bluuebunny/crossref_metadata_2025 huggingface dataset:
A purine-rich DNA sequence motif present in SV40 and lymphotropic papovavirus binds a lymphoid-specific factor and contributes to enhancer activity in lymphoid cells.
Authors: Petterson M , Schaffner W
Published: June 2007

The enhancer of simian virus 40 (SV40) is active in a wide variety of tissues and hosts and thus has been called a general enhancer. Previous work has established that this region contains a number of subsegments, each with a different cell type specificity. By analyzing enhancer deletion mutants of SV40 with a restricted cell type specificity, we have identified a purine-rich DNA motif (Pu box) that is essential for activity of the mutant enhancer in lymphoid cells and also obtained evidence for an independent element that confers activity in kidney CV-1 cells. The Pu box element is positively regulated since binding of a cognate factor(s) was only observed in lymphoid cell extracts. The Pu box is also present in the 63-bp enhancer repeat of lymphotropic papovavirus (LPV), and competition experiments show that the SV40 and LPV sequences bind the same factor(s). Thus, the Pu box is likely to be a major determinant of the lymphotropic host range of LPV. In SV40, however, the Pu box is one of several enhancer elements with different cell specificities. We suggest that such an arrangement reflects a diversification strategy of SV40 to maximize its chance of adaptation to various types of host cells.
Oct-1 POU domain-DNA interactions: cooperative binding of isolated subdomains and effects of covalent linkage.
Authors: Klemm J D , Pabo C O
Published: June 2007

Structural and biochemical studies of Oct-1 POU domain-DNA interactions have raised important questions about cooperativity and the role of the linker connecting the POU-specific domain and the POU homeo domain. To analyze these interactions, we have studied binding of the isolated domains. Surprisingly, we find that two unlinked polypeptides corresponding to the POU-specific domain and the POU homeo domain bind cooperatively to the octamer site and have a coupling energy of 1.6 kcal/mole. We suggest that overlapping DNA contacts near the center of the octamer site may be the source of this cooperativity, as there are no protein-protein contacts between the domains in the crystal structure of the Oct-1 POU domain-DNA complex. These studies also have allowed us to describe the thermodynamic contribution of the linker (present in the intact POU domain) in terms of an effective concentration (3.6 mM). The broader implications for understanding cooperativity in protein-DNA recognition and gene regulation are discussed.
NF-kappa B-mediated chromatin reconfiguration and transcriptional activation of the HIV-1 enhancer in vitro.
Authors: Pazin M J , Sheridan P L , Cannon K , Cao Z , Keck J G , Kadonaga J T , Jones K A
Published: June 2007

NF-kappa B is a potent inducible transcription factor that regulates many genes in activated T cells. In this report we examined the ability of different subunits of NF-kappa B to enhance HIV-1 transcription in vitro with chromatin templates. We find that the p65 subunit of NF-kappa B is a strong transcriptional activator of nucleosome-assembled HIV-1 DNA, whereas p50 does not activate transcription, and that p65 activates transcription synergistically with Sp1 and distal HIV-1 enhancer-binding factors (LEF-1, Ets-1, and TFE-3). These effects were observed with chromatin, but not with nonchromatin templates. Furthermore, binding of either p50 or p65 with Sp1 induces rearrangement of the chromatin to a structure that resembles the one reported previously for integrated HIV-1 proviral DNA in vivo. These results suggest that p50 and Sp1 contribute to the establishment of the nucleosomal arrangement of the uninduced provirus in resting T cells, and that p65 activates transcription by recruitment of the RNA polymerase II transcriptional machinery to the chromatin-repressed basal promoter.
The T/ebp null mouse: thyroid-specific enhancer-binding protein is essential for the organogenesis of the thyroid, lung, ventral forebrain, and pituitary.
Authors: Kimura S , Hara Y , Pineau T , Fernandez-Salguero P , Fox C H , Ward J M , Gonzalez F J
Published: June 2007

The thyroid-specific enhancer-binding protein (T/ebp) gene was disrupted by homologous recombination in embryonic stem cells to generate mice lacking T/EBP expression. Heterozygous animals developed normally, whereas mice homozygous for the disrupted gene were born dead and lacked the lung parenchyma. Instead, they had a rudimentary bronchial tree associated with an abnormal epithelium in their pleural cavities. Furthermore, the homozygous mice had no thyroid gland but had a normal parathyroid. In addition, extensive defects were found in the brain of the homozygous mice, especially in the ventral region of the forebrain. The entire pituitary, including the anterior, intermediate, and posterior pituitary, was also missing. In situ hybridization showed that the T/ebp gene is expressed in the normal thyroid, lung bronchial epithelium, and specific areas of the forebrain during early embryogenesis. These results establish that the expression of T/EBP, a transcription factor known to control thyroid-specific gene transcription, is also essential for organogenesis of the thyroid, lung, ventral forebrain, and pituitary.
MyoD is required for myogenic stem cell function in adult skeletal muscle.
Authors: Megeney L A , Kablar B , Garrett K , Anderson J E , Rudnicki M A
Published: June 2007

