bluuebunny/crossref_metadata_2025 huggingface dataset:
Binding of the CBP2 protein to a yeast mitochondrial group I intron requires the catalytic core of the RNA.
Authors: Gampel A , Cech T R
Published: June 2007

The yeast CBP2 gene product is required for the splicing of the terminal intron (bI5) of the mitochondrial cytochrome b pre-mRNA in vivo. In vitro, bI5 RNA self-splices efficiently only at high MgCl2 concentrations (50 mM); at 5 mM MgCl2, efficient splicing requires purified CBP2 protein. To determine the sequences within bI5 recognized by the protein, we have constructed deletion and substitution mutants of the RNA. Their binding to CBP2 was assessed by their ability to inhibit protein-dependent splicing of the wild-type bI5 RNA. Several regions, including the large L1 and L8 loops, can be deleted without affecting binding. They can therefore be eliminated from consideration as critical recognition elements. In contrast, other changes prevent the RNA from binding CBP2 and also impair self-splicing. Thus, either the catalytic core contacts the protein directly, or the integrity of the core is required for proper display of other RNA sequences that bind the protein. The results are consistent with a model in which the CBP2 protein facilitates splicing by binding to and stabilizing the active structure of the RNA. However, a more specific model is proposed in which the protein specifically enhances Mg2+ binding required for catalysis.
The dorsal morphogen gradient regulates the mesoderm determinant twist in early Drosophila embryos.
Authors: Jiang J , Kosman D , Ip Y T , Levine M
Published: June 2007

A gradient of the maternal morphogen dorsal (dl) initiates the differentiation of various tissues along the dorsal-ventral axis of early Drosophila embryos. dl is a sequence-specific DNA-binding protein that is related to the mammalian regulatory factor NF-kappa B. Previous studies suggest that dl can function as a transcriptional repressor. To determine how dl functions as an activator we have examined the promoter of the mesoderm determinant gene twist (twi). Genetic studies suggest that peak levels of dl protein in ventral regions of early embryos initiate twi expression. Using a combination of promoter fusion-P-transformation assays, and in vitro DNA-binding assays coupled with site-directed mutagenesis, we establish a direct link between dl-binding sites and twi expression in the early embryo. We also present evidence that the dorsal-ventral limits of twi expression depend on the number and affinity of dl-binding sites present in its promoter. A comparison of twi with a second dl target gene, zen, suggests a correlation between the affinities of dl-binding sites and response to different thresholds of dl morphogen.
Cloning and characterization of two mouse heat shock factors with distinct inducible and constitutive DNA-binding ability.
Authors: Sarge K D , Zimarino V , Holm K , Wu C , Morimoto R I
Published: June 2007

We have cloned two distinct mouse heat shock transcription factor genes, mHSF1 and mHSF2. The mHSF1 and mHSF2 open reading frames are similar in size, containing 503 and 517 amino acids, respectively. Although mHSF1 and mHSF2 are quite divergent overall (only 38% identity), they display extensive homology in the DNA-binding and oligomerization domains that are conserved in the heat shock factors of Saccharomyces cerevisiae, Kluyveromyces lactis, Drosophila, tomato, and human. The ability of these two mouse heat shock factors to bind to the heat shock element (HSE) is regulated by heat. mHSF1 is expressed in an in vitro translation system in an inactive form that is activated to DNA binding by incubation at temperatures greater than 41 degrees C, the same temperatures that activate heat shock factor DNA binding and the stress response in mouse cells in vivo. mHSF2, on the other hand, is expressed in a form that binds DNA constitutively but loses DNA binding by incubation at greater than 41 degrees C. Both mHSF1 and mHSF2 are encoded by single-copy genes, and neither is transcriptionally regulated by heat shock. However, there is a striking difference in the levels of mHSF1 mRNA in different tissues of the mouse.
MAT alpha 1 can mediate gene activation by a-mating factor.
Authors: Sengupta P , Cochran B H
Published: June 2007

In the yeast Saccharomyces cerevisiae, expression of alpha-specific genes is governed by the MAT alpha 1 and MCM1 gene products. MAT alpha 1 and MCM1 bind cooperatively to PQ elements upstream of alpha-specific genes. The PQ element not only directs alpha-specific expression but can also direct gene induction in response to treatment with a-mating pheromone. We have used gene fusions to investigate whether induction conferred by the PQ box is mediated through either MAT alpha 1 or MCM1, or a combination of both. When MCM1 is fused to the DNA-binding domain of the bacterial repressor LexA, this fusion protein is capable of trans-activating a lacZ reporter gene driven by a LexA operator. However, the transcriptional activity of the MCM1-LexA fusion is not further enhanced by treatment of cells with a-factor. A MAT alpha 1-LexA fusion protein is also capable of trans-activation through a LexA operator. Moreover, the activity of the MAT alpha 1-LexA fusion protein can be further induced by treatment with a-factor. When progressive deletions are made from the amino terminus of MAT alpha 1 in the fusion protein, the basal level of trans-activation progressively decreases, but the inducibility of the fusion protein increases. MAT alpha 1-LexA fusion proteins, which have greater than or equal to 57 amino acids deleted from the amino terminus of MAT alpha 1 are not capable of trans-activation. In addition, the activity of the MAT alpha 1-LexA fusion protein is dependent on the functions of the STE7, STE11, and STE12 genes that encode components of the pheromone response pathway.
The mammalian TFIID protein is present in two functionally distinct complexes.
Authors: Timmers H T , Sharp P A
Published: June 2007

