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W E Timberlake

Publications and source records attributed to W E Timberlake.

At least 19 recordsLinked to original sources
PubMed1996

Wild chromosomal variants in Aspergillus nidulans.

Pulsed-field gel electrophoresis and a chromosome-specific cosmid DNA library were used to determine the karyotypes of wild-type Aspergillus nidulans isolates from around the world. Overall, little structural variation was found, with a few major exceptions. One isolate possessed a non-essential B-chromosome of about 1.0 million base pairs (mb). Another isolate had undergone a non-reciprocal translocation of about 1.6 mb of chromosome VI onto chromosome VIII. Other than these chromosomal differences, these isolates appeared phenotypically normal. To analyze its effects on meiosis, the translocation isolate was outcrossed with another wild-type derivative that had a normal electrophoretic karyotype. This cross produced a range of phenotypes, including duplicated progeny that had a barren phenotype similar to that described for Neurospora partial disomics. The duplication was somewhat vegetatively unstable. This is the first association of sterility with chromosomal duplication in A. nidulans.

Aspergillus nidulans↗
PubMed1996

Saccharomyces cerevisiae TEC1 is required for pseudohyphal growth.

Diverse eukaryotic organisms share developmental transcription factors with homologous DNA-binding domains. We showed that the developmental regulator AbaA, a member of the ATTS/TEA (AbaA, TEF-1, TEC1, Scalloped/TEF-1, TEC1, AbaA) class of transcription factors of the filamentous fungus Aspergillus nidulans, induces pseudohyphal development in the yeast Saccharomyces cerevisiae. The S. cerevisiae homologue of AbaA, TEC1p, is required for this morphological transition. We provide evidence that TEC1p functions in co-operation with STE12p to induce pseudohyphal development.

Amino Acid Sequence↗
PubMed1996

catA, a new Aspergillus nidulans gene encoding a developmentally regulated catalase.

Aspergillus nidulans asexual sporulation (conidiation) is a model system for studying gene regulation and development. The CAN5 cDNA is one of several clones isolated based on transcript induction during conidiation. Here we present the molecular characterization of its corresponding gene, demonstrating that it encodes a developmentally regulated catalase, designated catA. The catA 744-amino-acid-residue polypeptide shows significant identity to other catalases. Its similarity to prokaryotic catalases is greater than to other fungal catalases. catA mRNA is barely detectable in growing mycelia, highly induced during sporulation, and present in isolated spores. However, catA expression is not dependent on the developmental regulatory genes brlA, abaA and wetA. Direct catalase activity determination in native gels revealed the existence of two bands of activity. One of these bands represented the major activity during vegetative growth and was induced during sporulation. The second catalase activity appeared after the induction of sporulation and was the predominant activity in spores. Disruption of catA abolished the major spore catalase without eliminating the vegetative activity, indicating the existence of at least two catalase genes in A. nidulans. catA-disrupted mutants produced spores that were sensitive to H2O2, as compared to wild-type spores. The increase in the activity of the vegetative catalase and the appearance of a second catalase during asexual sporulation is consistent with the occurrence of an oxidative stress during development.

Amino Acid Sequence↗
PubMed1995

Aspergillus nidulans apsA (anucleate primary sterigmata) encodes a coiled-coil protein required for nuclear positioning and completion of asexual development.

Many fungi are capable of growing by polarized cellular extension to form hyphae or by isotropic expansion to form buds. Aspergillus nidulans anucleate primary sterigmata (apsA) mutants are defective in nuclear distribution in both hyphae and in specialized, multicellular reproductive structures, called conidiophores. apsA mutations have a negligible effect on hyphal growth, unlike another class of nuclear distribution (nud) mutants. By contrast, they almost completely block entry of nuclei into primary buds, or sterigmata (bud nucleation), produced during development of conidiophores. Failure of the primary sterigmata to become nucleated results in developmental arrest and a failure to activate the transcriptional program associated with downstream developmental steps. However, occasionally in mutants a nucleus enters a primary bud and this event relieves the developmental blockage. Thus, there is a stringent developmental requirement for apsA function, but only at the stage of primary bud formation. apsA encodes a 183-kD coiled-coil protein with similarity to Saccharomyces cerevisiae NUM1p, required for nuclear migration in the budding process.

