Expression of qa-1F activator protein: identification of upstream binding sites in the qa gene cluster and localization of the DNA-binding domain.

Baum, James A.; Geever, Robert F.; Giles, Norman H.

doi:10.1128/mcb.7.3.1256

Cited by 100 publications

(43 citation statements)

References 44 publications

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“…Hence, the protein factors associated with the CTTI, CYC7, DAL5, and DAL7 5'-GATAA-3'-containing sequences are unlikely to be the same. A similar situation may also be occurring in Neurospora crassa, because the sequence 5'-GATAA-3' appears in the UAS sites of genes associated with the utilization of quinic acid as a carbon source (1).…”

Section: Methodsmentioning

confidence: 99%

Saturation mutagenesis of the UASNTR (GATAA) responsible for nitrogen catabolite repression-sensitive transcriptional activation of the allantoin pathway genes in Saccharomyces cerevisiae

1991

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Saturation mutagenesis of the UASNTR element responsible for GLN3-dependent, nitrogen catabolite repression-sensitive transcriptional activation of allantoin pathway genes in yeast cells identified the dodecanucleotide sequence 5'-TTNCTGATAAGG-3' as the minimum required for UAS activity. There was significant flexibility in mutant sequences capable of supporting UAS activity, which correlates well with the high variation in UASNTR homologous sequences reported to be upstream of the DAL and DUR genes. Three of nine UASNTR-like sequences 5' of the DAL5 gene supported high-level transcriptional activation. The others, which contained nonpermissive substitutions, were not active.

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Section: Methodsmentioning

confidence: 99%

Saturation mutagenesis of the UASNTR (GATAA) responsible for nitrogen catabolite repression-sensitive transcriptional activation of the allantoin pathway genes in Saccharomyces cerevisiae

1991

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“…NIT-4, the most extensively studied of the two, is required for nitrate assimilation and interacts with NIT-2, a GATA factor (see below), to activate expression of nitrate and nitrite reductases (230,257,892). The QA1F factor, which regulates quinic acid utilization, is another example where protein function and DNA binding properties have been determined (52). The fluffy gene product (FL), required for macroconidiation, is also a member of the Zn(II) 2 Cys 6 family (40) but has not been characterized at the protein level.…”

Section: Transcription Factorsmentioning

confidence: 99%

Lessons from the Genome Sequence ofNeurospora crassa: Tracing the Path from Genomic Blueprint to Multicellular Organism

Borkovich

Alex

Yarden

et al. 2004

Microbiol Mol Biol Rev

595

618

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We present an analysis of over 1,100 of the ∼10,000 predicted proteins encoded by the genome sequence of the filamentous fungus Neurospora crassa. Seven major areas of Neurospora genomics and biology are covered. First, the basic features of the genome, including the automated assembly, gene calls, and global gene analyses are summarized. The second section covers components of the centromere and kinetochore complexes, chromatin assembly and modification, and transcription and translation initiation factors. The third area discusses genome defense mechanisms, including repeat induced point mutation, quelling and meiotic silencing, and DNA repair and recombination. In the fourth section, topics relevant to metabolism and transport include extracellular digestion; membrane transporters; aspects of carbon, sulfur, nitrogen, and lipid metabolism; the mitochondrion and energy metabolism; the proteasome; and protein glycosylation, secretion, and endocytosis. Environmental sensing is the focus of the fifth section with a treatment of two-component systems; GTP-binding proteins; mitogen-activated protein, p21-activated, and germinal center kinases; calcium signaling; protein phosphatases; photobiology; circadian rhythms; and heat shock and stress responses. The sixth area of analysis is growth and development; it encompasses cell wall synthesis, proteins important for hyphal polarity, cytoskeletal components, the cyclin/cyclin-dependent kinase machinery, macroconidiation, meiosis, and the sexual cycle. The seventh section covers topics relevant to animal and plant pathogenesis and human disease. The results demonstrate that a large proportion of Neurospora genes do not have homologues in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. The group of unshared genes includes potential new targets for antifungals as well as loci implicated in human and plant physiology and disease