To investigate the function of MyoD in adult skeletal muscle, we interbred MyoD mutant mice with mdx mice, a model for Duchenne and Becker muscular dystrophy. Mice lacking both MyoD and dystrophin displayed a marked increase in severity of myopathy leading to premature death, suggesting a role for MyoD in muscle regeneration. Examination of MyoD mutant muscle revealed elevated numbers of myogenic cells; however, myoblasts derived from these cells displayed normal differentiation potential in vitro. Following injury, MyoD mutant muscle was severely deficient in regenerative ability, and we observed a striking reduction in the in vivo proliferation of myogenic cells during regeneration. Therefore, we propose that the failure of MyoD-deficient muscle to regenerate efficiently is not caused by a reduction in numbers of satellite cells, the stem cells of adult skeletal muscle, but results from an increased propensity for stem-cell self-renewal rather than progression through the myogenic program.
The XPB and XPD DNA helicases are components of the p53-mediated apoptosis pathway.
Authors: Wang X W , Vermeulen W , Coursen J D , Gibson M , Lupold S E , Forrester K , Xu G , Elmore L , Yeh H , Hoeijmakers J H , Harris C C
Published: June 2007

The molecular pathway of p53-dependent apoptosis (programmed cell death) is poorly understood. Because p53 binds to the basal transcription-repair complex TFIIH and modulates its DNA helicase activities, we hypothesized that TFIIH DNA helicases XPB and XPD are members of the p53-mediated apoptotic pathway. Whereas transfer of a wild-type p53 expression vector by microinjection or retroviral infection into primary normal human fibroblasts resulted in apoptosis, primary fibroblasts from individuals with xeroderma pigmentosum (XP), who are deficient in DNA repair and have germ-line mutations in the XPB or XPD gene, but not in the XPA or XPC gene, have a deficiency in the apoptotic response. This deficiency can be rescued by transferring the wild-type XPB or XPD gene into the corresponding mutant cells. XP-D lymphocytes also have a decreased apoptotic response to DNA damage by adriamycin, indicating a physiologically relevant deficiency. The XP-B or XP-D mutant cells undergo a normal apoptotic response when microinjected with the Ich-L, and ICE genes. Analyses of p53 mutants and the effects of microinjected anti-p53 antibody, Pab421, indicate that the carboxyl terminus of p53 may be required for apoptosis. Direct microinjection of the p53 carboxy-terminal-derived peptide (amino acid residues 319-393) resulted in apoptosis of primary normal human fibroblasts. These results disclose a novel pathway of p53-induced apoptosis.
A novel mechanism for telomere size control in Saccharomyces cerevisiae.
Authors: Li B , Lustig A J
Published: June 2007

One of the central requirements for eukaryotic chromosome stability is the maintenance of the simple sequence tracts at telomeres. In this study, we use genetic and physical assays to reveal the nature of a novel mechanism by which telomere length is controlled. This mechanism, telomeric rapid deletion (TRD), is capable of reducing elongated telomeres to wild-type tract length in an apparently single-division process. The deletion of telomeres to wild-type lengths is stimulated by the hpr1 mutation, suggesting that TRD in these cells is the consequence of an intrachromatid pathway. Paradoxically, TRD is also dependent on the lengths of the majority of nonhomologous telomeres in the cell. Defects in the chromatin-organizing protein Sir3p increase the rate of hpr1-induced rapid deletion and specifically change the spectrum of rapid deletion events. We propose a model in which interactions among telosomes of nonhomologous chromosomes form higher order complexes that restrict the access of the intrachromatid recombination machinery to telomeres. This mechanism of size control is distinct from that mediated through telomerase and is likely to maintain telomere length within a narrow distribution.
The transcriptional factor CF2 is a mediator of EGF-R-activated dorsoventral patterning in Drosophila oogenesis.
Authors: Hsu T , Bagni C , Sutherland J D , Kafatos F C
Published: June 2007

Establishment of dorsoventral polarity during Drosophila oogenesis requires localized intercellular communication between the follicular cells and the oocyte. This is initiated by the transmission of a "dorsal signal" from the oocyte to the anterior dorsal follicle cells by the EGF receptor (EGF-R) pathway and is followed by transmission of a second signal from the ventral follicle cells back to the embryo. We show that the zinc finger transcription factor CF2 participates in these processes. CF2 is suppressed by EGF-R signaling in the anterior dorsal follicle cells. Altered expression patterns of CF2 result in specific dorsoventral patterning defects in egg chambers and in embryos, as demonstrated phenotypically and with molecular markers. CF2 appears to act as a repressor of dorsal follicle cell fates and specifically as a repressor of the rhomboid gene transcription.
Protein kinase C-zeta reverts v-raf transformation of NIH-3T3 cells.
Authors: Kieser A , Seitz T , Adler H S , Coffer P , Kremmer E , Crespo P , Gutkind J S , Henderson D W , Mushinski J F , Kolch W , Mischak H
Published: June 2007

We have identified protein kinase C-zeta (PKC-zeta) as a novel suppressor of neoplastic transformation caused by the v-raf oncogene. PKC-zeta overexpression drastically retards proliferation, abolishes anchorage-independent growth, and reverts the morphological transformation of v-raf-transformed NIH-3T3 cells. The molecular basis for this effect appears to be a specific induction of junB and egr-1 expression, triggered synergistically by PKC-zeta via a Raf/Mek/MAPK-independent mechanism and v-raf. junB-promoter/CAT assays revealed that PKC-zeta directly targets the junB promoter. The induction of junB and egr-1 is linked to the v-raf transformation-suppressing effect of PKC-zeta as constitutive expression of junB and egr-1 but not of c-jun also abolishes anchorage-independent growth of v-raf-transformed NIH-3T3 cells. Moreover, junB overexpression leads to a retardation of proliferation in these cells. PKC-zeta interferes with the serum inducibility of an AP-1 reporter plasmid in v-raf-transformed NIH-3T3 cells, indicating that PKC-zeta antagonizes transformation and proliferation by down-modulating AP-1 function via induction of junB. In summary, our data suggest that PKC-zeta counteracts v-raf transformation by modulating the expression of the transcription factors junB and egr-1.
Essential role of stromal mesenchyme in kidney morphogenesis revealed by targeted disruption of Winged Helix transcription factor BF-2.
Authors: Hatini V , Huh S O , Herzlinger D , Soares V C , Lai E
Published: June 2007

