bp spacer as well as the presence of flanking AT-rich regions on both sides of the core sequence appear essential for optimal activation. Further evidence that this element is the target of Lys14p was provided by the demonstration that Lys14p binds to UAS LYS in vitro. The binding is independent of the presence of the co-inducer and is not affected by lysine. It depends on the integrity of the putative Zn(II) 2 Cys 6 binuclear cluster contained in the Lys14p.

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Section: Discussionmentioning

confidence: 93%

Section: Introductionmentioning

confidence: 99%

A nonameric core sequence is required upstream of the LYS genes of Saccharomyces cerevisiae for Lys14p‐mediated activation and apparent repression by lysine

Becker

Feller

Alami

et al. 1998

Molecular Microbiology

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“…These proteins are predicted to be involved in the transport of a wide range of substrates and several may function as nutrient sensors. Aspergillus species have also undergone a significant expansion in the number of fungal zinc binuclear cluster proteins (PF00172) 27 (Supplementary Table 14 online). This distribution is mirrored by a second PFAM domain (PF04082), which was originally identified as occurring in a proportion of proteins with PF00172 domain.…”

Section: Cell Wall Developmentmentioning

confidence: 99%

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

et al. 2007

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The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis.

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“…We collected from the literature a list of target genes (Table 1A), as well as a description of the known binding sites for each characterized zinc cluster protein (18,19,21). This list includes a second family of genes responding to galactose: the 'GAL-chip' family results from a DNA-chip experiment (14) that evaluates the ratio of expression of all yeast genes between galactose-rich and glucose-rich culture conditions.…”

Section: Families Of Co-regulated Genesmentioning

confidence: 99%

“…Such spaced dyad elements are *To whom correspondence should be addressed. Tel: +32 2 650 20 13; Fax: +32 2 648 89 54; Email: jvanheld@ucmb.ulb.ac.be common to a large class of transcription factors, found so far almost exclusively in fungi: the C 6 Zn 2 binuclear cluster proteins (18,19). This class encompasses 56 of the 170 transcription factors predicted from the genome of Saccharomyces cerevisiae.…”

Section: Introductionmentioning

confidence: 99%

Discovering regulatory elements in non-coding sequences by analysis of spaced dyads

Helden

Rios²,

Collado‐Vides³

2000

Nucleic Acids Research

261

207

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The application of microarray and related technologies is currently generating a systematic catalog of the transcriptional response of any single gene to a multiplicity of experimental conditions. Clustering genes according to the similarity of their transcriptional response provides a direct hint to the regulons of the different transcription factors, many of which have still not been characterized. We have developed a new method for deciphering the mechanism underlying the common transcriptional response of a set of genes, i.e. discovering cis-acting regulatory elements from a set of unaligned upstream sequences. This method, called dyad analysis, is based on the observation that many regulatory sites consist of a pair of highly conserved trinucleotides, spaced by a nonconserved region of fixed width. The approach is to count the number of occurrences of each possible spaced pair of trinucleotides, and to assess its statistical significance. The method is highly efficient in the detection of sites bound by C 6 Zn 2 binuclear cluster proteins, as well as other transcription factors. In addition, we show that the dyad and single-word analyses are efficient for the detection of regulatory patterns in gene clusters from DNA chip experiments. In combination, these programs should provide a fast and efficient way to discover new regulatory sites for as yet unknown transcription factors.

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Evolution of a Fungal Regulatory Gene Family: The Zn(II)2Cys6 Binuclear Cluster DNA Binding Motif

Cited by 260 publications

References 158 publications

A nonameric core sequence is required upstream of the LYS genes of Saccharomyces cerevisiae for Lys14p‐mediated activation and apparent repression by lysine

A nonameric core sequence is required upstream of the LYS genes of Saccharomyces cerevisiae for Lys14p‐mediated activation and apparent repression by lysine

Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88

Discovering regulatory elements in non-coding sequences by analysis of spaced dyads

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