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At least 901 records · Page 50Linked to original sources
PubMed2005

Hedgehog and retinoid signalling confines nkx2.2b expression to the lateral floor plate of the zebrafish trunk.

The ventral neural tube of vertebrates consists of distinct neural progenitor domains positioned along the dorsoventral (DV) axis that develop different types of moto- and interneurons. Several signalling molecules, most notably Sonic Hedgehog (Shh), retinoic acid (RA) and fibroblast growth factor (FGF) have been implicated in the generation of these domains. Shh is secreted from the floor plate, the ventral most neural tube structure that consists of the medial (MFP) and the lateral floor plate (LFP). While the MFP is well characterized, organization and function of the LFP remains unclear. Here, we describe the novel homeobox gene nkx2.2b that is strongly expressed in the trunk LFP of zebrafish and thus represents a unique marker for the characterization of LFP formation and the identification of LFP deficient mutants. nkx2.2b and its paralog nkx2.2a (formerly known as nk2.2 and nkx2.2) arose by gene duplication in zebrafish. Both duplicates show significant differences in their expression patterns. For example, while prominent nkx2.2a expression has been described in the ventral brain [Barth, K.A., Wilson, S.W., 1995. Expression of zebrafish nk2.2 is influenced by sonic hedgehog/vertebrate hedgehog-1 and demarcates a zone of neuronal differentiation in the embryonic forebrain. Development 121, 1755-1768], hardly any expression can be found in the trunk LFP, which is in contrast to nkx2.2b. Overexpression, mutant and inhibitor analyses show that nkx2.2b expression in the LFP is up-regulated by Shh, but repressed by retinoids and ectopic islet-1 (isl1) expression. In contrast to previously described zebrafish trunk LFP markers, like e.g. tal2 or foxa2, nkx2.2b is exclusively expressed in the LFP. Thus, it represents a unique tool to analyse the mechanisms of ventral neural tube patterning in zebrafish.

Amino Acid Sequence↗
PubMed2006

Identification of an effector protein and gain-of-function mutants that activate Pfmrk, a malarial cyclin-dependent protein kinase.

Cyclin-dependent protein kinases (CDKs) are key regulators of cell cycle control. In humans, CDK7 performs dual roles as the CDK activating kinase (CAK) responsible for regulating numerous CDKs and as the RNA polymerase II carboxyl-terminal domain (CTD) kinase involved in the regulation of transcription. Binding of an effector protein, human MAT1, stimulates CDK7 kinase activity and influences substrate specificity. In Plasmodium falciparum, CDKs and their roles in regulating growth and development are poorly understood. In this study, we characterized the regulatory mechanisms of Pfmrk, a putative homolog of human CDK7. We identified an effector, PfMAT1, which stimulates Pfmrk kinase activity in a cyclin-dependent manner. The addition of PfMAT1 stimulated RNA polymerase II CTD phosphorylation and had no effect on the inability of Pfmrk to phosphorylate PfPK5, a putative CDK1 homolog, which suggests that Pfmrk may be a CTD kinase rather than a CAK. In an attempt to abrogate the requirement for PfMAT1 stimulation, we mutated amino acids within the active site of Pfmrk. We found that two independent mutants, S138K and F143L, yielded a 4-10-fold increase in Pfmrk activity. Significant kinase activity of these mutants was observed in the absence of either cyclin or PfMAT1. Finally, we observed autophosphorylation of Pfmrk that is unaffected by the addition of either cyclin or PfMAT1.

Amino Acid Sequence↗
PubMed2007

Calcium/calmodulin kinase kinase beta has a male-specific role in memory formation.

