bluuebunny/crossref_metadata_2025 huggingface dataset:
Forespore-specific transcription of a gene in the signal transduction pathway that governs Pro-sigma K processing in Bacillus subtilis.
Authors: Cutting S , Driks A , Schmidt R , Kunkel B , Losick R
Published: June 2007

We present studies on the regulation of a developmental gene (spoIVB) whose product is required at a late stage of morphogenesis during the process of sporulation in Bacillus subtilis. Earlier work implicated the spoIVB gene product in a signal-transduction pathway that governs the conversion of pro-sigma K to the mature and active form of the mother cell sigma factor, sigma K, in response to a signal generated within the forespore chamber of the sporangium. We now show that (1) spoIVB is induced at the engulfment stage of sporulation, (2) this transcription is restricted to the forespore, and (3) spoIVB is under the direct control of the forespore sigma factor sigma G. The discovery that spoIVB is a forespore-expressed gene suggests that the spoIVB gene product, or a developmental event under its control, triggers the processing of pro-sigma K and thereby mediates the coupling of sigma K-directed gene expression in the mother cell to sigma G-directed gene expression in the forespore. We also show that spoIVB transcription is partially dependent on the action of the mother cell regulatory gene spoIIID, a finding that suggests that the transcription of certain forespore-expressed genes is influenced by events in the mother cell.
The carboxyl terminus of Scg1, the G alpha subunit involved in yeast mating, is implicated in interactions with the pheromone receptors.
Authors: Hirsch J P , Dietzel C , Kurjan J
Published: June 2007

The carboxyl termini of alpha subunits of mammalian G proteins have been implicated in receptor interactions. We have used a genetic analysis to test such a role for the carboxyl terminus of Scg1, the alpha subunit involved in the yeast pheromone response pathway. A 22-amino-acid truncation (scg1Amb451) resulted in defects in growth and cellular morphology. This phenotype is similar to the null phenotype and represents constitutive activation of the pheromone response pathway; it could result from various effects, including protein instability or constitutive guanine nucleotide exchange, as reported for some altered mammalian G alpha s constructs. A 5-amino-acid truncation (SCG1Och468) resulted in pheromone response and mating defects in both a and alpha cells, which is consistent with defects in interactions with the pheromone receptors. Lysine-to-proline mutations near the carboxyl terminus (SCG1Pro467 and SCG1Pro468) resulted in pheromone response and mating defects, the severity of which differed in a and alpha cells. This differential effect in the two mating types suggests that the specificity for the interactions with the two pheromone receptors may involve different residues of the Scg1 carboxyl terminus. Mutations leading to constitutive activation of the pathway were recessive, whereas mutations that result in decreased pheromone response and mating were partially dominant. These relationships are consistent with the model for the mechanism of action of the G protein subunits in the pheromone response pathway and indicate the importance of the stoichiometry of components of this system.
Mutations in the guanine nucleotide-binding domains of a yeast G alpha protein confer a constitutive or uninducible state to the pheromone response pathway.
Authors: Kurjan J , Hirsch J P , Dietzel C
Published: June 2007

Several domains of guanine nucleotide-binding proteins are conserved and form the guanine nucleotide-binding pocket. Mutations in these domains in EF-Tu, ras, and Gas have been shown to result in informative phenotypes. We made several analogous changes in SCG1, which encodes the alpha subunit of the G protein involved in pheromone response in yeast. The scg1Lys388 and scg1Ala391 mutations resulted in severe growth and cell morphology defects; this phenotype is similar to the null phenotype and results from constitutive activation of the pheromone response pathway. On the basis of the model for the action of the yeast G protein, the effect of these mutations is consistent with the effect of analogous mutations in ras, which result in a transforming phenotype. The SCG1Ala322 mutation resulted in pheromone response and mating defects. This effect is similar to the effect of the analogous G alpha s mutation, which results in a defect in stimulation of adenylate cyclase. The scg1Val50 mutation, which is analogous to the transforming mutation rasVal12, resulted in multiple effects, including defects in growth, cell morphology, and mating. Some of our results and interpretations are different from previously published results of others for the same mutation in SCG1; specifically, our gene replacement of this mutation resulted in high basal activation of the pheromone response pathway, consistent with a GTPase defect, which was not seen previously with scg1Val50 on a low-copy plasmid. Implications of these phenotypes are discussed.
The yeast MCK1 gene encodes a protein kinase homolog that activates early meiotic gene expression.
Authors: Neigeborn L , Mitchell A P
Published: June 2007

We have identified a yeast gene, MCK1, that encodes a positive regulator of meiosis and spore formation. Sequence analysis revealed that MCK1 encodes a protein kinase homolog identical to YPK1, a phosphotyrosyl protein with demonstrated protein kinase activity. Increased MCK1 gene dosage accelerates the sporulation program; mck1 mutations cause delayed and decreased levels of sporulation. MCK1 is required during sporulation for maximal transcript accumulation from IME1, which encodes a meiotic activator. MCK1 is required in vegetative cells for basal IME1 expression, as evidenced by functional assays of an ime1-HIS3 fusion gene. MCK1 is also required for efficient ascus maturation. Although expression of IME1 from the GAL1 promoter restored high-level sporulation to mck1 mutants, it did not correct the ascus-maturation defect. This observation indicates that MCK1 is required, independently, for both the activation of IME1 and subsequent ascus maturation. Expression of an mck1-lacZ fusion gene was not regulated by the signals that govern meiosis. This observation is consistent with evidence that MCK1 plays a role in governing centromere function during vegetative growth as well as sporulation.
Glass encodes a site-specific DNA-binding protein that is regulated in response to positional signals in the developing Drosophila eye.
Authors: Moses K , Rubin G M
Published: June 2007