The TFIID activity recognizes a TATA-box element and supports formation of an initiation complex containing RNA polymerase II. Antisera specific for the 38-kD human TFIID protein were used to determine whether this protein cofractionated with the TFIID activity. Surprisingly, the TFIID activity in HeLa whole-cell extracts was resolved into two different size complexes, one of 300 kD and one of greater than 700 kD. Cofractionation studies suggest that both complexes contain the 38-kD protein; thus, this component of the large complexes is probably responsible for recognition of the TATA sequence and interaction with the other general transcription factors in formation of the initiation complex. Interestingly, in contrast to the TFIID activity characterized previously, the 300-kD form of TFIID activity, B-TFIID, does not support stimulation of transcription by factors containing acidic or glutamine-rich activating motifs. We propose that the functional and physical differences between these two forms of TFIID activity are caused by differences in the protein composition of the TFIID complexes of which the 38-kD hTFIID protein is an integral part.
Mutation of the AAUAAA polyadenylation signal depresses in vitro splicing of proximal but not distal introns.
Authors: Niwa M , Berget S M
Published: June 2007

To investigate the relationship between splicing and polyadenylation during the production of vertebrate mRNAs, we examined the effect of mutation of a poly(A) site on splicing of upstream introns. Mutation of the AAUAAA polyadenylation consensus sequence inhibited in vitro splicing of an upstream intron. The magnitude of the depression depended on the magnesium concentration. Dependence of splicing on polyadenylation signals suggests the existence of interaction between polyadenylation and splicing factors. In multi-intron precursor RNAs containing duplicated splice sites, mutation of the poly(A) site inhibited removal of the last intron, but not the removal of introns farther upstream. Inhibition of removal of only the last intron suggests segmental recognition of multi-exon precursor RNAs and is consistent with previous suggestions that signals at both ends of an exon are required for effective splicing of an upstream intron.
Alternative splicing of beta-tropomyosin pre-mRNA: cis-acting elements and cellular factors that block the use of a skeletal muscle exon in nonmuscle cells.
Authors: Guo W , Mulligan G J , Wormsley S , Helfman D M
Published: June 2007

The rat beta-tropomyosin (beta-TM) gene encodes both skeletal muscle beta-TM and fibroblast TM-1 by an alternative RNA-splicing mechanism. This gene contains 11 exons. Exons 1-5, 8, and 9 are common to all mRNAs expressed from the gene. Exons 6 and 11 are used in fibroblasts as well as smooth muscle cells, whereas exons 7 and 10 are used in skeletal muscle cells. In this study we have carried out an extensive mutational analysis to identify cis-acting elements that block the use of the skeletal muscle-specific exon 7 in nonmuscle cells. These studies localize the critical elements for regulated alternative splicing to sequences within exon 7 and the adjacent upstream intron. In addition, mutations that inactivate the 5'- or 3'-splice sites of exon 6 do not result in the use of the skeletal muscle-specific exon 7 in nonmuscle cells, suggesting that splice-site selection in vivo is not regulated by a simple cis-acting competition mechanism but, rather, by a mechanism that inhibits the use of exon 7 in certain cellular environments. In support of this hypothesis we have identified sequence-specific RNA-binding proteins in HeLa cell nuclear extracts using native gel electrophoresis and binding competition assays. Mutations in the pre-mRNA that result in the use of the skeletal muscle exon in vivo also disrupt the binding of these proteins to the RNA in vitro. We propose that the binding of these proteins to the pre-mRNA is involved in regulated alternative splicing and that this interaction is required for blocking the use of the skeletal muscle exon in nonmuscle cells.
The cap and poly(A) tail function synergistically to regulate mRNA translational efficiency.
Authors: Gallie D R
Published: June 2007

The cap structure and the poly(A) tail are important regulatory determinants in establishing the translational efficiency of a messenger RNA. Although the mechanism by which either determinant functions remains poorly characterized, the interaction between the poly(A) tail-poly(A)-binding protein complex and events occurring at the 5' terminus during translation initiation has been an intriguing possibility. In this report, the mutual dependence of the cap and the poly(A) tail was studied. Poly(A)+ and poly(A)- luciferase (Luc) mRNAs generated in vitro containing or lacking a cap were translated in vivo in tobacco protoplasts, Chinese hamster ovary cells, and yeast following delivery by electroporation. The poly(A) tail-mediated regulation of translational efficiency was wholly dependent on the cap for function. Moreover, cap function was enhanced over an order of magnitude by the presence of a poly(A) tail. The relative differences in stability between the mRNAs could not account for the synergism. The synergism between the cap and poly(A) tail was not observed in yeast cells in which active translation had been disrupted. In addition, the synergism was not observed in in vitro translation lysates. These data demonstrate that the cap and the poly(A) tail are interdependent for optimal function in vivo and suggest that communication between the two regulatory determinants may be important in establishing efficient translation.
Cellular localization and cell cycle regulation by a temperature-sensitive p53 protein.
Authors: Martinez J , Georgoff I , Martinez J , Levine A J
Published: June 2007