Actins↗
PubMed1995

dewA encodes a fungal hydrophobin component of the Aspergillus spore wall.

An anonymous cDNA clone, pCAN4, was shown previously to correspond to an mRNA that accumulates preferentially during asexual sporulation of the filamentous fungus Aspergillus nidulans. The peptide encoded by pCAN4 is a fungal hydrophobin, a group of small, hydrophobic cell wall proteins. When the CAN4 gene was disrupted, conidia and conidiophores appeared to be normal, but sporulating colonies wetted more rapidly with detergent solutions than did the wild type. We renamed CAN4 dewA for the detergent wettable phenotype and mapped it to chromosome V, 24 map units from cysC. The A. nidulans rodA gene also encodes a sporulation-specific fungal hydrophobin. Spores of a dewA- rodA- double mutant were less hydrophobic than those of either mutant alone, showing that dewA and rodA contribute independently to spore-wall hydrophobicity. Immunolocalization of DewA by epitope tagging demonstrated that DewA is present in the spore wall, but not in the walls of germ tubes, hyphae or cells of the spore-producing conidiophore. We conclude that dewA encodes a new fungal hydrophobin component of the conidial wall.

Amino Acid Sequence↗
PubMed1994

A fast random cost algorithm for physical mapping.

Ordering clones from a genomic library into physical maps of whole chromosomes presents a central computational/statistical problem in genetics. Here we present a physical mapping algorithm for creating ordered genomic libraries or contig maps by using a random cost approach [Berg, A. (1993) Nature (London) 361, 708-710]. This random cost algorithm is 5-10 times faster than existing physical mapping algorithms and has optimization performance comparable to existing procedures. The speedup in the algorithm makes practical the widespread use of bootstrap resampling to assess the statistical reliability of links in the physical map as well as the use of more elaborate physical mapping criteria to improve map quality. The random cost algorithm is illustrated by its application in assembling a physical map of chromosome IV from the filamentous fungus Aspergillus nidulans.

Aspergillus nidulans↗
PubMed1994

The Penicillium chrysogenum and Aspergillus nidulans wetA developmental regulatory genes are functionally equivalent.

Aspergillus nidulans and Penicillium chrysogenum are related fungi that reproduce asexually by forming multicellular conidiophores and uninucleate conidia. In A. nidulans, spore maturation is controlled by the wetA (AwetA) regulatory gene. We cloned a homologous gene (PwetA) from P. chrysogenum to determine if spore maturation is regulated by a similar mechanism in this species. The PwetA and AwetA genes are similar in structure and functional organization. The inferred polypeptides share 77% overall amino acid sequence similarity, with several regions having > 85% similarity. The genes also had significant, local sequence similarities in their 5' flanking regions, including conserved binding sites for the product of the regulatory gene abaA. PwetA fully complemented an A. nidulans wetA deletion mutation, demonstrating that PwetA and its 5' regulatory sequences function normally in A. nidulans. These results indicate that the mechanisms controlling sporulation in A. nidulans and P. chrysogenum are evolutionarily conserved.

Amino Acid Sequence↗
PubMed1994

Sexual origins of British Aspergillus nidulans isolates.

Aspergillus nidulans is a holomorphic fungus, capable of producing both meiotically and mitotically derived spores. Meiosis may be an evolutionary relic in this species because it is potentially capable of mitotic recombination and because most Aspergilli lack the ability to produce meiotic spores. We tested the null hypothesis that meiosis has been a major factor in the origin of strains of A. nidulans from Great Britain by estimating linkage disequilibrium among restriction fragment length polymorphisms. These strains belong to different heterokaryon compatibility groups and are thus incapable of undergoing mitotic recombination with one another, so any recombination evidenced by linkage equilibrium is assumed to be the result of meiosis. Eleven cosmid clones of known chromosomal origin were used to generate multilocus genotypes based on restriction-pattern differences for each heterokaryon compatibility group. Low levels of genetic variation and little linkage disequilibrium were found, indicating that the heterokaryon compatibility groups represent recently diverged lineages that arose via meiotic recombination. The null hypothesis that loci are independent could not be rejected. Additionally, low levels of electrophoretic karyotype variation were indicative of meiosis. We conclude that although A. nidulans probably propagates in a primarily clonal fashion, recombination events are frequent enough to disrupt the stable maintenance of clonal genotypes. We further conclude that the British heterokaryon compatibility groups arose via recombination and not through novel mutation.