The glass gene encodes a zinc finger protein required for normal photoreceptor cell development in Drosophila. We show that glass transcripts are present in the third-instar eye-imaginal disc starting in the morphogenetic furrow and extending to the posterior margin of the disc; glass protein is detected in the nuclei of all cells in this region. We also show that glass encodes a site-specific DNA-binding protein. A 27-bp glass-binding site can confer glass-dependent expression on a reporter gene in developing photoreceptor cells, the particular subset of glass-expressing cells known to require glass function. This specificity may represent a regulation of glass protein activity after cells are recruited to the photoreceptor cell fate.
RAP1 protein activates and silences transcription of mating-type genes in yeast.
Authors: Kurtz S , Shore D
Published: June 2007

RAP1 is a sequence-specific DNA-binding protein essential for cell growth. The occurrence of RAP1-binding sites in many promoter regions, the mating-type gene silencer elements, and telomeres suggests that RAP1 has multiple functions in the cell. To assess its role in transcription, temperature-sensitive mutations in RAP1 were generated. Analysis of rap1ts strains provides evidence that RAP1 functions in both transcriptional activation and silencing of mating-type genes. Several observations indicate that rap1ts strains are defective in the expression of MAT alpha, whose upstream activation sequence (UAS) contains a RAP1-binding site. At nonpermissive temperatures, decreases in MAT alpha steady-state transcript levels can be detected in MAT alpha rap1ts strains. Furthermore, these strains are deficient in alpha-pheromone production and simultaneously express at least two alpha-specific genes. These phenotypes can be reversed by replacing the RAP1-binding site at MAT alpha with a binding site for the GAL4 transcriptional activator. Certain rap1ts alleles have an opposite effect on the silent mating-type locus HMR, which becomes partially derepressed at nonpermissive temperatures.
The Drosophila FGF-R homolog is expressed in the embryonic tracheal system and appears to be required for directed tracheal cell extension.
Authors: Glazer L , Shilo B Z
Published: June 2007

The Drosophila homolog of the vertebrate fibroblast growth factor receptor (FGF-R) was isolated by low-stringency hybridization. In contrast to the diversity of this subclass of receptor tyrosine kinases in vertebrates, the Drosophila genome appears to encode only a single homolog. Nucleotide sequence analysis demonstrates that the Drosophila FGF-R homolog (DFGF-R) protein has a conserved sequence, size, and organization. The extracellular region encodes three immunoglobulin-like domains, and the cytoplasmic kinase domain exhibits a high degree of similarity to the vertebrate FGF-Rs with the typical split kinase and comparably sized juxtamembrane and carboxy-terminal regions. The DFGF-R was mapped to position 70C on the third chromosome, and two overlapping chromosomal deficiencies that remove the gene were identified. Developmental Northern blots show that the gene has a single transcript of 4.3 kb and is expressed at all stages of development. Localization of the transcript and protein in embryos has shown that the gene is predominantly expressed in a restricted set of tissues: the developing tracheal system and the delaminating midline glial and neural cells. In embryos homozygous for a deletion of several genes including the DFGF-R locus, the initial formation of the tracheal pits is not affected. However, the extension of tracheal cell processes leading to the formation of the elaborate tree structure is blocked. The DFGF-R protein may thus participate in receiving spatial cues that guide tracheal cell outgrowth.
Secondary structure of the homeo domain of yeast alpha 2 repressor determined by NMR spectroscopy.
Authors: Phillips C L , Vershon A K , Johnson A D , Dahlquist F W
Published: June 2007

The yeast alpha 2 protein is a regulator of cell type in Saccharomyces cerevisiae. It represses transcription of a set of target genes by binding to an operator located upstream of each of these genes. The alpha 2 protein shares weak sequence similarity with members of the homeo domain family; the homeo domain is a 60-amino-acid segment found in many eukaryotic transcriptional regulators. In this paper we address the question of whether alpha 2 is structurally related to prototypical members of the homeo domain family. We used solution 1H and 15N nuclear magnetic resonance [NMR] spectroscopy to determine the secondary structure of an 83-amino-acid residue fragment of alpha 2 that contains the homeo domain homology. We have obtained resonance assignments for the backbone protons and nitrogens of the entire 60-residue region of the putative homeo domain and for most of the remainder of the alpha 2 fragment. The secondary structure was determined by using NOE connectivities between backbone protons, 3JHN-H alpha coupling constants, and dynamical information from the hydrogen exchange kinetics of the backbone amides. Three helical segments exist in the alpha 2 fragment consisting of residues 11-23, 32-42, and 46-60 (corresponding to residues 138-150, 159-169, and 173-187 of the intact protein). The positions of these three helices correspond extremely well to those of the Drosophila Antennapedia (Antp) and engrailed (en) homeo domains, whose three-dimensional structures have recently been determined by NMR spectroscopy and X-ray crystallography, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)
Suppressors of a U4 snRNA mutation define a novel U6 snRNP protein with RNA-binding motifs.
Authors: Shannon K W , Guthrie C
Published: June 2007

