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Query: UNIPROT:P06889 (Mol)
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During transcription elongation, eukaryotic RNA polymerase II (Pol II) must contend with the barrier presented by nucleosomes. The conserved Spt4-Spt5 complex has been proposed to regulate elongation through nucleosomes by Pol II. To help define the mechanism of Spt5 function, we have characterized proteins that coimmunopurify with Spt5. Among these are the general elongation factors TFIIF and TFIIS as well as Spt6 and FACT, factors thought to regulate elongation through nucleosomes. Spt5 also coimmunopurified with the mRNA capping enzyme and cap methyltransferase, and spt4 and spt5 mutations displayed genetic interactions with mutations in capping enzyme genes. Additionally, we found that spt4 and spt5 mutations lead to accumulation of unspliced pre-mRNA. Spt5 also copurified with several previously unstudied proteins; we demonstrate that one of these is encoded by a new member of the SPT gene family. Finally, by immunoprecipitating these factors we found evidence that Spt5 participates in at least three Pol II complexes. These observations provide new evidence of roles for Spt4-Spt5 in pre-mRNA processing and transcription elongation.
Mol Cell Biol 2003 Feb
PMID:Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins. 1255 96

SV2 (Synaptic Vesicle Protein 2) is expressed in neurons and endocrine cells where it is required for normal calcium-evoked neurosecretion. In mammals, there are three SV2 genes, denoted SV2A, B and C. SV2A interacts with synaptotagmin, the prime candidate for the calcium sensor in exocytosis. Here, we report that all isoforms of native SV2 bind synaptotagmin and that binding is inhibited by calcium, indicating that all isoforms contain a common calcium-inhibited synaptotagmin-binding site. The isolated amino termini of SV2A and SV2C supported an additional interaction with synaptotagmin, and binding at this site was stimulated by calcium. The amino-terminal binding site was mapped to the first 57 amino acids of SV2A, and removal of this domain decreased calcium-mediated inhibition of binding to synaptotagmin, suggesting that it modulates calcium's effect on the SV2-synaptotagmin interaction. Introduction of the amino terminus of SV2A or SV2C into cultured superior cervical ganglion neurons inhibited neurotransmission, whereas the amino terminus of SV2B did not. These observations implicate the SV2-synaptotagmin interaction in regulated exocytosis and suggest that SV2A and SV2C, via their additional synaptotagmin binding site, function differently than SV2B.
Mol Cell Neurosci 2005 May
PMID:SV2A and SV2C contain a unique synaptotagmin-binding site. 1586 46

Rapid progress in studies on flower development has resulted in refining the classical 'ABC model' into a new 'ABCDE model' to explain properly the regulation of floral organ identity. Conservation of E-function for flower organ identity among the dicotyledonous (dicot) plants has been revealed. However, its conservation in monocotyledonous (monocot) plants remains largely unknown. Here, we show the conservation of E-function in rice (Oryza sativaL.) by characterizing tissue culture-induced mutants of two MADS-box genes, OsMADS1and OsMADS5, which form a subclade within the well-supported clade of SEP-genes (E-function) phylogeny. Severe loss-of-function mutations of OsMADS1cause complete homeotic conversion of organs (lodicules, stamens, and carpels) of three inner whorls into lemma- and palea-like structures. Such basic deformed structure is reiterated along with the pedicel at the center of the same floret, indicating the loss of determinacy of the flower meristem. These phenotypes resemble the phenotypes caused by mutations of the dicot E-class genes, such as the Arabidopsis SEP123(SEPALLATA1/2/3) and the petunia FBP2(Floral Binding Protein 2), suggesting that OsMADS1play a very similar role in rice to that of defined E-class genes in dicot plants. In case of the loss-of-function mutation of OsMADS5, no defect in either panicles or vegetative organs was observed. These results demonstrate that OsMADS1clearly possesses E-function, and so, E-function is fundamentally conserved between dicot plants and rice, a monocot model plant.
Plant Mol Biol 2005 Sep
PMID:Conservation of the E-function for floral organ identity in rice revealed by the analysis of tissue culture-induced loss-of-function mutants of the OsMADS1 gene. 1621 7