Aspergillus nidulans↗
PubMed1994

ODS_BOOTSTRAP: assessing the statistical reliability of physical maps by bootstrap resampling.

In the program ODS_BOOTSTRAP we provide a methodology for quickly ordering clones in a genomic library into a physical map and for applying a statistical tool known as the bootstrap to assess the statistical reliability of a clonal ordering. Each clone is assigned a binary fingerprint by one of a variety of experimental approaches to physical mapping. For example, the binary fingerprints might be generated by hybridizing a panel of m probes to a library of n clones. The resulting n x m binary data matrix, X, is input to ODS_BOOTSTRAP, which utilizes the similarity in binary fingerprints of clones to construct a physical map. Under this particular implementation of bootstrap resampling, the m probes (or columns of the data matrix) are sampled randomly with replacement in the computer to generate a new n x m data matrix, X*, from which a second physical map is constructed. The resampling process is repeated 100 or more times to generate 100 or more X* matrices. The resulting 100 or more physical maps are compared with the original physical map based on the original data matrix X by counting how often links in the original physical map reappear. Three confidence statistics are introduced for each link in a physical map. The statistic C1 is defined as the percentage of time two neighboring clones on the original map reappear as neighbors under resampling. The statistic C2 is defined as the percentage of time that two neighboring clones i and j on the original map reappear as neighbors or that a clone with an identical binary fingerprint to clone i reappears as a neighbor to clone j. The statistic C3 is defined as the percentage of time that two neighboring clones on the original map reappear in the same contig under resampling.

Algorithms↗
PubMed1994

The Aspergillus nidulans abaA gene encodes a transcriptional activator that acts as a genetic switch to control development.

The Aspergillus nidulans abaA gene encodes a protein containing an ATTS DNA-binding motif and is required for the terminal stages of conidiophore development. Results from gel mobility shift and protection, missing-contact, and interference footprint assays showed that AbaA binds to the sequence 5'-CATTCY-3', where Y is a pyrimidine, making both major- and minor-groove contacts. Multiple AbaA binding sites are present in the cis-acting regulatory regions of several developmentally controlled structural genes as well as those of the upstream regulatory gene brlA, the downstream regulatory gene wetA, and abaA itself. These cis-acting regulatory regions confer AbaA-dependent transcriptional activation in a heterologous Saccharomyces cerevisiae gene expression system. From these observations, we propose that the AbaA transcription factor establishes a novel set of feedback regulatory loops responsible for determination of conidiophore development.

Base Sequence↗
PubMed1993

The Aspergillus nidulans yA gene is regulated by abaA.

The developmentally regulated Aspergillus nidulans yA gene encodes a p-diphenol oxidase that is needed for synthesis of green conidial pigment. We subjected the yA 5' flanking region to mutational analysis in A. nidulans and Saccharomyces cerevisiae to identify DNA sequence elements involved in its transcriptional control, and identified two functionally distinct elements. Element I contained potential BrlA binding sites and was required for full level yA transcription, but not for developmental regulation in the presence of element II. Element II contained putative TEF-1 binding sites flanking a CCAAT element and was sufficient for developmental regulation of transcription. Mutation of the TEF-1 binding sites eliminated developmental regulation, whereas mutation of the CCAAT element led to elevated levels of transcription. Element II was also sufficient to induce transcription in S. cerevisiae when the A.nidulans developmental regulatory gene abaA was expressed from the GAL1 promoter. As AbaA and TEF-1 possess similar DNA binding domains, the abaA-yA interaction in yeast is probably direct. Thus, abaA appears to be a direct activator of yA, but yA regulation may also involve interactions with BrlA and a member of the CCAAT class of DNA binding proteins.

Amino Acid Sequence↗
PubMed1993

The Aspergillus nidulans brlA regulatory locus consists of overlapping transcription units that are individually required for conidiophore development.