U4 and U6 small nuclear RNAs are associated by an extensive base-pairing interaction that must be disrupted and reformed with each round of splicing. U4 mutations within the U4/U6 interaction domain destabilize the complex in vitro and cause a cold-sensitive phenotype in vivo. Restabilization of the U4/U6 helix by dominant (gain-of-function), compensatory mutations in U6 results in wild-type growth. Cold-insensitive growth can also be restored by two classes of recessive (loss-of-function) suppressors: (1) mutations in PRP24, which we show to be a U6-specific binding protein of the RNP-consensus family; and (2) mutations in U6, which lie outside the interaction domain and identify putative PRP24-binding sites. Destabilization of the U4/U6 helix causes the accumulation of a PRP24/U4/U6 complex, which is undetectable in wild-type cells. The loss-of-function suppressor mutations inhibit the binding of PRP24 to U6, and thus presumably promote the release of PRP24 from the PRP24/U4/U6 complex and the reformation of the base-paired U4/U6 snRNP. We propose that the PRP24/U4/U6 complex is normally a highly transient intermediate in the spliceosome cycle and that PRP24 promotes the reannealing of U6 with U4.
Dominant and recessive mutations define functional domains of Toll, a transmembrane protein required for dorsal-ventral polarity in the Drosophila embryo.
Authors: Schneider D S , Hudson K L , Lin T Y , Anderson K V
Published: June 2007

The asymmetry of the dorsal-ventral pattern of the Drosophila embryo appears to depend on the ventral activation of the transmembrane Toll protein. The Toll protein is found around the entire dorsal-ventral circumference of the embryo, and it appears to act as a receptor for a ventral, extracellular signal and to then relay that signal to the cytoplasm in ventral regions of the embryo. Three of five recessive loss-of-function alleles of Toll are caused by point mutations in the region of the cytoplasmic domain of Toll that is similar to the mammalian interleukin-1 receptor, supporting the hypothesis that Toll acts as a signal-transducing receptor. Nine dominant gain-of-function alleles that cause Toll to be active in dorsal, as well as ventral, regions of the embryo are caused by mutations in the extracellular domain. Three of the dominant alleles appear to cause the protein to be constitutively active and are caused by cysteine-to-tyrosine changes immediately outside the transmembrane domain. All six of the remaining dominant alleles require the presence of a wild-type transmembrane Toll protein for their ventralizing effect and all encode truncated proteins that lack the transmembrane and cytoplasmic domains.
LEF-1, a gene encoding a lymphoid-specific protein with an HMG domain, regulates T-cell receptor alpha enhancer function [corrected]
Authors: Travis A , Amsterdam A , Belanger C , Grosschedl R
Published: June 2007

Lymphoid-specific cDNA clones were isolated that encode a nuclear protein with homology to the chromosomal nonhistone protein HMG-1 and to putative regulators of cell specialization, including the mammalian testis-determining factor SRY and fungal mating-type proteins. The gene represented by the isolated cDNA clones, termed LEF-1 (lymphoid enhancer-binding factor 1), is developmentally regulated and expressed in pre-B and T lymphocytes but not in later-stage B cells or nonlymphoid tissues. Both endogenous and recombinant LEF-1 were shown to bind to a functionally important site in the T-cell antigen receptor (TCR) alpha enhancer. Maximal TCR alpha enhancer activity was found to parallel the cell type-specific expression pattern of LEF-1. Moreover, forced expression of recombinant LEF-1 in late stage B cells increases TCR alpha enhancer function. Taken together, these data suggest that LEF-1 is a regulatory participant in lymphocyte gene expression and differentiation.
The Neurospora mitochondrial tyrosyl-tRNA synthetase is sufficient for group I intron splicing in vitro and uses the carboxy-terminal tRNA-binding domain along with other regions.
Authors: Kittle J D , Mohr G , Gianelos J A , Wang H , Lambowitz A M
Published: June 2007

Neurospora mitochondrial tyrosyl-tRNA synthetase (mt tyrRS), which is encoded by nuclear gene cyt-18, functions in splicing of group I introns in mitochondria. Here, we overproduced functional cyt-18 protein in Escherichia coli and purified it to near homogeneity. The purified protein has splicing and tyrRS activities similar to those of cyt-18 protein isolated from mitochondria and is by itself sufficient to splice the mitochondrial large rRNA intron in vitro. Structure-function relationships in the cyt-18 protein were analyzed by in vitro mutagenesis. We confirmed that a small amino-terminal domain not found in bacterial tyrRSs is required for splicing activity, but not tyrRS activity. Two linker insertion mutations, which disrupt the predicted ATP-binding site, completely inhibit tyrRS activity but leave substantial splicing activity. Finally, deletions or linker insertion mutations in the putative carboxy-terminal tRNA-binding domain inhibit both tyrRS and splicing activities, although some have differential effects on the two activities. Our results show that the normal catalytic activity of the cyt-18 protein is not required for splicing and are consistent with the hypothesis that the protein functions by binding to the precursor RNA and facilitating formation of the correct RNA structure. Regions required for splicing are distributed throughout the cyt-18 protein and overlap, but are not identical to, regions required for tyrRS activity. The finding that the putative carboxy-terminal tRNA-binding domain is required for both tyrRS and splicing activities suggests that the mechanism for binding the intron has similarities to the mechanism for binding tRNA(Tyr).
mRNA-type introns in U6 small nuclear RNA genes: implications for the catalysis in pre-mRNA splicing.
Authors: Tani T , Ohshima Y
Published: June 2007