In an effort to examine the molecular basis of gametogenesis, we screened Riken cDNA database and the clone 4930481F22 that is expressed preponderantly in mouse testis was identified. In the course of the research, a new isoform of 4930481F22 clone was found, isolated from mouse testis and sequenced. It only lacks the 7th exon of 4930481F22 transcript. The new isoform only has 837 bp and encodes a putative 28.4 kDa protein. We investigated the expression pattern at the mRNA level by RT-PCR and in situ hybridization in testis. The new isoform was only expressed in the gonad, where it began to be detected at day 8 after birth. In situ hybridization proved that the new isoform mostly expressed in spermatocytes. The structure of the predicted protein and the expression pattern of the mRNA suggest that the new isoform could have an important role in meiosis. We temporarily named it mmrp 2 (Mouse Meiosis Related Protein 2).
Mol Biol Rep 2005 Dec
PMID:Identification of a new transcript specifically expressed in mouse spermatocytes: mmrp2. 1632 86

The present study was conducted to investigate the relation between in vitro developmental competence and the expression of a panel of developmentally important genes in germinal vesicle (GV) stage oocytes. One-month-old prepubertal and adult sheep oocytes were used as models of low and high quality gametes, respectively. Cumulus-oocyte complexes (COCs) derived from lambs and ewes were in vitro matured and fertilized, and their cleavage rate at 22, 26, and 32 hr post fertilization and the blastocyst yield were observed to assess their developmental potential. In parallel, the relative abundance (RA) of 11 genes was analyzed by semi-quantitative Reverse Transcription Polymerase Chain Reaction (RT-PCR) assay in the two groups of oocytes. We observed similar maturation and fertilization rates in the two groups, but a significant lower rate of cleaved prepubertal oocytes (P < 0.05), a general delay in the timing of their first division (P < 0.01), and a lower blastocysts production (P < 0.05). The analysis of gene expression evidenced no difference in the RA of four transcripts [superoxide dismutase (SOD), ubiquitin, beta-actin, cyclin B] in the two classes of oocytes, but a statistically lower RA of seven messenger RNAs (mRNA) [Na(+)K(+)ATPase, p34(cdc2), Glucose-transporter I (Glut-1), Activin, Zona Occludens Protein 2 (PanZO2), Poli(A)Polymerase (PAP), E-Cadherin (E-Cad)] in the prepubertal oocytes compared to the adult ones. The present data show for the first time in the ovine species that the lower developmental competence is associated with deficiencies in the mRNAs storage during the oocyte growth.
Mol Reprod Dev 2007 Feb
PMID:Relations between relative mRNA abundance and developmental competence of ovine oocytes. 1694 75

To better understand the structure and the function of ovine glucose 6-phosphate dehydrogenase (G6PD) promoter region, a genome-walking procedure was followed to isolate and sequence a 1628 bp fragment, containing the 5' regulatory region of the G6PD gene. In silico analysis of the sequence showed many conserved blocks and features with other known mammalian G6PD promoter regions. The analysis also revealed the presence of one TATA box, three GC boxes, two E-boxes and several binding sites for Stimulating Protein 1 (Sp1) and Activator Protein 2 (AP2). Moreover, elements involved in the regulation of lipogenesis like USF (Upstream stimulating factor), HSF (Heat Shock Factor), F2F (Prolactin receptor), RAR (Retinoid Acid Receptor), STRE (STress Response Element), RORa (Retinoid related Orphan Receptor alpha), GATA (GATA binding factor), RFX (Regulatory Factor X), SREBP (Sterol Regulatory Element Binding Protein), MEP (Metal Element Protein), CREB (insulin receptor), PRE (Progesterone receptor), and HNF4 (Hepatic Nuclear Factor 4) were detected. The most important regulatory motifs were found to be conserved as compared to those in human and mouse counterparts. However, some differences were noted, likely indicating differences in the transcription regulation of G6PD gene between ruminant and non-ruminant species.
Comp Biochem Physiol B Biochem Mol Biol 2007 Aug
PMID:Cloning, characterization and computational analysis of the 5' regulatory region of ovine glucose 6-phosphate dehydrogenase gene. 1749 56

Clostridial neurotoxins are responsible for botulism and tetanus by cleaving the synaptic SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) synaptobrevin/VAMP2 (Vesicle-Associated Membrane Protein 2) and its partners SNAP-25 (synaptosome-associated protein of 25 kDa) and syntaxin 1. SNARE proteins mediate membrane fusion, a crucial step in intracellular trafficking. There are seven isotypes of botulinic neurotoxins with different target specificities and one tetanus neurotoxin (TeNT), which targets synaptobrevin. Regarding the high sequence similarities between synaptobrevin and its nonneuronal homolog cellubrevin/VAMP3, different groups developed the use of TeNT to study cellubrevin (Cb). Here, we show how we have introduced the light chain of the TeNT into nonneuronal cells and selected clones expressing this toxin by Western blotting and by immunofluorescence. We also present how we identified which cells express TeNT by searching for a soluble green fluorescent protein (GFP) pattern of expression corresponding to cleaved GFP-tagged cellubrevin in living GFP-cellubrevin and TeNT transfected cells.
Methods Mol Biol 2008
PMID:Targeting the epithelial SNARE machinery by bacterial neurotoxins. 1836 46