Primary rat embryo fibroblasts were transformed by a p53 mutant (alanine to valine change at amino acid 135) plus ras. This p53val135 mutant is temperature sensitive for a conformational change detected by the binding of a monoclonal antibody, PAb246, which recognizes the wild-type protein or the great majority of p53val135 at 32.5 degrees C. At 37 degrees C, both mutant and wild-type p53 conformational forms co-exist in the cells, while at 39.5 degrees C, the majority of the p53val135 in the cell is in a mutant conformation not recognized by PAb246 antibody. At 39.5 degrees C, the mutant p53 is localized in the cytoplasm of the cell. At 32.5 degrees C, the p53 protein enters the nucleus and stops the growth of these cells. At 37 degrees C where there is a mixture of mutant and wild-type p53, the wild-type p53 protein is in a complex with hsc70 and mutant p53 protein in the cytoplasm of the cell during G1. This wild-type protein enters the nucleus as the cells enter the S-phase of the cell cycle. At 32.5 degrees C, the cells stop replication and arrest at the G1/S border. After 48 hr at 32.5 degrees C, 91% of the cells are in the G1 fraction of the cell cycle. The S-phase cells appear to be immune to the p53 negative regulation of growth until they enter the next G1 period.(ABSTRACT TRUNCATED AT 250 WORDS)
A central role for chromosome breakage in gene amplification, deletion formation, and amplicon integration.
Authors: Windle B , Draper B W , Yin Y X , O'Gorman S , Wahl G M
Published: June 2007

A CHO cell line with a single copy of the DHFR locus on chromosome Z2 was used to analyze the structure of the amplification target and products subsequent to the initial amplification event. Dramatic diversity in the number and cytogenetic characteristics of DHFR amplicons was observed as soon as eight to nine cell doublings following the initial event. Two amplicon classes were noted at this early time: Small extrachromosomal elements and closely spaced chromosomal amplicons were detected in 30-40% of metaphases in six of nine clones, whereas three of nine clones contained huge amplicons spanning greater than 50 megabases. In contrast, the incidence of metaphases containing extrachromosomal amplicons fell to 1-2% in cells analyzed at 30-35 cell doublings, and most amplicons localized to rearranged or broken derivatives of chromosome Z2 at this time. Breakage of the Z2 chromosome near the DHFR gene, and deletion of the DHFR gene and flanking DNA was also observed in cells that had undergone the amplification process. To account for these diverse cytogenetic and molecular consequences of gene amplification, we propose that chromosome breakage plays a central role in the amplification process by (1) generating intermediates that are initially acentric and lead to copy number increase primarily by unequal segregation, (2) creating atelomeric ends that are either incompletely replicated or resected by exonucleases to generate deletions, and (3) producing recombinogenic ends that provide preferred sites for amplicon relocalization.
Occlusion of the HIV poly(A) site.
Authors: Weichs an der Glon C , Monks J , Proudfoot N J
Published: June 2007

To investigate the selective use of poly(A) sites in the 3' long terminal repeat (LTR) but not the 5' LTR of retroviruses, we have studied the poly(A) site of the human immunodeficiency virus (HIV-1). Using hybrid HIV/alpha-globin gene constructs, we demonstrate that the HIV poly(A) site is inactive or occluded when adjacent to an active promoter, either the homologous HIV promoter or the alpha-globin gene promoter. Furthermore, this occlusion of the HIV poly(A) site occurs over a considerable distance of up to at least 500 bp. In contrast, two nonretroviral poly(A) sites [alpha-globin and a synthetic poly(A) site] are active when close to a promoter. We also show that a short fragment of approximately 60 nucleotides containing the HIV poly(A) site is fully active when placed at the 3' end of the human alpha-globin gene or within the rabbit beta-globin gene. This result rules out the requirement of more distant upstream elements for the activity of the HIV poly(A) site, as has been suggested for other viral poly(A) sites. Finally, we show that the GT-rich downstream region of the HIV poly(A) site confers poly(A) site occlusion properties on a synthetic poly(A) site. This result focuses attention on this more variable part of a poly(A) site in retroviruses as a possible general signal for poly(A) site occlusion.
Activation and repression of transcription by the gap proteins hunchback and Krüppel in cultured Drosophila cells.
Authors: Zuo P , Stanojević D , Colgan J , Han K , Levine M , Manley J L
Published: June 2007

We have studied the ability of the Drosophila gap proteins Krüppel and hunchback to function as transcriptional regulators in cultured cells. Both proteins bind to specific sites in a 100-bp DNA fragment located upstream of the segment polarity gene engrailed, which also contains functional binding sites for a number of homeo box proteins. The hunchback protein is a strikingly concentration-dependent activator of transcription, capable of functioning both by itself and also synergistically with the pair-rule proteins fushi tarazu and paired. In contrast, Krüppel is a transcriptional repressor that can block transcription induced either by hunchback or by several different homeo box proteins. While repression of the homeo box protein activators requires a Krüppel-binding site on the DNA, repression of hunchback can occur efficiently in the absence of a Krüppel-binding site. We discuss the possible molecular mechanisms underlying these activities, as well as the potential significance of these results with respect to segmentation in Drosophila.
Autoregulation of a segmentation gene in Drosophila: combinatorial interaction of the even-skipped homeo box protein with a distal enhancer element.
Authors: Jiang J , Hoey T , Levine M
Published: June 2007