U6 small nuclear RNA is one of the spliceosomal RNAs involved in pre-mRNA splicing. In the fission yeast Schizosaccharomyces pombe, the U6 RNA gene was found to have an intron similar to a nuclear pre-mRNA intron, and it was proposed that the U6 intron might be inserted erroneously during pre-mRNA splicing. Using the polymerase chain reaction, we analyzed the U6 RNA genes of 52 organisms. In addition to the five species of Schizosaccharomyces, we found that the yeast species Rhodotorula hasegawae and Rhodosporidium dacryoidum also have mRNA-type introns in their U6 genes; however, in all the other organisms tested, we found no intron within the region of the U6 gene examined. Four introns and one intron are present in the R. hasegawae and R. dacryoidum U6 genes, respectively; and these introns are located at sites differing from the location of the Schizosaccharomyces U6 intron. Most of the U6 introns locate within the conserved domain, which is strikingly similar in structure to the catalytic center of the negative strand of the satellite RNA of tobacco ring spot virus. The introns of the S. pombe and R. dacryoidum U6 genes are located immediately adjacent to the nucleotides that were shown to be essential for the second step of the splicing reaction. These results support the notion that U6 RNA has a catalytic role in pre-mRNA splicing and that U6 introns originated from insertion of an excised intron during pre-mRNA splicing.
The leucine zipper of TFE3 dictates helix-loop-helix dimerization specificity.
Authors: Beckmann H , Kadesch T
Published: June 2007

TFE3 is a DNA-binding protein that activates transcription through the muE3 site of the immunoglobulin heavy-chain enhancer. Its amino acid sequence reveals two putative protein dimerization motifs: a helix-loop-helix (HLH) and an adjacent leucine zipper. We show here that both of these motifs are necessary for TFE3 to homodimerize and to bind DNA in vitro. Using a dominant negative TFE3 mutant, we also demonstrate that both the HLH and the leucine zipper motifs are necessary and sufficient for protein-protein interactions in vivo. TFE3 is unable to form stable heterodimers with a variety of other HLH proteins, including USF, a protein that is structurally similar to TFE3 and binds a common DNA sequence. The analysis of "zipper swap" proteins in which the TFE3 HLH was fused to the leucine zipper region of USF indicates that dimerization specificity is mediated entirely by the identity of the leucine zipper and its position relative to the HLH. Hence, in this "b-HLH-zip" class of proteins, the leucine zipper functions in concert with the HLH both to stabilize protein-protein interactions and to establish dimerization specificity.
Ectopic expression of the H19 gene in mice causes prenatal lethality.
Authors: Brunkow M E , Tilghman S M
Published: June 2007

The mouse H19 gene is expressed in a broad array of tissues of both endoderm and mesoderm origin in the developing mouse embryo. Its expression is repressed in all tissues except skeletal muscle shortly after birth. This gene is unusual in that it may not encode a protein, despite its conservation in mammals. The RNA product is found as a spliced and polyadenylated RNA in a cytoplasmic particle. To probe whether this unusual gene is functional, excess copies were introduced into mouse zygotes. Transgenic progeny were obtained at a very low frequency, but in no instance was the transgene expressed. That the gene itself was deleterious to embryos was established by introducing into zygotes a mutant of the structural gene in which its most conserved segment was deleted. Transgenic founders were obtained at a higher frequency, and these expressed the altered transgene at high rates in a subset of the tissues that express the endogenous H19 gene. The lethal effects are manifested late in gestation, between day 14 and birth.
Regulation of achaete-scute gene expression and sensory organ pattern formation in the Drosophila wing.
Authors: Skeath J B , Carroll S B
Published: June 2007

Adult Drosophila possess a large number of sensory organs, including large and small bristles and other types of sensilla, each arising from a single mother cell at particular positions in a reproducible pattern. Genetic studies have shown that sensory organ pattern formation is partly coordinated by a number of structurally similar, potential heterodimer-forming, helix-loop-helix (HLH) regulatory proteins. Here, by localizing regulatory gene expression during the development of normal and mutant imaginal discs, we show that two positive regulators of sensory neurogenesis, the proneural achaete and scute proteins, initially trans-activate each other and are transiently expressed in identical patterns, including clusters of wing ectodermal cells and the individual sensory mother cells that arise from them. Two negative regulators, hairy and extramacrochaete, suppress sensory neurogenesis by selectively repressing achaete and scute gene expression, respectively, but in different spatial domains and at different developmental stages. Surprisingly, we also find that the level of achaete-scute activity influences the level of hairy expression, thereby providing feedback control upon achaete-scute activity and sensory organ formation. Some or all of these interactions may involve specific dimerization reactions between different combinations of HLH proteins.
Proneural clusters of achaete-scute expression and the generation of sensory organs in the Drosophila imaginal wing disc.
Authors: Cubas P , de Celis J F , Campuzano S , Modolell J
Published: June 2007