During folliculogenesis, oocytes accumulate maternal mRNAs in preparation for the first steps of early embryogenesis. The processing of oocyte mRNAs is ensured by heterogeneous nuclear ribonucleoproteins (hnRNPs) genes that encode RNA binding proteins implied in mRNA biogenesis, translation, alternative splicing, nuclear exportation, and degradation. In the present work, by combining phylogenetic analyses and, when available, in silico expression data, we have identified three new oocyte-expressed genes encoding RNA binding proteins by using two strategies. Firstly, we have identified mouse orthologs of the Car1 gene, known to be involved in regulation of germ cell apoptosis in C. elegans, and of the Squid gene, required for the establishment of anteroposterior polarity in the Drosophila oocyte. Secondly, we have identified, among genes whose ESTs are highly represented in oocyte libraries, a paralog of Poly(A) binding protein--Interacting Protein 2 (Paip2) gene, known to inhibit the interaction of the Poly(A)-Binding Protein with Poly(A) tails of mRNAs. For all of these genes, the expression in oocyte was verified by in situ hybridization. Overall, this work underlines the efficiency of in silico methodologies to identify new genes involved in biological processes such as oogenesis.
Mol Reprod Dev 2008 Dec
PMID:Use of combined in silico expression data and phylogenetic analysis to identify new oocyte genes encoding RNA binding proteins in the mouse. 1838 49

Retinoblastoma protein (pRB) mediates cell-cycle withdrawal and differentiation by interacting with a variety of proteins. RB-Binding Protein 2 (RBP2) has been shown to be a key effector. We sought to determine transcriptional regulation by RBP2 genome-wide by using location analysis and gene expression profiling experiments. We describe that RBP2 shows high correlation with the presence of H3K4me3 and its target genes are separated into two functionally distinct classes: differentiation-independent and differentiation-dependent genes. The former class is enriched by genes that encode mitochondrial proteins, while the latter is represented by cell-cycle genes. We demonstrate the role of RBP2 in mitochondrial biogenesis, which involves regulation of H3K4me3-modified nucleosomes. Analysis of expression changes upon RBP2 depletion depicted genes with a signature of differentiation control, analogous to the changes seen upon reintroduction of pRB. We conclude that, during differentiation, RBP2 exerts inhibitory effects on multiple genes through direct interaction with their promoters.
Mol Cell 2008 Aug 22
PMID:Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation. 1872 78

Mdm30p, a nucleus-encoded F-box protein, which binds to the substrate for ubiquitin-mediated proteolysis, is involved in maintenance of fusion-competent mitochondria for various cellular functions. Recently, Mdm30p has been implicated in regulation of gene expression. However, its mode of action in gene regulation is not clearly known in vivo. With this view, we have systematically analyzed here the role of Mdm30p in regulation of transcriptional initiation, elongation, mRNA processing, and export in Saccharomyces cerevisiae, using a formaldehyde-based in vivo cross-linking and chromatin immunoprecipitation assay in conjunction with RT-PCR and fluorescence in situ hybridization. We show that Mdm30p is dispensable for formation of the preinitiation complex assembly, association of elongating RNA polymerase II, and recruitment of mRNA capping enzyme, cap-binding complex, and 3' end formation machinery at the transcriptionally active genes such as ADH1, PHO84, and RPS5. Intriguingly, we find that Mdm30p facilitates the recruitment of the transcription-export complex at these genes. Consistently, the export of mRNAs of these genes is significantly impaired in the absence of Mdm30p as revealed by fluorescence in situ hybridization and RT-PCR analysis of cytoplasmic mRNA. However, such an impaired mRNA export is not dependent on mitochondrial fusion, as the deletion of FZO1, an essential gene for mitochondrial fusion, does not alter the export of ADH1, PHO84, and RPS5 mRNAs. Together, our data demonstrate that Mdm30p selectively controls mRNA export independently of mitochondrial fusion, revealing a novel function of an F-box protein in mRNA export.
J Mol Biol 2009 Jun 05
PMID:Stimulation of mRNA export by an F-box protein, Mdm30p, in vivo. 1937 28


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