Metanephric mesenchyme gives rise to both the epithelial cells of the nephron and the stromal cells of the mature kidney. The function of the stroma. in kidney morphogenesis is poorly understood. We have generated mice with a null mutation in the Winged Helix (WH) transcription factor BF-2 to examine its function during development. BF-2 expression within the developing kidney is restricted to the stromal cell lineage. Homozygotes die within the first 24 hr after birth with abnormal kidneys. Mutant kidneys are small, fused longitudinally, and rotated 90 degrees ventrally. Histological examination reveals a smaller collecting system, numerous large condensations of mesenchyme, and a decrease in the number of nephrons. Using molecular markers we show that induction and condensation of the nephrogenic mesenchyme occurs normally in mutant. The disruption of BF-2 reduces the rate of differentiation of the condensed mesenchyme into tubular epithelium, as well as the rate of growth and branching of the ureter and collecting system. Our findings demonstrate that BF-2 and stromal cells have essential functions during kidney morphogenesis. Furthermore, they suggest that BF-2 controls the production, by the stroma, of signals or factors that are required for the normal transition of induced mesenchyme into tubular epithelium and full growth and branching of the collecting system.
Mammalian p50Cdc37 is a protein kinase-targeting subunit of Hsp90 that binds and stabilizes Cdk4.
Authors: Stepanova L , Leng X , Parker S B , Harper J W
Published: June 2007

CDC37, an essential gene in Saccharomyces cerevisiae, interacts genetically with multiple protein kinases and is required for production of Cdc28p/cyclin complexes through an unknown mechanism. We have identified mammalian p50Cdc37 as a protein kinase-targeting subunit of the molecular chaperone Hsp90. Previously, p50 was observed in complexes with pp60v-src and Raf-1, but its identity and function have remained elusive. In mouse fibroblasts, a primary target of Cdc37 is Cdk4. This kinase is activated by D-type cyclins and functions in passage through G1. In insect cells, Cdc37 is sufficient to target Hsp90 to Cdk4 and both in vitro and in vivo, Cdc37/Hsp90 associates preferentially with the fraction of Cdk4 not bound to D-type cyclins. Cdc37 is coexpressed with cyclin Dl in cells undergoing programmed proliferation in vivo, consistent with a positive role in cell cycle progression. Pharmacological inactivation of Cdc37/Hsp90 function decreases the half-life of newly synthesized Cdk4, indicating a role for Cdc37/Hsp90 in Cdk4 stabilization. This study suggests a general role for p50Cdc37 in signaling pathways dependent on intrinsically unstable protein kinases and reveals a previously unrecognized chaperone-dependent step in the production of Cdk4/cyclin D complexes.
Selective translation initiation by ribosome jumping in adenovirus-infected and heat-shocked cells.
Authors: Yueh A , Schneider R J
Published: June 2007

Translation initiation on eukaryotic mRNAs usually occurs by 5'-processive scanning of 40S ribosome subunits from the m7GTP-cap to the initiating AUG. In contrast, picornavirus and some specialized mRNAS initiate translation by internally binding ribosomes. A poorly described third mechanism of initiation, referred to as ribosome shunting or jumping, involves discontinuous scanning by 40S ribosome subunits, in which large segments of the 5' noncoding region are bypassed. Ribosome shunting has only been observed to date on a cauliflower mosaic virus mRNA. In this report we show that the family of adenovirus late mRNAs, which are preferentially translated during infection, use a ribosome jumping mechanism to initiate protein synthesis. Late adenovirus mRNAs contain a common 5'-noncoding region known as the tripartite leader, which confers preferential translation by reducing the requirement for the rate-limiting initiation factor eIF-4F (cap-binding protein complex). Adenovirus inhibits cell protein synthesis largely by inactivating eIF-4F. We show that the tripartite leader directs both 5' linear ribosome scanning and ribosome jumping when eIF-4F is abundant but exclusively uses a ribosome jumping mechanism during late adenovirus infection or heat shock (stress) of mammalian cells, when eIF-4F is altered or inactivated. Shunting is directed by a complex group of secondary structures in the tripartite leader and is facilitated by one or more unidentified viral late gene products. We propose that shunting may represent a widespread mechanism to facilitate selective translation of specialized classes of capped mRNAs, including some stress and developmentally regulated mRNAs, which possess little requirement for eIF-4F but do not initiate by internal ribosome binding.
Regulation of cell-cell contacts in developing Drosophila eyes by Dsrc41, a new, close relative of vertebrate c-src.
Authors: Takahashi F , Endo S , Kojima T , Saigo K
Published: June 2007

In Drosophila, Dsrc64 is considered a unique ortholog of the vertebrate c-src; however, we show evidence to the contrary. The closest relative of vertebrate c-src so far found in Drosophila is not Dsrc64, but Dsrc41, a gene identified for the first time here. In contrast to Dsrc64, overexpression of wild-type Dsrc41 caused little or no appreciable phenotypic change in Drosophila. Both gain-of-function and dominant-negative mutations of Dsrc41 caused the formation of supernumerary R7-type neurons, suppressible by one-dose reduction of boss, sev, Ras1, or other genes involved in the Sev pathway. Dominant-negative mutant phenotypes were suppressed and enhanced, respectively, by increasing and decreasing the copy number of wild-type Dsrc41. Colocalization of Dsrc41 protein, actin fibers and DE-cadherin, and Dsrc41-dependent disorganization of actin fibers and putative adherens junctions in precluster cells suggested that Dsrc41 may be involved in the regulation of cytoskeleton organization and cell-cell contacts in developing ommatidia.
The Drosophila tamou gene, a component of the activating pathway of extramacrochaetae expression, encodes a protein homologous to mammalian cell-cell junction-associated protein ZO-1.
Authors: Takahisa M , Togashi S , Suzuki T , Kobayashi M , Murayama A , Kondo K , Miyake T , Ueda R
Published: June 2007