The proneural genes achaete (ac) and scute (sc) confer to Drosophila epidermal cells the ability to become sensory mother cells (SMCs). In imaginal discs, ac-sc are expressed in groups of cells, the proneural clusters, which are thought to delimit the areas where SMCs arise. We have visualized with the resolution of single cells the initial stages of sensory organ development by following the evolving pattern of proneural clusters and the emergence of SMCs. At reproducible positions within clusters, a small number of cells accumulate increased amounts of ac-sc protein. Subsequently, one of these cells, the SMC, accumulates the highest amount. Later, at least some SMCs become surrounded by cells with reduced ac-sc expression, a phenomenon probably related to lateral inhibition. Genetic mosaic analyses of cells with different doses of ac-sc genes, the sc expression in sc mutants, and the above findings show that the levels of ac-sc products are most important for SMC singling-out and SMC state maintenance. These products do not intervene in the differentiation of SMC descendants. The extramacrochaetae gene, an antagonist of proneural genes, negatively regulates sc expression, probably by interfering with activators of this gene.
Xenopus embryos contain a somite-specific, MyoD-like protein that binds to a promoter site required for muscle actin expression.
Authors: Taylor M V , Gurdon J B , Hopwood N D , Towers N , Mohun T J
Published: June 2007

We identify the "M region" of the muscle-specific Xenopus cardiac actin gene promoter from -282 to -348 as necessary for the embryonic expression of a cardiac actin-beta-globin reporter gene injected into fertilized eggs. Four DNA-binding activities in embryo extracts, embryonic M-region factors 1-4 (EMF1-4), are described that interact specifically with this region. One of these, EMF1, is detected in extracts from microdissected somites, which differentiate into muscle, but not in extracts from the adjacent neurectoderm, which differentiates into a variety of other cell types. Moreover, EMF1 is detected in embryo animal caps induced to form mesoderm, which includes muscle, and in which the cardiac actin gene is activated, but not in uninduced animal caps. EMF1 is also first detectable when cardiac actin transcripts begin to accumulate; therefore, both its temporal and spatial distributions during Xenopus development are consistent with a role in activating cardiac actin expression. Two lines of evidence suggest that EMF1 contains the myogenic factor Xenopus MyoD (XMyoD): (1) XMyoD synthesized in vitro can bind specifically to the same site as EMF1; and (2) antibodies raised against XMyoD bind to EMF1. DNA-binding studies indicate that EMF1 may be a complex between XMyoD and proteins found in muscle and other tissues. Our results suggest that the myogenic factor XMyoD, as a component of somite EMF1, regulates the activation of the cardiac actin gene in developing embryonic muscle by binding directly to a necessary region of the promoter.
A novel mechanism regulating growth factor association with the cell surface: identification of a PDGF retention domain.
Authors: LaRochelle W J , May-Siroff M , Robbins K C , Aaronson S A
Published: June 2007

Platelet-derived growth factor (PDGF) chimeras were used to map a domain responsible for either efficient secretion of PDGF-A or the tight cell association of PDGF-B to their carboxy-terminal domains. Introduction of stop codons within PDGF-A or PDGF-B further dissected their respective carboxy-terminal domains. Although successive deletions of the PDGF-A carboxyl terminus did not impair its secretion, incremental deletions from the carboxyl terminus of PDGF-B abrogated its membrane retention properties and promoted secretion. By this approach, PDGF-B retention properties could be localized to PDGF-B residues 212-226. A processed form of PDGF-B, which contained this domain, was expressed at the cell surface but not released. Comparison of PDGF-B with PDGF-A revealed an analogous sequence located at the PDGF-A carboxyl terminus. We demonstrated that this PDGF-A domain also acts as a retention sequence under conditions that inhibit its proteolytic cleavage. Thus, differences in PDGF-A and PDGF-B secretion relate to differential proteolytic processing of analogous retention domains. All of these findings establish a new mechanism for stable growth factor presentation at the cell surface.
POU-domain proteins Pit-1 and Oct-1 interact to form a heteromeric complex and can cooperate to induce expression of the prolactin promoter.
Authors: Voss J W , Wilson L , Rosenfeld M G
Published: June 2007

Two members of the POU-domain family of transcriptional activators, Pit-1 and Oct-1, are coexpressed in cells of the anterior pituitary gland. We demonstrate that the pituitary-specific developmental regulator Pit-1 can bind as a heterodimer with the widely expressed 100-kD Oct-1 protein to critical tissue-specific cis-active elements in the rat prolactin gene. Pit-1 and Oct-1 can also associate, in the absence of DNA, via their POU domains. Coexpression of Pit-1 and Oct-1 in a heterologous cell type results in reproducible 2- to 2.5-fold synergistic transcriptional effects on genes under control of the native prolactin promoter or of a single Pit-1 response element. These results suggest that a combinatorial pattern of heterodimeric and homodimeric interactions between different members of the POU-domain gene family can result when members of this large family are coexpressed in cells of developing and established organ systems, potentially regulating differential developmental gene activation.
Expression of the Wilms' tumor gene WT1 in the murine urogenital system.
Authors: Pelletier J , Schalling M , Buckler A J , Rogers A , Haber D A , Housman D
Published: June 2007