Autoregulation has been implicated in the expression of many patterning genes in Drosophila, but the molecular details of this process are largely unknown. In the case of the segmentation gene even-skipped (eve), autoregulation is important for the specification of sharp stripes of gene expression at the onset of gastrulation. Here, we use a combination of DNA binding and P-transformation assays to characterize the cis- and trans-acting factors responsible for autoregulation. We show that eve autoregulation is mediated, at least in part, by a 100-bp minimal autoregulatory sequence (MAS) located approximately 5 kb upstream from the eve transcription start site. Multimerization of a 200-bp DNA fragment that encompasses the MAS drives optimal autoregulatory activity, comparable to that obtained with the native distal enhancer element located between -5.9 and -5.2 kb. The MAS contains two eve protein-binding sites, as well as binding sites for two nuclear factors present in early embryos. Directed mutagenesis of these binding sites suggests that both the eve protein and nuclear factors are essential for autoregulation. These results provide evidence that the eve protein acts combinatorially with other transcription factors to enhance its own expression.
High-affinity binding sites for the Deformed protein are required for the function of an autoregulatory enhancer of the Deformed gene.
Authors: Regulski M , Dessain S , McGinnis N , McGinnis W
Published: June 2007

The homeotic selector gene Deformed (Dfd) is required to specify the identity of head segments during Drosophila development. Previous experiments have shown that for the Dfd segmental identity function to operate in epidermal cells, the Dfd gene must be persistently expressed. One mechanism that provides persistent embryonic expression of Dfd is an autoregulatory circuit. Here, we show that the control of this autoregulatory circuit is likely to be directly mediated by the binding of Dfd protein to an upstream enhancer in Dfd locus DNA. In a 25-kb region around the Dfd transcription unit, restriction fragments with the highest binding affinity for Dfd protein map within the limits of the upstream autoregulatory element at approximately -5 kb. A minimal autoregulatory element, within a 920-bp segment of upstream DNA, has four moderate- to high-affinity binding sites for Dfd protein, with the two highest affinity sites sharing an ATCATTA consensus sequence. Site-specific mutagenesis of these four sites results in an element that has low affinity for Dfd protein when assayed in vitro and is nonfunctional when assayed in embryos.
An arginine to lysine substitution in the bZIP domain of an opaque-2 mutant in maize abolishes specific DNA binding.
Authors: Aukerman M J , Schmidt R J , Burr B , Burr F A
Published: June 2007

The opaque-2 (o2) locus in maize encodes a transcription factor involved in the regulation of zein storage proteins. We have shown previously that the O2 protein contains a leucine zipper domain that binds to promoters of 22-kD zein genes. In this paper we characterize an EMS-induced o2 allele, o2-676, that causes a 50% reduction in zein. We have found that the o2-676 mutant protein does not show specific recognition of zein promoter fragments because of the substitution of a lysine residue for an arginine residue within the bZIP domain of o2-676. This particular arginine is conserved within the bZIP domains of all mammalian, fungal, and plant DNA binding proteins of this class. The correlation between this mutation in o2 and the altered pattern of zein expression strongly suggests that O2 regulates transcription of certain members of the zein multigene family through direct interaction with the zein promoters and not through the transcriptional activation of some other regulator of zein gene expression.
Characterization of a gene controlling heterocyst differentiation in the cyanobacterium Anabaena 7120.
Authors: Buikema W J , Haselkorn R
Published: June 2007

Anabaena 7120 mutant 216 fails to differentiate heterocyst. We previously identified a 2.4-kb wild-type DNA fragment able to complement this mutant. We show here that the sequence of this fragment contains a single open reading frame (hetR), encoding a 299-amino-acid protein. Conjugation of deletion subclones of this fragment into strain 216 showed that the hetR-coding region is both necessary and sufficient for complementation of the Het- phenotype. The mutation in 216 is located at nucleotide 535 in the hetR gene, converting a serine at position 179 in the wild-type protein to an asparagine in the mutant. Interruption of the hetR gene in wild-type cells results in a mutant phenotype identical to that of 216. Both 216 and wild-type cells containing wild-type hetR on a plasmid display increased frequency of heterocysts, even on media containing fixed nitrogen. These results suggest that hetR encodes a product that is not only essential for but also controls heterocyst development. This putative regulatory protein lacks known structural motifs characteristic of transcription factors and probably acts at a level one or more steps removed from its target genes.
A pairing-sensitive element that mediates trans-inactivation is associated with the Drosophila brown gene.
Authors: Dreesen T D , Henikoff S , Loughney K
Published: June 2007