In Drosophila sensory organ development, the balance of activities between proneural genes and repressor genes defines a proneural cluster as a population of competent cells for neural development. In this study, we report the isolation and analysis of the tamou (tam) gene that encodes a cell-cell junction-associated protein, which is homologous to mammalian ZO-1, a member of the membrane-associated guanylate kinase homolog family. The tam mutation reduces the transcription of a repressor gene, extramacrochaetae, and causes enlargement of a proneural cluster where supernumerary precursor cells emerge, resulting in extra mechanosensory organs in the fly. These results suggest that the membrane-associated Tam protein is involved in the signaling pathway that activates emc expression.
Nuclear localization of the Arabidopsis APETALA3 and PISTILLATA homeotic gene products depends on their simultaneous expression.
Authors: McGonigle B , Bouhidel K , Irish V F
Published: June 2007

The Arabidopsis APETALA3 (AP3) and PISTILLATA (PI) proteins are thought to act as transcription factors and are required for specifying floral organ identities. To define the nuclear localization signals within these proteins, we generated translational fusions of the coding regions of AP3 and PI to the bacterial uidA gene that encodes beta-glucuronidase (GUS). Transient transformation assays of either the AP3-GUS or PI-GUS fusion protein alone resulted in cytoplasmic localization of GUS activity. However, coexpression of AP3-GUS with PI, or PI-GUS with AP3, resulted in nuclear localization of GUS activity. Stable transformation with these fusion proteins in Arabidopsis showed similar results. The nuclear colocalization signals in AP3 and PI were mapped to the amino-terminal regions of each protein. These observations suggest that the interaction of the AP3 and PI gene products results in the formation of a protein complex that generates or exposes a colocalization signal required to translocate the resulting complex into the nucleus. The colocalization phenomenon that we have described represents a novel mechanism to coordinate the functions of transcription factors within the nucleus.
Early loss of the retinoblastoma gene is associated with impaired growth inhibitory innervation during melanotroph carcinogenesis in Rb+/- mice.
Authors: Nikitin AYu  , Lee W H
Published: June 2007

To better understand the cell lineage-specific character of retinoblastoma (Rb) gene inactivation during tumor formation, the earliest stages of spontaneous melanotroph carcinogenesis in Rb+/- heterozygous mice have been subjected to sequential analyses. The first atypical cells are detected in the pituitary intermediate lobe during a period corresponding to the cessation of melanotroph proliferation between 35 and 60 days after birth. Atypical cells contain no wild-type copy of the Rb gene and synchronously form early atypical proliferates (EAP) in the subsequent 30-60 day period. In contrast to surrounding mature melanotrophs with the wild-type Rb gene, Rb-negative cells in EAP continue to proliferate well past postnatal day 60, and fail to be innervated by growth inhibitory dopaminergic nerve terminals. Atypical melanotrophs remain competent for dopamine D2 receptor stimulation and undergo S-phase apoptosis in close proximity to nerve terminals. These results indicate a key role for the Rb protein in the onset of neuron-neuroendocrine cell interactions. This role may explain cell-type-specific neuroendocrine carcinogenesis associated with inactivation of the ubiquitously expressed Rb gene.
In vitro selection of preferred DNA pairing sequences by the Escherichia coli RecA protein.
Authors: Tracy R B , Kowalczykowski S C
Published: June 2007

The RecA protein and other DNA strand exchange proteins are characterized by their ability to bind and pair DNA in a sequence-independent manner. In vitro selection experiments demonstrate, unexpectedly, that RecA protein has a preferential affinity for DNA sequences rich in GT composition. Such GT-rich sequences are present in loci that display increased recombinational activity in both eukaryotes and prokaryotes, including the Escherichia coli recombination hotspot, chi (5'-GCTGGTGG-3'). Interestingly, these selected sequences, or chi-containing substrates, display both an enhanced rate and extent of homologous pairing in RecA protein-dependent homologous pairing reactions. Thus, the binding and pairing of DNA by RecA protein is composition-dependent, suggesting that a component of the elevated recombinational activity of chi and increased genomic rearrangements at certain DNA sequences in eukaryotes is contributed by enhanced DNA pairing activity.
The Caenorhabditis elegans gene sem-4 controls neuronal and mesodermal cell development and encodes a zinc finger protein.
Authors: Basson M , Horvitz H R
Published: June 2007

Neuronal and mesodermal cell types are generated in separate cell lineages during the larval development of Caenorhabditis elegans. Here we demonstrate that the gene sem-4 is required in both types of lineages for the normal development of neuronal and mesodermal cell types. The sem-4 gene encodes a protein containing seven zinc finger motifs of the C2H2 class, four of which are arranged in two pairs widely separated in the primary sequence of the protein. These pairs of zinc fingers are similar to pairs of zinc fingers in the protein encoded by the Drosophila homeotic gene spalt and in the human transcription factor PRDII-BF1. Analysis of sem-4 alleles suggests that different zinc fingers in the SEM-4 protein may function differentially in neuronal and mesodermal cell types. We propose that sem-4 interacts with different transcription factors in different cell types to control the transcription of genes that function in the processes of neuronal and mesodermal cell development.
Zygotic degradation of two maternal Cdc25 mRNAs terminates Drosophila's early cell cycle program.
Authors: Edgar B A , Datar S A
Published: June 2007