The Wilms' tumor gene WT1 is a recessive oncogene that encodes a putative transcription factor implicated in nephrogenesis during kidney development. In this report we analyze expression of WT1 in the murine urogenital system. WT1 is expressed in non-germ-cell components of the testis and ovaries in both young and adult mice. In situ mRNA hybridization studies demonstrate that WT1 is expressed in the granulosa and epithelial cells of ovaries, the Sertoli cells of the testis, and in the uterine wall. In addition to the 3.1-kb WT1 transcript detected by Northern blotting of RNA from kidney, uterus, and gonads, there is an approximately 2.5-kb WT1-related mRNA species in testis. The levels of WT1 mRNA in the gonads are among the highest observed, surpassing amounts detected in the embryonic kidney. During development, these levels are differentially regulated, depending on the sexual differentiation of the gonad. Expression of WT1 mRNA in the female reproductive system does not fluctuate significantly from days 4 to 40 postpartum. In contrast, WT1 mRNA levels in the tesis increase steadily after birth, reaching their highest expression levels at day 8 postpartum and decreasing slightly as the animal matures. Expression of WT1 in the gonads is detectable as early as 12.5 days postcoitum (p.c.). As an initial step toward exploring the tissue-specific expression of WT1, DNA elements upstream of WT1 were cloned and sequenced. Three putative transcription initiation sites, utilized in testis, ovaries, and uterus, were mapped by S1 nuclease protection assays. The sequences surrounding these sites have a high G + C content, and typical upstream CCAAT and TATAA boxes are not present. These studies allowed us to identify the translation initiation site for WT1 protein synthesis. We have also used an epitope-tagging protocol to demonstrate that WT1 is a nuclear protein, consistent with its role as a transcription factor. Our results demonstrate regulation of WT1 expression during development of the gonads, implicate WT1 in genitourinary development, and provide a molecular framework toward understanding genitourinary defects observed among hereditary cases of Wilms' tumor.
Helix-loop-helix transcription factor E47 activates germ-line immunoglobulin heavy-chain gene transcription and rearrangement in a pre-T-cell line.
Authors: Schlissel M , Voronova A , Baltimore D
Published: June 2007

E47 is a helix-loop-helix transcription factor that binds to sites in the immunoglobulin heavy-chain and kappa light-chain gene enhancers. Other proteins of this type are involved in cell-type determination. A possible role for E47 in B-cell development was tested by overexpressing a cDNA encoding E47 in the pre-T-cell line 2017. We found a dramatic activation of a germ-line heavy-chain gene transcript in these stable transfectants and an equally large induction of immunoglobulin D-to-J rearrangement, the first recognized step in B-cell development. Germ-line kappa light-chain gene transcription and rearrangement were unaffected, but transcription of the recombination-activating genes RAG-1 and RAG-2 and the lymphoid-specific transcription factor Oct-2 was increased. These T cells did not transcribe their rearranged DJ alleles, however, and failed to progress to the next stage of heavy-chain gene assembly, V-to-DJ rearrangement. Because transcription factor E47 can induce pre-T cells to carry out events of B-cell differentiation, it may be a crucial determinant of the earliest stages of B-cell development.
Immunoaffinity purification of a [U4/U6.U5] tri-snRNP from human cells.
Authors: Behrens S E , Lührmann R
Published: June 2007

We describe the isolation and biochemical characterization of [U4/U6.U5] tri-snRNP complexes from HeLa cells under nondenaturing conditions using a monoclonal antibody reacting with the U5-specific 100-kD protein. We show that the [U4/U6.U5] complex contains five previously unobserved proteins with molecular masses of 90, 60, 27, 20, and 15.5 kD, in addition to the core proteins, common to the U4/U6, U5, U1, and U2 snRNPs, and the U5-specific proteins, as found in 20S U5 snRNPs. With approximately 20 distinct snRNP proteins the complexity of the [U4/U6.U5] tri-snRNP is surprising. One or more of the five proteins found exclusively in the 25S [U4/U6.U5] tri-snRNP appears to be involved in the assembly of the tri-snRNP complex, as, in an in vitro reconstitution assay, purified 20S U5 and 10S U4/U6 snRNPs formed stable 25S [U4/U6.U5] complexes only in the presence of the free tri-snRNP-specific proteins. The formation of the [U4/U6.U5] complex in vitro does not require ATP, and the stability of the purified tri-snRNP complex is not affected by ATP to a measurable extent. However, the native [U4/U6.U5] displays a kinase activity that is absent in isolated U5: A 52-kD protein present in both U5 and [U4/U6.U5] is phosphorylated only in the latter. The function of this phosphorylation is unclear thus far; it may be involved in the activation of [U4/U6.U5] in the spliceosome.
Mammalian achaete-scute homolog 1 is transiently expressed by spatially restricted subsets of early neuroepithelial and neural crest cells.
Authors: Lo L C , Johnson J E , Wuenschell C W , Saito T , Anderson D J
Published: June 2007

Using monoclonal antibodies, we have examined the expression pattern of MASH1, a basic helix-loop-helix protein that is a mammalian homolog of the Drosophila achaete-scute proteins. In Drosophila, achaete-scute genes are required for the determination of a subset of neurons. In the rat embryo, MASH1 expression is confined to subpopulations of neural precursor cells. The induction of MASH1 precedes, but is extinguished upon, overt neuronal differentiation. MASH1 is expressed in the forebrain by spatially restricted domains of neuroepithelium and in the peripheral nervous system exclusively by precursors of sympathetic and enteric neurons. The features of early and transient expression, in spatially restricted subpopulations of neural precursors, are similar to those observed for achaete-scute. Thus, the amino acid sequence conservation between MASH1 and achaete-scute is reflected in a parallel conservation of cell type specificity of expression, similar to the case of mammalian MyoD and Drosophila nautilus. These data support the idea that helix-loop-helix proteins may represent an evolutionarily conserved family of cell-type determination genes, of which MASH1 is the first neural-specific member identified in vertebrates.
Multiple processing-defective mutations in a mammalian histone pre-mRNA are suppressed by compensatory changes in U7 RNA both in vivo and in vitro.
Authors: Bond U M , Yario T A , Steitz J A
Published: June 2007