Position-effect variegation in Drosophila is the mosaic expression of a gene juxtaposed to heterochromatin by chromosome rearrangement. The brown (bw+) gene is unusual in that variegating mutations are dominant, causing "trans-inactivation" of the homologous allele. We show that copies of bw+ transposed to ectopic sites are not trans-inactivated by rearrangements affecting the endogenous gene. However, when position-effect variegation is induced on an ectopic copy by chromosome rearrangement, the allele on its paired homolog is trans-inactivated, whereas other copies of bw+ are not. This confirms that trans-inactivation is "chromosome local" and maps the responsive element to the immediate vicinity of brown. Subsequent P-transposase-induced deletions within the ectopic copy in cis to the rearrangement breakpoint caused partial suppression of trans-inactivation. Surprisingly, the amount of suppression was correlated with deletion size, with some degree of trans-inactivation persisting even when the P[bw+] transposon was completely excised. The chromosome-local nature of the phenomenon and its extreme sensitivity to small disruptions of somatic pairing leads to a model in which a regulator of the brown gene is inactivated by direct contact with heterochromatic proteins.
wimp, a dominant maternal-effect mutation, reduces transcription of a specific subset of segmentation genes in Drosophila.
Authors: Parkhurst S M , Ish-Horowicz D
Published: June 2007

wimp is a dominant maternal-effect mutation that interacts with a specific subset of early-acting maternal and zygotic Drosophila genes. We show that wimp is a change-of-function mutation, allelic to mutations of the 140-kD subunit of RNA polymerase, which causes reduced transcription of interacting genes. Loci that do not interact with wimp are expressed at normal levels. We discuss these results in terms of specific interactions between transcription factors and RNA polymerase. Embryos from wimp mothers show unaltered fate maps and develop normally, despite the reduction of transcript levels at least twofold. We suggest that spatial cues are determined by a balance of segmentation gene products rather than their absolute concentrations. We also demonstrate powerful genetic screens for otherwise undetected loci required for segmentation, sex determination, and other early functions.
Identification of a potent adipocyte-specific enhancer: involvement of an NF-1-like factor.
Authors: Graves R A , Tontonoz P , Ross S R , Spiegelman B M
Published: June 2007

The molecular basis for adipocyte-specific gene expression is not known. We have demonstrated that while short (-168) segments of the 5'-flanking sequence of the adipocyte P2 gene containing AP-1- and C/EBP-binding sites can direct expression of a heterologous gene in cultured adipocytes, they cannot support tissue-specific expression in a transgenic mouse. We have therefore analyzed larger segments of the aP2 5'-flanking region by transfection into adipocytes and have found an enhancer at -5.4 kb. This 500-bp enhancer directs expression of the bacterial chloramphenicol acetyltransferase (CAT) gene in a differentiation-dependent fashion when linked to its own minimal promoter or to an enhancerless SV40 promoter. Moreover, this enhancer stimulates very strong and highly specific expression from the CAT gene in the adipose tissues of transgenic mice. A smaller fragment (190 bp) having enhancer activity in adipocytes was defined and demonstrated to contain a binding site for an abundant nuclear protein. This factor has the binding specificity and several other properties characteristic of the nuclear factor 1 (NF-1) transcription/replication factor family, and mutation of this NF-1-binding site greatly reduces the function of the 500-bp enhancer. These results identify and characterize the first functional enhancer with specificity for adipose cells and also demonstrate that a member(s) of the NF-1 family is involved in adipocyte-specific gene expression.
Inactivation of auxin in tobacco transformed with the indoleacetic acid-lysine synthetase gene of Pseudomonas savastanoi.
Authors: Romano C P , Hein M B , Klee H J
Published: June 2007

The iaaL gene of Pseudomonas syringae, subspecies savastanoi, encodes an indoleacetic acid (IAA)-lysine synthetase. To determine the effects of converting IAA to IAA-lysine in whole plants, the iaaL gene was fused to a constitutive plant promoter and introduced into tobacco plants. Biochemical analyses show that endogenous IAA is reduced by up to 19-fold in iaaL plants. Tobacco plants expressing the iaaL gene display reduced apical dominance, reduced rooting, and inhibition of vascular differentiation. The phenotypic effects of iaaL gene expression are reverted by crossing iaaL plants with plants that overproduce IAA. These data indicate that iaaL can act as an anti-auxin gene in vivo and confirm the role of auxin in the control of apical dominance, root growth, and vascular differentiation in whole plants.
FtsZ in Bacillus subtilis is required for vegetative septation and for asymmetric septation during sporulation.
Authors: Beall B , Lutkenhaus J
Published: June 2007

A Bacillus subtilis strain was constructed in which the cell division gene, ftsZ, was placed under control of the isopropyl-beta-D-thiogalactoside (IPTG)-inducible spac promoter. This strain was dependent upon the presence of IPTG for cell division and colony formation indicating that ftsZ is an essential cell division gene in this organism. In sporulation medium this strain increased in mass and reached stationary phase in the presence or absence of IPTG, but only sporulated in the presence of IPTG. The expression of the sporulation genes spoIIG, spoIIA, and spoIIE occurred normally in the absence of IPTG as monitored by spo-lacZ fusions. However, expression of lacZ fusions to genes normally induced later in the developmental pathway, and that required processed pro-sigma E for expression, was inhibited. Immunoblot analysis revealed that pro-sigma E was not processed to its active form (sigma E) under these experimental conditions. Electron microscopy revealed that these FtsZ-depleted cells did not initiate asymmetric septation, suggesting that FtsZ has a common role in the initiation of both the vegetative and sporulation septa.
Novel murine homeo box gene on chromosome 1 expressed in specific hematopoietic lineages and during embryogenesis.
Authors: Allen J D , Lints T , Jenkins N A , Copeland N G , Strasser A , Harvey R P , Adams J M
Published: June 2007