In Drosophila embryos the maternal/zygotic transition (MZT) in cell cycle control normally follows mitosis 13. Here we show that this transition requires degradation of two maternal mRNAs, string and twine, which encode Cdc25 phosphatases. Although twine is essential for meiosis and string is essential for most mitotic cycles, the two genes have mutually complementing, overlapping functions in the female germ line and the early embryo. Deletion of both gene products from the female germ line arrests germ-line development. Reducing the maternal dose of both products can lower the number of early embryonic mitoses to 12, whereas increasing maternal Cdc25(twine) can increase the number of early mitoses to 14. Blocking the activation of zygotic transcription stabilizes maternal string and twine mRNAs and also allows an extra maternal mitosis, which is Cdc25 dependent. We propose that Drosophila's MZT comprises a chain reaction in which (1) proliferating nuclei deplete factors (probably mitotic cyclins) required for cell cycle progression; (2) this depletion causes the elongation of interphases and allows zygotic transcription; (3) new gene products accumulate that promote degradation of maternal mRNAs, including string and twine; and (4) consequent loss of Cdc25 phosphatase activity allows inhibitory phosphorylation of Cdc2 by Dwee1 kinase, effecting G2 arrest. Unlike timing or counting mechanisms, this mechanism can compensate for losses or additions of nuclei by altering the timing and number of the maternal cycles and thus will always generate the correct cell density at the MZT.
Turnover of cyclin E by the ubiquitin-proteasome pathway is regulated by cdk2 binding and cyclin phosphorylation.
Authors: Clurman B E , Sheaff R J , Thress K , Groudine M , Roberts J M
Published: June 2007

Cyclin E is a mammalian G1 cyclin that is both required and rate limiting for entry into S phase. The expression of cyclin E is periodic, peaking at the G1-S transition and then decaying as S phase progresses. To understand the mechanisms underlying cyclin E periodicity, we have investigated the regulation of cyclin E degradation. We find that cyclin E is degraded by the ubiquitin-proteasome system, and that this degradation is regulated by both cdk2 binding and cdk2 catalytic activity. Free cyclin E is readily ubiquitinated and degraded by the proteasome. Binding to cdk2 protects cyclin E from ubiquitination, and this protection is reversed by cdk2 activity in a process that involves phosphorylation of cyclin E itself. The data are most consistent with a model in which cdk2 activity initiates cyclin E degradation by promoting the disassembly of cyclin E-cdk2 complexes, followed by the ubiquitination and degradation of free cyclin E.
Essential role of Swp73p in the function of yeast Swi/Snf complex.
Authors: Cairns B R , Levinson R S , Yamamoto K R , Kornberg R D
Published: June 2007

Swi/Snf protein was purified previously from the yeast Saccharomyces cerevisiae as an 11-polypeptide complex, including five novel Swp polypeptides. Here we present evidence concerning the role of Swp73p in the function of the complex. Deletion mutants in the SWP73 gene display phenotypes similar to those of swi and snf mutants, and in addition are temperature-sensitive. Swp73p is required for transcriptional activation by full-length glucocorticoid receptor (GR), but not by all GR derivatives. Swp73p is also required for activation with an enhancer element that binds the transcription factors Swi5p and Pho2p, which may underlie the defects in HO expression observed with swi and snf mutants. A single amino acid change in the protein confers phenotypes that are similar to those observed in the swp73 delta strain, but in some cases the two strains behave differently. The extent to which Swp73p is required for assisting transcriptional activation depends on the activator and promoter tested. Homologs of SWP73 are present in S. cerevisiae, Ashbya gossypii, Caenorhabditis elegans, and mice, indicating that SWP73 may belong to a family of related genes encoding proteins with analogous functions.
Conjugating plasmids are preferred targets for Tn7.
Authors: Wolkow C A , DeBoy R T , Craig N L
Published: June 2007

Most transposons display target site selectivity, inserting preferentially into sites that contain particular features. The bacterial transposon Tn7 possesses the unusual ability to recognize two different classes of target sites. Tn7 inserts into these classes of target sites through two transposition pathways mediated by different combinations of the five Tn7-encoded transposition proteins. In one transposition pathway, Tn7 inserts into a unique site in the bacterial chromosome, attTn7, through specific recognition of sequences in attTn7; the other transposition pathway ignores the attTn7 target. Here we examine targets of the non-attTn7 pathway and find that Tn7 preferentially inserts into bacterial plasmids that can conjugate between cells. Furthermore, Tn7 appears to recognize preferred targets through the conjugation process, as we show that Tn7 inserts poorly into plasmids containing mutations that block plasmid transfer. We propose that Tn7 recognizes preferred targets through features of the conjugation process, a distinctive target specificity that offers Tn7 the ability to spread efficiently through bacterial populations.
Exon coconversion biases accompanying intron homing: battle of the nucleases.
Authors: Mueller J E , Smith D , Belfort M
Published: June 2007