The calcium/calmodulin (CaM) kinase cascade regulates gene transcription, which is required for long-term memory formation. Previous studies with Camkk2 null mutant mice have shown that in males calcium/calmodulin kinase kinase beta (CaMKKbeta) is required for spatial memory formation and for activation of the transcription factor cyclic AMP-responsive element binding protein (CREB) in the hippocampus by spatial training. Here we show that CaMKKbeta is not required for spatial memory formation in female mice as female Camkk2 null mutants were not impaired in spatial memory formation and they had the same level of hippocampal CREB phosphorylation after spatial training as female wild-type mice. Furthermore, we show that male but not female Camkk2 null mutants were impaired in long-term potentiation (LTP) at hippocampal CA1 synapses. Finally, a transcriptional analysis of male Camkk2 null mutants led to the identification of a gene, glycosyl phosphatidyl-inositol anchor attachment protein 1 (GAA1), whose hippocampal mRNA expression was up-regulated by spatial and contextual training in male but not in female wild-type mice. Taken together, we conclude that CaMKKbeta has a male-specific function in hippocampal memory formation and we have identified male-restricted transcription occurring during hippocampal memory formation.

Animals↗
PubMed2004

New aspects of sterol biosynthesis in growth and development of higher plants.

The characterization of the enzymatic components of plant sterol biosynthesis, the phenotypic description of a set of Arabidopsis thaliana sterol mutants, and consequently, the identification of aspects of growth and development influenced by sterols have been in recent years a very fruitful area of research. The overall data obtained in the field have shown an essential role of sterols at the cellular level in hormone signaling, organized divisions and embryo patterning. Indeed, current research efforts strongly suggest that membrane bound proteins implicated in polarized auxin transport or ethylene signaling have altered activity or functionality in a modified sterolic environment.

Arabidopsis↗
PubMed1999

Identification of a hydrogen bond in the phe M197-->Tyr mutant reaction center of the photosynthetic purple bacterium Rhodobacter sphaeroides by X-ray crystallography and FTIR spectroscopy.

In bacterial reaction centers the charge separation process across the photosynthetic membrane is predominantly driven by the excited state of the bacteriochlorophyll dimer (D). An X-ray structure analysis of the Phe M197-->Tyr mutant reaction center from Rhodobacter sphaeroides at 2.7 A resolution suggests the formation of a hydrogen bond as postulated by Wachtveitl et al. [Biochemistry 32, 12875-12886, 1993] between the Tyr M197 hydroxy group and one of the 2a-acetyl carbonyls of D. In combination with electrochemically induced FTIR difference spectra showing a split band of the pi-conjugated 9-keto carbonyl of D, there is clear evidence for the existence of such a hydrogen bond.

Crystallography, X-Ray↗
PubMed2003

Molecular and cell biology of phosphatidylserine and phosphatidylethanolamine metabolism.

In this review, the pathways for phosphatidylserine (PS) and phosphatidylethanolamine (PE) biosynthesis, as well as the genes and proteins involved in these pathways, are described in mammalian cells, yeast, and prokaryotes. In mammalian cells, PS is synthesized by a base-exchange reaction in which phosphatidylcholine or PE is substrate for PS synthase-1 or PS synthase-2, respectively. Isolation of Chinese hamster ovary cell mutants led to the cloning of cDNAs and genes encoding these two PS synthases. In yeast and prokaryotes PS is produced by a biosynthetic pathway completely different from that in mammals: from a reaction between CDP-diacylglycerol and serine. The major route for PE synthesis in cultured cells is from the mitochondrial decarboxylation of PS. Alternatively, PE can be synthesized in the endoplasmic reticulum (ER) from the CDP-ethanolamine pathway. Genes and/or cDNAs encoding all the enzymes in these two pathways for PE synthesis have been isolated and characterized. In mammalian cells, PS is synthesized on the ER and/or mitochondria-associated membranes (MAM). PS synthase-1 and -2 are highly enriched in MAM compared to the bulk of ER. Since MAM are a region of the ER that appears to be in close juxtaposition to the mitochondrial outer membrane, it has been proposed that MAM act as a conduit for the transfer of newly synthesized PS into mitochondria. A similar pathway appears to operate in yeast. The use of yeast mutants has led to identification of genes involved in the interorganelle transport of PS and PE in yeast, but so far none of the corresponding genes in mammalian cells has been identified. PS and PE do not act solely as structural components of membranes. Several specific functions have been ascribed to these two aminophospholipids. For example, cell-surface exposure of PS during apoptosis is thought to be the signal by which apoptotic cells are recognized and phagocytosed. Translocation of PS from the inner to outer leaflet of the plasma membrane of platelets initiates the blood-clotting cascade, and PS is an important activator of several enzymes, including protein kinase C. Recently, exposure of PE on the cell surface was identified as a regulator of cytokinesis. In addition, in Escherichia coli, PE appears to be involved in the correct folding of membrane proteins; and in Drosophila, PE regulates lipid homeostasis via the sterol response element-binding protein.