We describe here a new murine homeo box gene, denoted Hlx, which is expressed within specific hematopoietic lineages. The cDNA sequence indicates that Hlx differs markedly from known vertebrate homeo box genes, and linkage analysis of an interspecific murine backcross showed that it resides at a novel homeo box locus on the distal portion of mouse chromosome 1. The Hlx homeo domain is most similar to that of the Drosophila H2.0 gene, but outside this region the two polypeptides are related only within a few short segments, the most notable being a motif (denoted Hep) also partially conserved in the engrailed and invected homeo proteins and possibly related to an octapeptide in certain paired box proteins. The presence of an intron within the Hlx homeo box at the same position as in several divergent Drosophila genes (H2.0, labial, Distal-less, proboscipedia, Abdominal-B, NK-1) suggests an ancient evolutionary relationship between these genes. RNA analysis of 67 murine hematopoietic cell lines and normal hematopoietic cells revealed Hlx expression throughout the myeloid/macrophage lineage and at early stages of B lymphocyte development but not in T lymphocytes, erythroid cells, or mast cells. Hence, Hlx is a candidate regulator of hematopoietic lineage commitment and maturation. It probably also functions outside the hematopoietic system, however, because Hlx mRNA could be detected in diverse adult tissues and in embryos from as early as day 8 of development.
Gene targeting of the aggregation stage cAMP receptor cAR1 in Dictyostelium.
Authors: Sun T J , Devreotes P N
Published: June 2007

cAR1, a G-protein-linked surface cAMP receptor, plays a central role in the development of Dictyostelium. To investigate its role, we sought to target the cAR1 gene by homogolous recombination. Transformation of these amoebas with appropriately designed vectors results in integration into the cAR1 locus with high frequency. cAR1 "null" mutants, resulting from double crossover events, fail to bind or sense cAMP and arrest in early development. The null mutants can be rescued by constitutive expression of a wild-type cAR1 cDNA. Carboxy-terminal deletion mutants, derived from single crossover events, express a truncated form of cAR1 that binds and senses cAMP. These cells proceed through the developmental program, albeit with a delay. Constitutive expression of a similar truncated form of cAR1 also rescues the null mutant. These observations prove that cAR1-mediated signal transduction controls the development of Dictyostelium and allow structural/functional studies of a G-protein-linked receptor in its natural context.
The paired box encodes a second DNA-binding domain in the paired homeo domain protein.
Authors: Treisman J , Harris E , Desplan C
Published: June 2007

The homeo box, which encodes the DNA-binding homeo domain, is a DNA sequence motif present in several Drosophila developmental genes; it has been used to identify many homologous genes involved in mammalian development. The paired box is another conserved sequence motif, first identified in the paired (prd) and gooseberry (gsb) Drosophila homeo domain genes. It encodes a 128-amino-acid domain, the paired domain, which has since been found in other fly and mouse gene products, in association with the homeo domain or in its absence. We show that the paired box of the prd gene encodes a DNA-binding activity, independent of the DNA-binding activity of the Paired (Prd) homeo domain and with a different sequence specificity. The amino-terminal region of the paired domain, including one of the three predicted alpha-helices, is necessary and sufficient for binding. We investigate the binding of the Prd protein to two sites in the even-skipped promoter, which are composed of overlapping sequences bound by the homeo domain and by the paired domain. We also show that a mutation in the paired box of Prd, corresponding to the mutation in the paired box of the mouse Pax-1 gene thought to cause the undulated skeletal phenotype, destroys the ability of the Prd protein to bind to the paired domain-specific site. This supports the view that the undulated phenotype results from the inactivation of the DNA-binding activity of the paired domain of Pax-1.
A cold-sensitive mRNA splicing mutant is a member of the RNA helicase gene family.
Authors: Strauss E J , Guthrie C
Published: June 2007

We have isolated a cold-sensitive mutant of Saccharomyces cerevisiae in which the first step of mRNA splicing is inhibited. The growth and splicing defects are recessive and cosegregate, thus defining a single essential gene (PRP28). The wild-type PRP28 gene was cloned, and sequence analysis reveals extensive homology to a family of proteins that are thought to function as ATP-dependent RNA helicases. The cold sensitivity is caused by a glycine-to-glutamic acid change in a conserved sequence motif. Interestingly, double mutants containing conditional alleles of PRP28 and PRP24, which encodes a U6 snRNA-binding protein, are inviable. In addition, a suppressor of prp28-1 is a mutant allele of PRP8, which encodes a U5 protein, thus linking PRP28 with U5. These data are consistent with a scenario in which PRP28 acts to unwind the U4/U6 base-pairing interaction in the U4/U6/U5 snRNP, facilitating the first covalent step of splicing.
A thymus-specific member of the HMG protein family regulates the human T cell receptor C alpha enhancer.
Authors: Waterman M L , Fischer W H , Jones K A
Published: June 2007