Intron homing in phage T4 occurs in the context of recombination-dependent replication, by virtue of intron-encoded endonucleolytic activity. After the td intron endonuclease I-TevI cleaves the intronless recipient 23 and 25 nucleotides upstream of the intron insertion site, exonucleolytic degradation is required for recombination to proceed. This resection process results in coconversion of exon sequences flanking the intron. In a genetic system designed to study coconversion of flanking markers, we demonstrate that although there is a bidirectional polarity gradient, coconversion can be highly asymmetric. Furthermore, we show that the coconversion of flanking markers favors exon I sequences, upstream of the I-TevI cleavage site. These data are consistent with the asymmetric features of the homing pathways that have been invoked for intron mobility in phage T4. Moreover, these results are in accord with the finding that once the td homing-site substrate is cleaved, I-TevI remains bound to the downstream cleavage product, protecting against exonucleolytic degradation, and thereby limiting the extent of coconversion into exon II. The results suggest that recombination events are influenced by a competition between the homing endonuclease and exonucleases for sequences downstream of the I-TevI cleavage site, thereby implying a role for the homing endonuclease in the repair process.
Pax-5 (BSAP) recruits Ets proto-oncogene family proteins to form functional ternary complexes on a B-cell-specific promoter.
Authors: Fitzsimmons D , Hodsdon W , Wheat W , Maira S M , Wasylyk B , Hagman J
Published: June 2007

The paired box transcription factor Pax-5 (B-cell-specific activator protein) is a key regulator of lineage-specific gene expression and differentiation in B-lymphocytes. We show that Pax-5 functions as a cell type-specific docking protein that facilitates binding of the early B-cell-specific mb-1 promoter by proteins of the Ets proto-oncogene family. Transcriptional activity of the mb-1 promoter in pre-B-cells is critically dependent on binding sites for Pax-5:Ets complexes. Ternary complex assembly requires only the Pax-5 paired box and ETS DNA-binding domains. Mutation of a single base pair in the ternary complex binding site allows for independent binding by Ets proteins but, conversely, inhibits the binding of Pax-5 by itself. Strikingly, the mutation reverses the pattern of complex assembly: Ets proteins recruit Pax-5 to bind the mutated sequence. Recruitment of Net and Elk-1, but not SAP1a, by Pax-5 defines a functional difference between closely related Ets proteins. Replacement of a valine (V68) in the ETS domain of SAP1a by aspartic acid (as found in c-Ets-1, Elk-1, and Net) enhanced ternary complex formation by more than 60-fold. Together, these observations define novel transcription factor interactions that regulate gene expression in B cells.
Human HPK1, a novel human hematopoietic progenitor kinase that activates the JNK/SAPK kinase cascade.
Authors: Hu M C , Qiu W R , Wang X , Meyer C F , Tan T H
Published: June 2007

The c-Jun amino-terminal kinases (JNKs)/stress-activated protein kinases (SAPKs) play a crucial role in stress responses in mammalian cells. The mechanism underlying this pathway in the hematopoietic system is unclear, but it is a key in understanding the molecular basis of blood cell differentiation. We have cloned a novel protein kinase, termed hematopoietic progenitor kinase 1 (HPK1), that is expressed predominantly in hematopoietic cells, including early progenitor cells. HPK1 is related distantly to the p21(Cdc42/Rac1)-activated kinase (PAK) and yeast STE20 implicated in the mitogen-activated protein kinase (MAPK) cascade. Expression of HPK1 activates JNK1 specifically, and it elevates strongly AP-1-mediated transcriptional activity in vivo. HPK1 binds and phosphorylates MEKK1 directly, whereas JNK1 activation by HPK1 is inhibited by a dominant-negative MEKK1 or MKK4/SEK mutant. Interestingly, unlike PAK65, HPK1 does not contain the small GTPase Rac1/Cdc42-binding domain and does not bind to either Rac1 or Cdc42, suggesting that HPK1. activation is Rac1/Cdc42-independent. These results indicate that HPK1 is a novel functional activator of the JNK/SAPK signaling pathway.
Conjugation, meiosis, and the osmotic stress response are regulated by Spc1 kinase through Atf1 transcription factor in fission yeast.
Authors: Shiozaki K , Russell P
Published: June 2007

The stress-activated Wis1-Spc1 protein kinase cascade links mitotic control with environmental signals in Schizosaccharomyces pombe. Fission yeast spc1- mutants are delayed in G2 during normal growth and undergo G2 arrest when exposed to osmotic or oxidative stress. Here we report that Spc1 also has an important role in regulating sexual development in S. pombe. This discovery arose from the observation that Spc1 is activated in response to nitrogen limitation, a key signal that promotes conjugation in fission yeast. Mutant spc1- cells are defective at arresting in G2 during nitrogen starvation and exhibit a poor mating ability. These deficiencies correlate with a failure to induce transcription of ste11+, a gene that encodes a transcription factor responsible for expression of various meiotic genes. Two genes, atf1+ and atf21+, were cloned as multicopy suppressors of the spc1- mating defect. Atf1 and Atf21 are bZIP transcription factors that are most closely related to human ATF-2/CRE-BP1. Spc1 is required for stress-induced phosphorylation of Atf1. Atf1 is required for induction of meiotic genes and stress-response genes, such as gpd1+ and pyp2+, that are transcriptionally regulated by Spc1. atf1- and spc1- mutants are sensitive to osmotic stress and impaired for sexual development, showing that fission yeast uses a common pathway to respond to cytotoxic stress and nitrogen starvation. However, unlike spc1- mutants, atf1- cells have no mitotic cell-cycle defect, indicating that the stress response pathway bifurcates at Spc1 to regulate independently meiosis and mitosis.
The Atf1 transcription factor is a target for the Sty1 stress-activated MAP kinase pathway in fission yeast.
Authors: Wilkinson M G , Samuels M , Takeda T , Toone W M , Shieh J C , Toda T , Millar J B , Jones N
Published: June 2007