To study the role of base-pairing between the mammalian U7 snRNA and the highly variable histone downstream element (HDE) during the 3'-end maturation of mammalian histone pre-mRNAs, we mutated the HDE of the mouse H2A-614 gene and assayed processing in HeLa cells both in vivo and in vitro. Either a 9-nucleotide deletion or a block substitution of pyrimidines for 6 purines within the HDE abolished all 3'-end processing. Compensatory changes were introduced into a synthetic human U7 gene, whose transcripts assemble into Sm snRNPs in vivo. Suppression of the 6-purine substitution as well as a 3-purine substitution within the HDE was obtained in vivo by coexpressing the corresponding U7 suppressor RNAs and in vitro by using nuclear extracts prepared from HeLa cells containing U7 suppressor genes. Our results not only provide genetic evidence for base-pairing between the U7 snRNP and the HDE of mammalian histone pre-mRNAs but reveal an unexpected tolerance to drastic changes in the nature of the base-paired region.
The chicken limb deformity gene encodes nuclear proteins expressed in specific cell types during morphogenesis.
Authors: Trumpp A , Blundell P A , de la Pompa J L , Zeller R
Published: June 2007

The chicken limb deformity (ld) mutation affects morphogenesis of both limbs and kidneys and is one of few murine mutations for which the affected gene has been isolated. Analysis of the chicken homolog reveals evolutionary conservation of large parts of the encoded ld gene products. This is the first study of these proteins, their intracellular localization, and their temporal and spatial distribution during embryogenesis. A major 180-kD protein is expressed in chicken embryos and certain adult tissues. The proteins are localized in the nuclei of different embryonic cell types in a characteristic punctate pattern. In the developing chicken limb bud, they are expressed in the newly differentiated apical ectodermal ridge and the mesenchymal compartment, where an unequal distribution along the anteroposterior and, subsequently, the dorsoventral axes, is observed. During kidney morphogenesis, expression is initially restricted to the epithelial compartment of the pronephros and mesonephros. These results correlate well with the previous analysis of the murine ld phenotype and imply determinative roles for ld gene products during the morphogenesis of limbs and kidneys. Unexpected expression in the notochord, floor plate, and ventral horns suggests an involvement of the ld gene products in establishment of the dorsoventral polarity of the neural tube.
Dual Bar homeo box genes of Drosophila required in two photoreceptor cells, R1 and R6, and primary pigment cells for normal eye development.
Authors: Higashijima S , Kojima T , Michiue T , Ishimaru S , Emori Y , Saigo K
Published: June 2007

In the Bar mutation of Drosophila, ommatidial differentiation is known to be suppressed in the anterior portion of the eye. Our structural analysis shows that the Bar region contains a pair of homeo box genes, BarH1 and BarH2. These genes encode polypeptides similar in size and sequence and share a common homeo domain that is identical in sequence except for putative trans-activator-binding sites. We also show, by mosaic analysis and immunostaining with anti-BarH1/BarH2 antibodies, that BarH1 and BarH2 are not only specifically coexpressed but also functionally required in R1/R6 prephotoreceptors and primary pigment cells in developing ommatidia. In R1/R6, the expression of BarH1 and BarH2 appears to be regulated by rough and glass gene products. BarH1 and BarH2 proteins are essential to normal lens formation, formation of three types of pigment cells, and elimination of excess cells from mature ommatidia. Taken together, our results suggest that Bar homeo domain proteins may play key roles in the fate-determination processes of pigment cells and cone cells.
Interleukin-7 induces N-myc and c-myc expression in normal precursor B lymphocytes.
Authors: Morrow M A , Lee G , Gillis S , Yancopoulos G D , Alt F W
Published: June 2007

Expression of both N-myc and c-myc is induced rapidly and dramatically in normal pre-B cells after stimulation with interleukin-7 (IL-7), a pre-B cell-specific growth factor. These IL-7-induced increases in N-myc and c-myc expression are mediated at the transcriptional level; for N-myc, a major portion of the induction results from release of an attenuation block between exons 1 and 2. Although c-myc expression has been shown to be regulated by many factors, these studies provide the first demonstration of N-myc regulation by a growth factor. Furthermore, mitogen-induced proliferation of more mature B-lineage cells is accompanied by induction of c-myc expression in the complete absence of N-myc expression. Thus, N-myc expression in normal B-lineage cells, as in transformed cells, is limited to cells that represent the precursor stages of this differentiation pathway. Together, these findings imply a specific function for N-myc in the early stages of B-cell development.
Yeast site-specific ribonucleoprotein endoribonuclease MRP contains an RNA component homologous to mammalian RNase MRP RNA and essential for cell viability.
Authors: Schmitt M E , Clayton D A
Published: June 2007

RNase MRP is a site-specific ribonucleoprotein endoribonuclease that cleaves RNA sequence complementary to mammalian mitochondrial origins of replication in a manner consistent with a role in primer RNA metabolism. The same activity in the yeast Saccharomyces cerevisiae has recently been identified; it cleaves an RNA substrate complementary to a yeast mitochondrial origin of replication at an exact site of linkage of RNA to DNA. We have purified this yeast enzyme further and detect a single, novel RNA of 340 nucleotides associated with the enzymatic activity. The single-copy nuclear gene for this RNA was sequenced and mapped to the right arm of chromosome XIV. The identity of the clone, as encoding the RNA copurifying with enzymatic activity, was confirmed by a match to the directly determined sequence of the RNA. The gene sequence also identified a 340-nucleotide RNA in total yeast RNA and in purified RNase MRP enzyme preparations. Inspection of the sequence of the yeast RNA revealed homologies to the RNA component of mouse RNase MRP, 49% overall with specific regions of much greater similarity. The flanking regions of the gene showed characteristics of an RNA polymerase II transcription unit, including a TATAAA box and a 7/8 match to the yeast cell cycle box UAS. The RNase MRP RNA gene was deleted by insertional replacement and found to be essential for cellular viability, indicating a critical nuclear role for RNase MRP.
Escherichia coli single-stranded DNA-binding protein is a supercoiled template-dependent transcriptional activator of N4 virion RNA polymerase.
Authors: Markiewicz P , Malone C , Chase J W , Rothman-Denes L B
Published: June 2007