The human T cell-specific transcription factor TCF-1 alpha plays a key role in the tissue-specific activation of the T cell receptor (TCR) C alpha enhancer and binds to pyrimidine-rich elements (5'-PyCTTTG-3') present in a variety of other T cell-specific control regions. Using amino acid sequence information derived from the DNA affinity-purified protein, we have now isolated cDNA clones encoding TCF-1 alpha. The TCF-1 alpha cDNA contains a single 68-amino-acid domain that is homologous to a region conserved among high-mobility group (HMG) and nonhistone chromosomal proteins. Expression of full-length and mutant cDNA clones in bacteria reveal that the single HMG motif, which is predicted to contain two extended alpha-helical segments, is sufficient to direct the sequence-specific binding of TCF-1 alpha to DNA. Northern blot experiments demonstrate further that TCF-1 alpha mRNA is highly tissue specific, found primarily in the thymus or T cell lines. The immature CEM T cell line expresses relatively low levels of TCF-1 alpha mRNA, which are increased upon activation of these cells by phorbol esters. Interestingly, the cloned TCF-1 alpha protein is a potent transcriptional activator of the human TCR alpha enhancer in nonlymphoid cell lines, whereas the activity of the endogenous protein in T cell lines is strongly dependent on an additional T cell-specific protein that interacts with the core enhancer. TCF-1 alpha is currently unique among the newly emerging family of DNA-binding regulatory proteins that share the HMG motif in that it is a highly tissue-specific RNA polymerase II transcription factor.
Transgenic mice provide new insights into the role of TGF-alpha during epidermal development and differentiation.
Authors: Vassar R , Fuchs E
Published: June 2007

Transforming growth factor-alpha (TGF-alpha) is thought to be the major autocrine factor controlling growth in epidermal cells. To explore further the role of TGF-alpha in epidermal growth and differentiation, we used a human keratin K14 promoter to target expression of rat TGF-alpha cDNA to the stratified squamous epithelia of transgenic mice. Unexpectedly, the only regions of epidermis especially responsive to TGF-alpha overexpression were those that were normally thick and where hair follicle density was typically low. This included most, if not all, body skin from 2-day- to 2-week-old mice, and ear, footpad, tail, and scrotum skin in adult mice. In these regions, excess TGF-alpha resulted in thicker epidermis and more stunted hair growth. Epidermal thickening was attributed both to cell hypertrophy and to a proportional increase in the number of basal, spinous, granular, and stratum corneum cells. During both postnatal development and epidermal differentiation, responsiveness to elevated TGF-alpha seemed to correlate with existing epidermal growth factor (EGF) receptor levels, and we saw no evidence for TGF-alpha-mediated control of EGF receptor (EGFR) expression. In adults, no squamous cell carcinomas were detected, but benign papillomas were common, developing primarily in regions of mechanical irritation or wounding. In addition, adult transgenic skin that was still both sensitive to TGF-alpha and subject to mild irritation displayed localized regions of leukocytic infiltration and granular layer loss, characteristics frequently seen in psoriasis in humans. These unusual regional and developmental effects of TGF-alpha suggest a natural role for the growth factor in (1) controlling epidermal thickness during development and differentiation, (2) involvement in papilloma formation, presumably in conjunction with TGF-beta, and (3) involvement in psoriasis, in conjunction with some as yet unidentified secondary stimulus stemming from mild mechanical irritation/bacterial infection.
Hematopoietic development of embryonic stem cells in vitro: cytokine and receptor gene expression.
Authors: Schmitt R M , Bruyns E , Snodgrass H R
Published: June 2007

A novel system to study early hematopoietic development is described. This report documents the in vitro capacity of murine embryonic stem (ES) cells to differentiate into hematopoietic precursors of most, if not all, of the colony-forming cells found in normal bone marrow. This system is used to correlate the genetic expression of cytokines, their receptors, the beta-globins, and the hematopoietic cell surface markers throughout the time course of ES cell differentiation with the hematopoietic development that occurs in these cultures. Our results indicate that there is a strong transcriptional activation, in a well-defined temporal order, of most of these genes including erythropoietin (Epo), CSF-1, IL-4, beta-globins, as well as the receptors for Epo, CSF-1, and IL-4. IL-3 and GM-CSF were not expressed during the first 24 days of ES cell differentiation. In contrast, the Steel (Sl) factor (SLF) was expressed early and underwent substantial up-regulation during this differentiation, and its receptor, c-kit, was expressed relatively constantly throughout the culture period. Our results are consistent with the conclusion that SLF, Epo, IL-4, and IL-6 are important during the early stages of ES cell differentiation and hematopoietic development. Furthermore, these results argue strongly that IL-3 and GM-CSF are not critical to early hematopoiesis. This system offers a unique in vitro model for studying hematopoietic development at the earliest possible stages.
Autoregulation of the splicing of transcripts from the transformer-2 gene of Drosophila.
Authors: Mattox W , Baker B S
Published: June 2007