The atf1+ gene of Schizosaccharomyces pombe encodes a bZIP transcription factor with strong homology to the mammalian factor ATF-2. ATF-2 is regulated through phosphorylation in mammalian cells by the stress-activated mitogen-activated protein (MAP) kinases SAPK/JNK and p38. We show here that the fission yeast Atf1 factor is also regulated by a stress-activated kinase, Sty1. The Sty1 kinase is stimulated by a variety of different stress conditions including osmotic and oxidative stress and heat shock. Deletion of the atf1+ gene results in many, but not all, of the phenotypes associated with loss of Sty1, including sensitivity to environmental stress and inability to undergo sexual conjugation. Furthermore, we identify a number of target genes that are induced rapidly in a manner dependent upon both the Sty1 kinase and the Atf1 transcription factor. These genes include gpd1+, which is important for the response of cells to osmotic stress, the catalase gene lambda important for cells to combat oxidative stress, and pyp2+, which encodes a tyrosine-specific MAP kinase phosphatase. Induction of Pyp2 by Atf1 is direct in that it does not require de novo protein synthesis and results in a negative feedback loop that serves to control signaling through the Sty1/Wis1 pathway. We show that Atf1 associates stably and is phosphorylated by the Sty1 kinase in vitro. Taken together, these results indicate that the interaction between AM and Sty1 is direct. These findings highlight a remarkable level of conservation in transcriptional control by stress-activated MAP kinase pathways between fission yeast and mammalian cells.
Yeast TAF(II)90 is required for cell-cycle progression through G2/M but not for general transcription activation.
Authors: Apone L M , Virbasius C M , Reese J C , Green M R
Published: June 2007

The RNA polymerase II general transcription factor TFIID is a multisubunit complex comprising TATA-box binding protein and associated factors (TAFIIs). In vitro experiments have suggested that TAFIIs are essential coactivators required for RNA polymerase II-directed transcription activation. Here, for the first time, we analyze systematically the in vivo function of a specific TAFII, yeast TAFII90 (yTAFII90). We show that functional inactivation of yTAFII90 by temperature-sensitive mutations or depletion leads to arrest at the G2/M phase of the cell cycle. Unexpectedly, in the absence of functional yTAFII90, a variety of endogenous yeast genes were all transcribed normally, including those driven by well-characterized activators. Taken together, our results indicate that yTAFII90 is not required for transcription activation in general, and reveal linkages between TAF function and cell-cycle progression.
Targeted disruption of ATM leads to growth retardation, chromosomal fragmentation during meiosis, immune defects, and thymic lymphoma.
Authors: Xu Y , Ashley T , Brainerd E E , Bronson R T , Meyn M S , Baltimore D
Published: June 2007

ATM, the gene mutated in the inherited human disease ataxia-telangiectasia, is a member of a family of kinases involved in DNA metabolism and cell-cycle checkpoint control. To help clarify the physiological roles of the ATM protein, we disrupted the ATM gene in mice through homologous recombination. Initial evaluation of the ATM knockout animals indicates that inactivation of the mouse ATM gene recreates much of the phenotype of ataxia-telangiectasia. The homozygous mutant (ATM-/-) mice are viable, growth-retarded, and infertile. The infertility of ATM-/- mice results from meiotic failure. Meiosis is arrested at the zygotene/pachytene stage of prophase I as a result of abnormal chromosomal synapsis and subsequent chromosome fragmentation. Immune defects also are evident in ATM-/- mice, including reduced numbers of B220+CD43- pre-B cells, thymocytes, and peripheral T cells, as well as functional impairment of T-cell-dependent immune responses. The cerebella of ATM-/- mice appear normal by histologic examination at 3 to 4 months and the mice have no gross behavioral abnormalities. The majority of mutant mice rapidly develop thymic lymphomas and die before 4 months of age. These findings indicate that the ATM gene product plays an essential role in a diverse group of cellular processes, including meiosis, the normal growth of somatic tissues, immune development, and tumor suppression.
TGF-beta1 and Ha-Ras collaborate in modulating the phenotypic plasticity and invasiveness of epithelial tumor cells.
Authors: Oft M , Peli J , Rudaz C , Schwarz H , Beug H , Reichmann E
Published: June 2007

Metastasis of epithelial tumor cells can be associated with the acquisition of fibroblastoid features and the ability to invade stroma and blood vessels. Using matched in vivo and in vitro culture systems employing fully polarized, mammary epithelial cells, we report here that TGF-beta1 brings about these changes in Ras-transformed cells but not in normal cells. When grown in collagen gels in the absence of TGF-beta, both normal and Ras-transformed mammary epithelial cells form organ-like structures in which the cells maintain their epithelial characteristics. Under these conditions, treatment of normal cells with TGF-beta results in growth arrest. The same treatment renders Ras-transformed epithelial cells fibroblastoid, invasive, and resistant to growth inhibition by TGF-beta. After this epithelial-fibroblastoid conversion, the Ras-transformed cells start to secrete TGF-beta themselves, leading to autocrine maintenance of the invasive phenotype and recruitment of additional cells to become fibroblastoid and invasive. More important, this cooperation of activated Ha-Ras with TGF-beta1 is operative during in vivo tumorigenesis and, as in wound healing processes, is dependent on epithelial-stromal interactions.
E2F-induced S phase requires cyclin E.
Authors: Duronio R J , Brook A , Dyson N , O'Farrell P H
Published: June 2007