Coliphage N4 is a double-stranded DNA virus that requires the sequential activity of three different RNA polymerases during infection. The N4 virion RNA polymerase, which is carried in the virion and is injected with the DNA at the start of infection, is responsible for the synthesis of N4 early RNAs. In vitro, the virion RNA polymerase can transcribe double-stranded N4 DNA accurately and efficiently but only when the DNA is denatured. We have shown previously that the activity of DNA gyrase is required for in vivo early N4 transcription. We report here that Escherichia coli single-stranded DNA-binding protein (SSB) is also required for N4 early transcription. In vitro, linear or relaxed templates cannot be activated by SSB; however, supercoiled template and SSB allow the virion polymerase to recognize its promoters on duplex DNA and activate transcription. The effects of supercoiling are limited to transcript initiation and are not required for transcript elongation. The activation is specific for SSB; no other single-stranded DNA-binding proteins can substitute. Therefore, SSB is one of a small number of proteins that function to stimulate both replication and transcription. The basis for the specificity of SSB, the mechanism of transcriptional activation by SSB and template supercoiling, and their role in the N4 transcriptional program during development are discussed.
Fission yeast genes involved in coupling mitosis to completion of DNA replication.
Authors: Enoch T , Carr A M , Nurse P
Published: June 2007

We have isolated fission yeast mutants that enter mitosis when DNA replication is blocked with hydroxyurea. The mutants define eight linkage groups, three of which consist of alleles of the rad1, rad3, and rad17 genes. Recently, these fission yeast genes have been shown to be required for radiation-induced cell cycle arrest, as is the budding yeast RAD9 gene. The other five genes are called hus (hydroxyurea sensitive) 1-5. We propose that these genes participate in an intracellular signal transduction pathway that monitors the completion of DNA replication and transmits information to the mitotic control protein cdc2. Mutations that bypass the requirement for cdc25 (an activator of the mitotic regulator cdc2) also uncouple mitosis from DNA replication. However, mitosis is blocked by inhibitors of DNA replication in strains in which the cdc25 gene has been deleted, indicating that although cdc25 influences the coupling of mitosis to the completion of DNA replication, it is not essential for this control.
Mutations affecting stability and deadenylation of the yeast MFA2 transcript.
Authors: Muhlrad D , Parker R
Published: June 2007

Decay rates of individual mRNAs in the yeast Saccharomyces cerevisiae can vary by 10- to 20-fold. To determine the basis for the rapid degradation of the mRNA encoded by the yeast MFA2 gene we have used a genetic screen to isolate mutations that increase the stability of this transcript. Analysis of point mutations obtained from this screen, and of additional lesions constructed in vitro, indicated that the MFA2 3'-untranslated region (UTR) contains sequences that specify rapid mRNA decay. Moreover, the lesions that affected mRNA decay rate also affected the process of mRNA deadenylation. Mutations in one region of the 3' UTR both decreased the rate of poly(A) shortening and increased the stability of an intermediate form in the decay pathway with an oligo(A) tail (approximately 10 nucleotides). Mutations in a second region primarily increased the stability of the oligo(A) form. These results suggest that the decay of the MFA2 mRNA initiates with the shortening of the poly(A) tail and there are specific sequences within the 3' UTR that stimulate poly(A) tail shortening as well as subsequent steps in the decay pathway. Given the similarity of this decay pathway to that seen for some mammalian mRNAs, these results suggest that mRNA deadenylation may be a common mechanism of mRNA turnover.
An essential splicing factor, SLU7, mediates 3' splice site choice in yeast.
Authors: Frank D , Guthrie C
Published: June 2007

Recently, we have reported the identification of several genes that exhibit genetic interactions with the U5 snRNA. Two of these genes, SLU4 and SLU7 (SLU: synergistic lethal with U5 snRNA), encode products required for the second catalytic step of splicing. To analyze the specific roles of SLU4 and SLU7, we have determined how mutants influence the relative usage of competing 3' splice sites. We find that mutations in SLU7 eliminate the normal 20-fold preference for 3' splice sites located > 22 nucleotides downstream of the branchpoint. In contrast, mutations in SLU4 inhibit usage of all 3' splice sites, regardless of their location. This suggests that SLU7 is involved in the process of 3' splice site choice, whereas SLU4 fulfills a generic requirement for the second step. We show that SLU7 is an essential gene that contains a small motif with striking similarity to the cysteine-rich zinc knuckle of retroviral nucleocapsid proteins, which has been implicated in RNA binding. Mutational analysis of SLU7 indicates that this motif influences the efficiency, but not the sequence specificity, of 3' splice site selection. The identification of a component of the constitutive splicing machinery that can promote 3' splice site choice has potentially important implications for alternative splicing.