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“…Soluble extracts of strain EG7686 were used as a source of TnpI protein for DNA binding studies aimed at identifying TnpI binding sites in Tn5401 and localizing the IRS of Tn5401. TnpI binding to a DNA fragment (nt 554 to 768 of Tn5401) containing the putative IRS was first assessed by the gel mobility shift assay (5). In this assay, specific binding of a protein to a radiolabeled DNA fragment results in a reduced electrophoretic mobility of that DNA fragment, observed as a discrete shift in the DNA band detected by autoradiography.…”

Section: And 5)mentioning

confidence: 99%

TnpI recombinase: identification of sites within Tn5401 required for TnpI binding and site-specific recombination

Baum

1995

J Bacteriol

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The Bacillus thuringiensis class II transposon Tn5401 encodes a recombinase protein, TnpI, that mediates the resolution of cointegrate molecules generated as intermediates during Tn5401 transposition by the TnpA transposase. This recombination event requires a specific target site, or internal resolution site, at which TnpI binds and catalyzes the exchange of DNA strands. Gel mobility shift assays and DNase I footprinting analyses were used to localize the TnpI binding region to the sequence extending from nucleotides 637 to 747 of Tn5401. Deletions within this region blocked TnpI-mediated recombination in vivo. The 12-bp sequence ATGTCC RCTAAY, present in four copies within the TnpI binding region, is proposed to be the recognition sequence for TnpI binding. TnpI also binds to a single copy of this sequence located within the 53-bp terminal inverted repeats of Tn5401. The unique juxtaposition of recombinase and transposase binding sites at the terminal inverted repeats of Tn5401 suggests that TnpI regulates the binding and/or catalytic activity of TnpA transposase.Tn5401 is a class II (15) (Tn3-like) transposable element indigenous to the CryIIIA-producing Bacillus thuringiensis subsp. morrisoni strain EG2158 (3). The 4,837-bp transposon encodes both a transposase protein (TnpA) and a recombinase protein (TnpI) that are required for Tn5401 transposition in B. thuringiensis. The structural organization of Tn5401 resembles that of another B. thuringiensis transposon, Tn4430, but the two transposons are only distantly related as judged by nucleotide and amino acid sequence identity (3).The TnpI recombinase, related to the phage integrase family of site-specific recombinases, catalyzes a recombination event that resolves cointegrate molecules formed as intermediates during Tn5401 transposition. Previously, it was shown that a mutation in the tnpI gene of the Tn5401-based transposon vector pEG922 leads to the accumulation of cointegrate molecules in B. thuringiensis (3), as would be predicted from the Tn3 model of replicative transposition (9,22). This recombination event presumably occurs at a specific site, referred to as an internal resolution site (IRS).Sequence analysis of Tn5401 has revealed a likely candidate for the IRS (3). A 12-bp sequence element, ATGTCCRCT AAY, occurs four times in the intergenic region between the orf1 coding region and the tnpI gene (Fig. 1), two copies of which form a 28-bp imperfect inverted repeat (IR). A similar sequence arrangement, albeit a different conserved sequence, is found in the tnpI promoter region of Tn4430 (17) as well as in the target sites of other site-specific recombinases of the integrase-like recombinase family (see reference 23 and references therein). In Tn5401, direct repeats of the 12-bp sequence are also positioned between the Ϫ10 and Ϫ35 sites of the divergent promoters for orf1 and tnpI (Fig. 1), an observation consistent with studies implicating TnpI as a negative regulator of transcription from these promoters (3).In addition, one copy of the conserved se...

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Expression of qa-1F activator protein: identification of upstream binding sites in the qa gene cluster and localization of the DNA-binding domain.

Cited by 100 publications

References 44 publications

Saturation mutagenesis of the UASNTR (GATAA) responsible for nitrogen catabolite repression-sensitive transcriptional activation of the allantoin pathway genes in Saccharomyces cerevisiae

Saturation mutagenesis of the UASNTR (GATAA) responsible for nitrogen catabolite repression-sensitive transcriptional activation of the allantoin pathway genes in Saccharomyces cerevisiae

Lessons from the Genome Sequence ofNeurospora crassa: Tracing the Path from Genomic Blueprint to Multicellular Organism

TnpI recombinase: identification of sites within Tn5401 required for TnpI binding and site-specific recombination

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