The Drosophila transformer-2 gene uses alternative promoters and splicing patterns to generate four different mRNAs that together encode three putative RNA-binding polypeptides. The transformer-2 products expressed in somatic tissues function to regulate the RNA splicing of the sex determination gene doublesex, whereas products expressed in the male germ line play an unknown, but essential, role in spermatogenesis. Two alternatively spliced transformer-2 transcripts, each encoding a different putative RNA-binding protein, are found only in the male germ line. These male germ line-specific mRNAs differ from each other by the presence or absence of a single intron called M1. We show that M1-containing transcripts make up a majority of transformer-2 germ-line transcripts in wild-type males but fail to accumulate in males homozygous for transformer-2 null mutations. Germ-line transformation experiments using a variety of reporter gene constructs demonstrate that specific polypeptide products of the transformer-2 gene itself normally repress M1 splicing in the male germ line. Thus, in addition to its role in the sex-specific control of doublesex RNA splicing in somatic tissues, the transformer-2 gene also regulates the splicing of its own transcripts in the male germ line. We propose that this autoregulatory function may serve in negative feedback control of transformer-2 activity during spermatogenesis. The finding that transformer-2 controls multiple splicing decisions suggests that a variety of different alternative splicing choices could be regulated by a relatively limited number of trans-acting factors.
DNA looping between sites for transcriptional activation: self-association of DNA-bound Sp1.
Authors: Su W , Jackson S , Tjian R , Echols H
Published: June 2007

The Sp1 protein activates transcription from many eukaryotic promoters. Sp1 can act in vivo from enhancer sites that are distal to the promoter and exhibit synergistic interaction with promoter-proximal binding sites. To investigate possible protein-protein interactions between DNA-bound Sp1 molecules, we have used electron microscopy to visualize the DNA-protein complexes. At the SV40 promoter, we observed the expected localized interaction at the Sp1 sites; in addition, we found that DNA-bound Sp1 served to associate two or more DNA molecules. At a modified thymidine kinase promoter, we observed a localized interaction at each of two binding locations that were separated by 1.8 kbp; in addition, we noted a substantial fraction of DNA molecules in which the distant binding regions were joined by a DNA loop. As judged by studies with mutant Sp1 proteins, the distant interactions depended on the glutamine-rich regions of Sp1 required for transcriptional activation. We conclude that DNA-bound Sp1 can self-associate, bringing together distant DNA segments. From the correlation between DNA looping in vitro and synergistic activation of the modified thymidine kinase promoter shown previously in vivo, we suggest that Sp1 exerts its transcriptional synergism by a direct protein-protein association that loops the intervening DNA. Our experiments support the DNA-looping model for the function of transcriptional enhancers.
Individual stripe regulatory elements in the Drosophila hairy promoter respond to maternal, gap, and pair-rule genes.
Authors: Riddihough G , Ish-Horowicz D
Published: June 2007

Striped expression of the pair-rule gene hairy (h) plays a central role in regulating segmentation in Drosophila. We have used h-lacZ reporter gene fusions to delineate h sequences that drive individual stripe expression. We show that 14 kb of 5'-flanking DNA directs expression of seven lacZ stripes in the blastoderm embryo. Within this region, we identify discrete sequences required for expression of individual stripes 1, 5, 6, and 7, and dispersed elements active in the stripe 2 domain. Only the stripe 1 element directs lacZ expression in an accurate h stripe; stripes 5, 6, and 7 are displaced by one to two cells relative to their h counterparts. These results indicate that regulatory sequences are dispersed within the h promoter. We have determined the sensitivity of the lacZ stripes to maternal, gap, and pair-rule gene mutations. Our results suggest that different but overlapping subsets of gap genes regulate each stripe and that activation and repression are both important in generating the stripe pattern.
Synthetic oligonucleotides recreate Drosophila fushi tarazu zebra-stripe expression.
Authors: Topol J , Dearolf C R , Prakash K , Parker C S
Published: June 2007

A complex array of activator and repressor elements located within 669 bp proximal to the fushi tarazu (ftz) transcriptional start site is sufficient to generate the "zebra-stripe" expression pattern characteristic of the ftz gene. P-element-mediated transformation and ftz promoter/lacZ fusion genes were used to characterize, in detail, several of these transcriptional control elements. By reconstructing promoters with synthetic oligonucleotides containing cis-regulators of stripe expression, we show that these regulatory sites can function as independent units to direct position-specific transcription in the Drosophila embryo. In particular, we demonstrate that multiple copies of a positive regulatory site can mediate expression in both the odd- and even-numbered parasegments throughout most of the germ band and that negative regulatory sites can transform a continuous pattern of gene expression into discrete stripes. The reconstructed promoter system presented provides an effective means of studying molecular mechanisms governing spatially restricted transcription in the early embryo.
Identification and characterization of a novel repressor of beta-interferon gene expression.
Authors: Keller A D , Maniatis T
Published: June 2007

We have identified and characterized a novel repressor of human beta-interferon (beta-IFN) gene expression. This protein, designated PRDI-BF1, binds specifically to the PRDI element of the beta-IFN gene promoter and is distinct from previously reported proteins that bind to this sequence. PRDI-BF1 is an 88-kD protein containing five zinc-finger motifs. Cotransfection experiments in cultured mammalian cells revealed that PRDI-BF1 is a potent repressor of PRDI-dependent transcription. PRDI-BF1 blocks virus induction of the intact beta-IFN gene promoter and of synthetic promoters containing multiple PRDI sites. PRDI-BF1 can also block the SV40 enhancer when PRDI sites are located between the enhancer and the promoter. This repression is highly dependent on the location of the PRDI sites, however, indicating that PRDI-BF1 cannot act at a distance. On the basis of the properties of PRDI-BF1 and the observation that PRDI-BF1 mRNA accumulation is virus inducible, we propose that PRDI-BF1 may act as a postinduction repressor of the beta-IFN gene by displacing positive regulatory proteins from the PRDI site of the promoter.