The Aspergillus nidulans brlA locus controls conidiophore development in conjunction with the products of several other regulatory loci. In this paper, we show that the brlA locus consists of overlapping transcription units, designated alpha and beta, with alpha transcription initiating within beta intronic sequences. The predicted BrlA polypeptides differ by 23 amino acid residues at their N-termini. Targeted mutations specifically eliminating either the alpha or beta transcript led to developmental abnormalities similar to those produced by previously identified hypomorphic mutants, showing that both transcripts have essential functions for normal development. However, provision of additional doses of alpha in a beta- strain or of beta in an alpha- strain remediated the developmental defects, indicating that the polypeptides have redundant functions. It is likely that differential regulation of alpha and beta expression in the wild type is important for the initiation and temporal regulation of development.

Amino Acid Sequence↗
PubMed1993

PCAP: probe choice and analysis package--a set of programs to aid in choosing synthetic oligomers for contig mapping.

In the program, PCAP, we provide a methodology for choosing synthetic oligonucleotide probes to be used in contig mapping experiments. The package serves the purpose of presenting a series of short oligonucleotides (8-12mers) that are chosen based on constraints with respect to frequency of occurrence within a particular genome and the G+C content of the oligonucleotides. The four programs contained within the package: (i) convert GenBank files to a format useable by the package; (ii) calculate trinucleotide and tetranucleotide frequencies in available sequence data on a particular species; (iii) present the user with upper and lower bounds on the frequencies of hybridization sites for oligonucleotide probes of length 8-12, (iv) allow the user to place constraints on site frequency and G+C content and provides a list of short probe sequences that fit these criteria. These sequences can then be synthetically produced and used in hybridization experiments to carry out contig mapping.

Base Sequence↗
PubMed1993

ODS: ordering DNA sequences--a physical mapping algorithm based on simulated annealing.

In the program ODS we provide a methodology for quickly ordering random clones into a physical map. The process of ordering individual clones with respect to their position along a chromosome is based on the similarity of binary signatures assigned to each clone. This binary signature is obtained by hybridizing each clone to a panel of oligonucleotide probes. By using the fact that the amount of overlap between any two clones is reflected in the similarity of their binary signatures, it is possible to reconstruct a chromosome by minimizing the sum of linking distances between an ordered sequence of clones. Unlike other programs for physical mapping, ODS is very general in the types of data that can be utilized for chromosome reconstruction. Any trait that can be scored in a presence--absence manner, such as hybridized synthetic oligonucleotides, restriction endonuclease recognition sites or single copy landmarks, can be used for analysis. Furthermore, the computational requirements for the construction of large physical maps can be measured in a matter of hours on work-stations such as the VAX2000.

Algorithms↗
PubMed1993

Identification of Aspergillus brlA response elements (BREs) by genetic selection in yeast.

The brlA gene of Aspergillus nidulans plays a central role in controlling conidiophore development. To test the hypothesis that brlA encodes a transcriptional regulator and to identify sites of interaction for the BrlA polypeptide, we expressed brlA in Saccharomyces cerevisiae (yeast) strains containing Aspergillus DNA sequences inserted upstream of a minimal yeast promoter fused to the Escherichia coli lacZ gene. Initially, a DNA fragment from the promoter region of the developmentally regulated rodA gene was tested and shown to mediate brlA-dependent transcriptional activation. Two additional DNA fragments were selected from an Aspergillus genomic library by their ability to respond to brlA in yeast. These fragments contained multiple copies of a sequence motif present in the rodA fragment, which we propose to be sites for BrlA interaction and designate brlA response elements (BREs). DNA fragments containing BREs upstream of a minimal Aspergillus promoter were capable of conferring developmental regulation in Aspergillus. Deletion of BREs from the upstream region of rodA greatly decreased its developmental induction. Multiple copies of a synthetic oligonucleotide with the consensus sequence identified among the BREs mediated brlA-dependent transcriptional activation in yeast. The results show that a primary activity of brlA is transcriptional activation and tentatively identify sites of interaction for the BrlA polypeptide.

Aspergillus nidulans↗