Animals↗
PubMed1997

An improved colony-PCR method for filamentous fungi for amplification of PCR-fragments of several kilobases.

A method was developed to perform PCR directly on mycelial pellets or colonies treated with NOVOzym 234. The method allows rapid screening of large numbers of transformants of both sporulating and non-sporulating fungi for the presence of (co)transforming plasmid copies or for specific genetic modifications such as gene disruption and site specific integration. PCR fragments of at least 3.2 kb can be obtained. Using this method the identification of specific disruption mutants from Aspergillus niger and Beauveria bassiana was carried out.

Aspergillus niger↗
PubMed1996

Recent advances in systemic acquired resistance research--a review.

Little is known about the signal transduction events that lead to the establishment of the broad-spectrum, inducible plant immunity called systemic acquired resistance (SAR). Salicylic acid (SA) accumulation has been shown to be essential for the expression of SAR and plays a key role in SAR signaling. Hydrogen peroxide has been proposed to serve as a second messenger of SA. However, our results do not support such a role in the establishment of SAR. Further elucidation of SAR signal transduction has been facilitated by the identification and characterization of mutants. The lesions simulating disease (lsd). resistance response mutant class exhibits spontaneous lesions similar to those that occur during the hypersensitive response. Interestingly, some lsd mutants lose their lesioned phenotype when SA accumulation is prevented by expression of the nahG gene (encoding salicylate hydroxylase), thereby providing evidence for a feedback loop in SAR signal transduction. Characterization of a mutant non-responsive to SAR activator treatments has provided additional evidence for common signaling components between SAR and gene-for-gene resistance.

Cell Death↗
PubMed1997

Analysis of the alcABC operon encoding alcaligin biosynthesis enzymes in Bordetella bronchiseptica.

We previously cloned a B. bronchiseptica (Bb) genomic DNA fragment that complements a Bb alcaligin biosynthesis mutant, and reported the identification of a gene, alcA, with predicted protein sequence similarity to siderophore biosynthesis enzymes from other organisms. In the present study we show that further nt sequencing of this region revealed two open reading frames (ORFs) 3' to alcA that encode putative proteins AlcB and AlcC, with significant sequence similarity to the aerobactin biosynthesis enzymes IucB and IucC, respectively. RT-PCR analysis indicated that the three ORFs are encoded on a single transcript, and that this operon is repressed at the transcriptional level by Fe. Primer extension analysis placed the transcriptional start point (tsp) 35 nt from the 5' end of the Fur consensus sequence and 188 nt from the putative start of translation of AlcA.

Amino Acid Sequence↗
PubMed1996

A Drosophila dystrophin-related protein, MSP-300, is required for embryonic muscle morphogenesis.

Proteins from the spectrin superfamily contribute to cell polarity and shape during the morphogenetic that accompany embryogenesis. Drosophila MSP-300, a member of the spectrin superfamily, is expressed in somatic, visceral and heart embryonic muscles. Cloning and sequence analysis of various spliced forms of MSP-300 reveals functional and structural similarities between MSP-300 and vertebrate Dystrophin, the product of the Duchenne Muscular Dystrophy gene. The identification of a strain mutant for the MSP-300 gene is described. Analysis of the somatic muscle phenotype in MSP-300 mutant embryos suggests that the protein contributes to the integrity of the somatic and visceral muscle during periods of significant morphogenetic change. Functional synergism between MSP-300 and laminin is demonstrated by the analysis of the phenotype of embryos mutant for both genes. The enhancement of aberrant muscle phenotype in the double mutants suggests a link between MSP-300 and laminin function in mediating proper extension of the myotube towards the epidermal muscle attachment site. In addition, both genes function to establish gut integrity. In view of the functional and structural similarities between MSP-300 and Dystrophin, it is postulated that Dystrophin is not only required for proper muscle function in adult life but also contributes to muscle morphogenesis during the development of the vertebrate embryo.