Both the heterodimeric transcription factor, E2F, and the G1 cyclin, cyclin E, are required for the G1-S transition at the start of the metazoan cell cycle. It has been established that cyclin E can act as an upstream activator of E2F. In addition to this action, we show here that cyclin E has an essential role in DNA replication distinct from activating E2F. We have created transgenic Drosophila capable of inducible, ectopic production of E2F activity. Simultaneous overexpression of both Drosophila E2F subunits, dE2F and dDP, in embryos stimulated the expression of multiple E2F-target genes including cyclin E, and also caused the initiation of S phase. Mutation of cyclin E prevented the initiation of S phase after overexpression of dE2F/dDP without affecting induction of target gene expression. Thus, E2F-directed transcription cannot bypass loss of cyclin E in Drosophila embryos.
Switching transcription on and off during the yeast cell cycle: Cln/Cdc28 kinases activate bound transcription factor SBF (Swi4/Swi6) at start, whereas Clb/Cdc28 kinases displace it from the promoter in G2.
Authors: Koch C , Schleiffer A , Ammerer G , Nasmyth K
Published: June 2007

When yeast cells reach a critical size in late G1 they simultaneously start budding, initiate DNA synthesis, and activate transcription of a set of genes that includes G1 cyclins CLN1, CLN2, and many DNA synthesis genes. Cell cycle-regulated expression of CLN1, CLN2 genes is attributable to the heteromeric transcription factor complex SBF. SBF is composed of Swi4 and Swi6 and binds to the promoters of CLN1 and CLN2. Different cyclin-Cdc28 complexes have different effects on late G1-specific transcription. Activation of transcription at the G1/S boundary requires Cdc28 and one of the G1 cyclins Cln1-Cln3, whereas repression of SBF-regulated genes in G2 requires the association of Cdc28 with G2-specific cyclins Clb1-Clb4. Using in vivo genomic footprinting, we show that SBF (Swi4/Swi6) binding to SCB elements (Swi4/Swi6 cell cycle box) in the CLN2 promoter is cell cycle regulated. SBF binds to the promoter prior to the activation of transcription in late G1, suggesting that Cln/Cdc28 kinase regulates the ability of previously bound SBF to activate transcription. In contrast, SBF dissociates from the CLN2 promoter when transcription is repressed during G2 and M phases, suggesting that Clb1-Clb4 repress SBF activity by inhibiting its DNA-binding activity. Switching transcription on and off by different mechanisms could be important to ensure that Clns are activated only once per cell cycle and could be a conserved feature of cell cycle-regulated transcription.
Transcriptional activation of the Cdk inhibitor p21 by vitamin D3 leads to the induced differentiation of the myelomonocytic cell line U937.
Authors: Liu M , Lee M H , Cohen M , Bommakanti M , Freedman L P
Published: June 2007

The hormonal form of vitamin D, 1,25-dihydroxyvitamin D3, acting through its cognate nuclear receptor (vitamin D3 receptor, VDR) will induce myeloid leukemic cell lines to terminally differentiate into monocytes/macrophages. Because VDR acts by transcriptionally regulating responsive genes in a ligand-dependent manner, we sought target genes of the receptor that initiate, the differentiation process in response to ligand. We screened a cDNA library prepared from the myelomonocytic U937 cell line with probes generated from either 1,25-dihydroxyvitamin D3-treated or untreated cells. We report here that a candidate clone that hybridized differentially is the Cdk inhibitor p21WAF1, CIP1. Furthermore, we show that p21 is transcriptionally induced by 1,25-dihydroxyvitamin D3 in a VDR-dependent, but not p53-dependent, manner, and we identify a functional vitamin D response element in the p21 promoter. Transient overexpression of p21 and/or the related Cdk inhibitor p27 in U937 cells in the absence of 1,25-dihydroxyvitamin D3 results in the cell-surface expression of monocyte/macrophage-specific markers, suggesting that ligand-modulated transcriptional induction of the p21 gene facilitates the induced differentiation of this monoblastic cell line. We believe that this is the first report demonstrating that the ectopic overexpression of a Cdk inhibitor such as p21 or p27 directly leads to a terminal differentiation program.
Differential effects of an erythropoietin receptor gene disruption on primitive and definitive erythropoiesis.
Authors: Lin C S , Lim S K , D'Agati V , Costantini F
Published: June 2007

Although the hormone erythropoietin (Epo) and its receptor (EpoR) are known to play important roles in the regulation of erythropoiesis, several questions remain concerning the developmental role of Epo/EpoR signaling. As the functions of Epo have been defined primarily through studies of definitive erythroid cells, its importance for primitive, embryonic erythropoiesis remains uncertain, as does the significance of EpoR expression in several nonerythroid cell types. To address these questions, mouse embryonic stem cells and embryos lacking a functional EpoR gene were produced by gene targeting. The effects of the mutation were examined in embryos developing in vivo, in chimeric adult mice produced with homozygous mutant embryonic stem cells, and in hemopoietic cells cultured in vitro. No defects were apparent in nonerythroid cell lineages in which the EpoR normally is expressed, including megakaryocytes and endothelial cells. In the mutant yolk sac, primitive erythrocytes were produced in normal numbers, they underwent terminal differentiation, and expressed near normal levels of embryonic globins, although they were reduced in size and their proliferation was severely retarded after E9.5. In contrast, in the fetal liver, definitive erythropoiesis beyond the late progenitor (CFU-E) stage was drastically inhibited by the EpoR mutation, and virtually no definitive erythrocytes were produced in vivo, leading to embryonic death by E13.5. Thus, our results suggest a fundamental difference in the molecular mechanisms stimulating primitive and definitive erythropoiesis. It was also observed that a few mutant definitive erythroid cells could terminally differentiate when cultured with additional cytokines, demonstrating that although Epo/EpoR signaling is important for definitive erythroid cell survival and proliferation, it is not an obligatory step in differentiation.