Amino Acid Sequence↗
PubMed1993

Differential regulation of Bordetella pertussis virulence factors.

Bordetella pertussis, the causative agent of whooping cough, regulates its virulence factors coordinately according to environmental parameters such as temperature and certain chemicals. A regulatory locus has been characterized which is essential for this regulation. This bvg locus codes for a two-component regulatory system composed of the sensor protein BvgS and the transcriptional activator protein BvgA. It has been shown that the BvgA and BvgS proteins are sufficient for the transcriptional regulation of some virulence factors such as the filamentous haemagglutinin (FHA) involved in adhesion. The recent identification of new regulatory mutants demonstrates that the regulation of some virulence factors such as the pertussis toxin (PTX) and the adenylate cyclase toxin (CYA) is more complex and involves additional regulatory factor(s). This finding suggests that the regulation of the various virulence factors is coordinated at the highest level of regulation, but there may be differences in the fine regulation of some of the factors such as the adhesins and the toxins.

Bacterial Proteins↗
PubMed2000

Forest tree biotechnology.

The past year has seen the fruits of biotechnological manipulation of forest trees approach commercial application. Advances in somatic embryogenesis have brought mass clonal propagation of the top commercial trees closer to reality, and efficient gene transfer systems have been developed for a number of conifers and hardwoods. Radical alterations in the quantity and quality of lignin in wood have been shown to be possible in softwoods and hardwoods through identification of naturally occurring mutants, as well as by engineering the lignin biosynthetic pathway with transgenes. The potential environmental and social impacts of the release of transgenic trees have become an increasingly contentious issue that will require more attention if we are to use these technologies to their full advantage.

Biotechnology↗
PubMed1998

Genetic dissection of familial Parkinson's disease.

In the past few years, the genetic contribution to Parkinson's disease (PD) has gained major attention and has resulted in the identification of the first mutant gene, called alpha-synuclein, involved in the pathogenesis of autosomal-dominant PD. alpha-Synuclein is a major component of Lewy bodies, which are a neuropathological feature of PD. Furthermore, deletions in the parkin gene have been identified as the primary cause in rare forms of autosomal-recessive juvenile PD. The elucidation of polygenic changes in the dopamine pathway, mitochondrial dysfunction, and metabolism of xenobiotics is now technically possible by means of association and genotype studies. The increasing knowledge of the pathogenesis of PD at a molecular level will have important implications for the development of individual therapeutic strategies to prevent disease progression.

Amino Acid Sequence↗
PubMed2001

Genetic interactions between ABA, ethylene and sugar signaling pathways.

The identification of genes through mutant screens is beginning to reveal the structure of a number of signaling pathways in plants. In the past year, genes that determine the plant's response to the hormones ethylene and abscisic acid have also been shown to be involved in sugar sensing in early seedlings. These results suggest that hormone signaling and carbon homeostasis are tightly coupled but that the architecture of these interactions is complex. Part of this complexity may be because some genetic screens on exogenous compounds produce signaling linkages that are not necessarily pertinent under normal growth conditions. Because many of the genes identified in these screens are cloned, the relevance of these interactions can now be unraveled at the molecular level.

Abscisic Acid↗
PubMed2003

Understanding the molecular responses to hypoxia using Drosophila as a genetic model.

We have previously discovered that Drosophila melanogaster could recover from extended periods of anoxia (0% oxygen) with no apparent consequential injuries. We have since employed forward and reverse genetic approaches to decipher the molecular basis for anoxia tolerance. In so doing, we have identified several independent mutant lines that demonstrated increased sensitivity to anoxia. Characterization of one of these mutants resulted in the identification of a dADAR gene that plays a role in the sensitivity to low levels of oxygen. We have also used microarrays to study all known Drosophila genes, the expression of which may be altered by hyoxia. Microarrays experiments have generated a large body of information that is being currently analyzed. We believe that these undertakings will provide insight into the genetic mechanisms of hypoxia tolerance and ischemic injuries.

Adenosine Deaminase↗
PubMed1990

Mechanistic studies of ionizing radiation and oxidative mutagenesis: genetic effects of a single 8-hydroxyguanine (7-hydro-8-oxoguanine) residue inserted at a unique site in a viral genome.

T4 RNA ligase was used to construct a deoxypentanucleotide containing a single 8-hydroxyguanine (7-hydro-8-oxoguanine; G8-OH) residue, which is one of the putatively mutagenic DNA adducts produced by oxidants and ionizing radiation. The pentamer d(GCTAG8-OH)p was prepared by the ligation of a chemically synthesized acceptor molecule, d(GCTA), to an adducted donor, 8-hydroxy-2'-deoxyguanosine 5',3'-bisphosphate. The acceptor was efficiently converted to the reaction product (greater than 95%), and the final product yield was 50%. Following 3'-dephosphorylation, the pentamer was characterized by UV spectroscopy, by high-pressure liquid chromatography, and by gas chromatography-mass spectrometry of the nucleosides released by enzymatic hydrolysis. Both d(GCTAG8-OH) and an unmodified control were 5'-phosphorylated by using [gamma -32P]ATP and incorporated covalently by DNA ligase into a five-base gap at a unique NheI restriction site in the otherwise duplex genome of an M13mp19 derivative. The ligation product contained G8-OH at the 3' residue of an in-frame amber codon (5'-TAG-3') (genome position 6276) of the phage lacZ alpha gene. The adduct was part of a nonsense codon in a unique restriction site in order to facilitate the identification and selection of mutants generated by the replication of the modified genome in Escherichia coli. Both control and adducted pentamers ligated into the genome at 50% of the maximum theoretical efficiency, and nearly all (approximately 90%) of the site-specifically adducted products possessed pentanucleotides that were covalently linked at both 5' and 3' termini. The G8-OH lesion in the NheI site inhibited the cleavage of the site by a 200-fold excess of NheI.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗
PubMed2004

Identification of membrane-anchoring domains of RLIP76 using deletion mutant analyses.

RLIP76 (RALBP1) is a multifunctional transporter involved in signaling and transmembrane movement of solute allocrites, which include glutathione conjugates and several natural product antineoplastic agents [Awasthi, S., et al. (2000) Biochemistry 39, 9327-9334; (2001) Biochemistry 40, 4159-4168]. Our previous studies suggested that the membrane-anchoring domain resides in the N-terminus of RLIP76, despite the lack of identifiable membrane-spanning domains. Amino acid sequence analysis indicated that this region of RLIP76 contains sequences that are similar to those of vector peptides. We, therefore, have studied the effect of a series of deletion mutant proteins on hydrophobicity and transport activity. RLIP76 or one of its derived deletion mutants was expressed in Escherichia coli, and bacteria were lysed and extracted in buffer without or with the nonionic detergent polidocanol. The ratio of RLIP76 in the detergent/aqueous extracts was found to be 2.5 for the wild-type protein, but decreased to 0.7 in the mutant in which amino acids 154-219 were deleted. Deletion of only one segment of this region (amino acids 171-185) alone resulted in a significant decrease in this ratio to 1.0. For the mutants with deletions within the region from amino acid 154 to 219, loss of hydrophobicity correlated with less incorporation of mutants into artificial liposomes, and decreased transport activity toward doxorubicin and dinitrophenyl-S-glutathione. In contrast, deletion of one of the two ATP-binding sites (at amino acids 65-80 or 415-448) or both sites did not affect hydrophobicity but reduced or abrogated transport activity. NSCLC (H358) stably transfected with del171-185 and del154-219 showed that loss of these regions results in a decrease in the extent of membrane association of RLIP76. Confocal laser immunohistochemistry colocalized amino acids 171-185 with her2/neu on the cell surface. Depletion of wild-type RLIP76 using si-RNA directed to this region in cells transfected with del171-185 resulted in the loss of cell surface expression. These finding demonstrate that amino acids 171-185 constitute a cell surface epitope which is necessary for optimal transport of anthracycline and glutathione conjugates by RLIP76, and that this peptide could be a novel target for antineoplastic therapy.

ATP-Binding Cassette Transporters↗