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At least 1,675 records · Page 93Linked to original sources
PubMed2005

Rice proteome database: a step toward functional analysis of the rice genome.

The technique of proteome analysis using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) has the power to monitor global changes that occur in the protein complement of tissues and subcellular compartments. In this study, the proteins of rice were cataloged, a rice proteome database was constructed, and a functional characterization of some of the identified proteins was undertaken. Proteins extracted from various tissues and subcellular compartments in rice were separated by 2D-PAGE and an image analyzer was used to construct a display of the proteins. The Rice Proteome Database contains 23 reference maps based on 2D-PAGE of proteins from various rice tissues and subcellular compartments. These reference maps comprise 13129 identified proteins, and the amino acid sequences of 5092 proteins are entered in the database. Major proteins involved in growth or stress responses were identified using the proteome approach. Some of these proteins, including a beta-tubulin, calreticulin, and ribulose-1,5-bisphosphate carboxylase/oxygenase activase in rice, have unexpected functions. The information obtained from the Rice Proteome Database will aid in cloning the genes for and predicting the function of unknown proteins.

Calreticulin↗
PubMed1998

Structural and functional analysis of the 1:1 growth hormone:receptor complex reveals the molecular basis for receptor affinity.

The designed G120R mutant of human growth hormone (hGH) is an antagonist and can bind only one molecule of the growth hormone receptor. We have determined the crystal structure of the 1:1 complex between this mutant and the receptor extracellular domain (hGHbp) at 2.6 A resolution, and used it to guide a detailed survey of the structural and functional basis for hormone-receptor recognition. The overall structure of the complex is very similar to the equivalent portion of the 1:2 complex, showing that formation of the active complex does not involve major conformational changes. However, a segment involved in receptor-receptor interactions in the 1:2 complex is disordered in this structure, suggesting that its productive conformation is stabilized by receptor dimerization. The hormone binding site of the receptor comprises a central hydrophobic patch dominated by Trp104 and Trp169, surrounded by a hydrophilic periphery containing several well-ordered water molecules. Previous alanine scanning showed that the hydrophobic "hot spot" confers most of the binding energy. The new structural data, coupled with binding and kinetic analysis of further mutants, indicate that the hot spot is assembled cooperatively and that many residues contribute indirectly to binding. Several hydrophobic residues serve to orient the key tryptophan residues; kinetic analysis suggests that Pro106 locks the Trp104 main-chain into a required conformation. The electrostatic contacts of Arg43 to hGH are less important than the intramolecular packing of its alkyl chain with Trp169. The true functional epitope that directly contributes binding energy may therefore comprise as few as six side-chains, participating mostly in alkyl-aromatic stacking interactions. Outside the functional epitope, multiple mutation of residues to alanine resulted in non-additive increases in affinity: up to tenfold for a hepta-alanine mutant. Contacts in the epitope periphery can therefore attenuate the affinity of the central hot spot, perhaps reflecting a role in conferring specificity to the interaction.

Binding Sites↗
PubMed1996

Functional analysis of vitamin D response elements in the parathyroid hormone gene and a comparison with the osteocalcin gene.

We have previously localised two putative vitamin D response elements (VDRE) in the bovine parathyroid hormone (PTH) gene to within -485 to -452 and -451 to -348 base pairs (bp). To confirm the functional significance of these elements, a series of reporter gene constructs were generated and the ability of 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) to suppress gene transcription was assessed. These data confirmed the presence of two regions within -485 to -348 bp which confer responsiveness to 1,25(OH)2D3 and mediate its down-regulatory effect on PTH gene transcription. Second, we investigated whether the putative bovine PTH VDRE and the osteocalcin VDRE require the same nuclear proteins in their interaction with VDR. In gel shift assays, three specific DNA-protein complexes were formed using CV-1 nuclear extract and PTH VDRE. However, unlabelled osteocalcin VDRE (50-fold) failed to inhibit the formation of these complexes. These results suggest that interactions of VDR with the PTH and osteocalcin genes require different accessory factors.

Animals↗
PubMed2005

Three-dimensional structure of nanocomposites from atomic pair distribution function analysis: study of polyaniline and (polyaniline)(0.5)V(2)O(5) x 1.0 H(2)O.

The three-dimensional structures of emeraldine base polyaniline (PANI) and (polyaniline)(0.5)V(2)O(5) x 1.0 H(2)O have been determined by total X-ray scattering experiments. Atomic pair distribution functions (PDF) were measured to obtain experimental observables against which structural models were tested and refined. The PDF approach is necessary because of the limited structural coherence in these nanostructured materials. Polyaniline possesses a well-defined local atomic arrangement that can be described in terms of an 84-atom orthorhombic unit cell. The nanocomposite (PANI)(0.5)V(2)O(5) x 1.0 H(2)O too is locally well ordered and may be described in terms of a small number of structure-sensible parameters. The PDF approach allows the construction of structure models of PANI and (PANI)(0.5)V(2)O(5) x 1.0 H(2)O on the basis of which important materials' properties can be explained predicted and possibly improved.

Journal Article↗
PubMed2001

Functional analysis of polar amino-acid residues in membrane associated regions of the NHE1 isoform of the mammalian Na+/H+ exchanger.

The NHE1 isoform of the Na+/H+ exchanger is a ubiquitous plasma membrane protein that regulates intracellular pH in mammalian cells. Site-specific mutagenesis was used to examine the functional role of conserved, polar amino-acid residues occurring in segments of the protein associated with the membrane. Seventeen mutant proteins were assessed by characterization of intracellular pH changes in stably transfected cells that lacked an endogenous Na+/H+ exchanger. All of the mutant proteins were targeted correctly to the plasma membrane and were expressed at similar levels. Amino-acid residues Glu262 and Asp267 were critical to Na+/H+ exchanger activity while mutation of Glu391 resulted in only a partial reduction in activity. The Glu262-->Gln mutant was expressed partially as a deglycosylated protein with increased sensitivity to trypsin treatment in presence of Na+. Substitution of mutated Glu262, Asp267 and Glu391 with alternative acidic residues restored Na+/H+ exchanger activity. The Glu262-->Asp mutant had a decreased affinity for Li+, but its activity for Na+ and H+ ions was unaffected. The results support the hypothesis that side-chain oxygen atoms in a few, critically placed amino acids are important in Na+/H+ exchanger activity and the acidic amino-acid residues at positions 262, 267 and 391 are good candidates for being involved in Na+ coordination by the protein.

Amino Acid Sequence↗
PubMed1998

Neonatal fulminant hepatitis B: structural and functional analysis of complete hepatitis B virus genomes from mother and infant.

Transmission of hepatitis B virus (HBV) from anti-hepatitis B e (anti-HBe)-positive carrier mothers to their infants may result in neonatal fulminant hepatitis B (FHB). We investigated whether HBV variants with a particular DNA sequence and functional phenotype, responsible for FHB, are selected during transmission. Full-length HBV genomes from a mother-infant pair were completely sequenced and transfected into human hepatoma cells. The dominant neonatal and maternal HBV populations were nearly identical (homology 99.8%) and showed a precore stop codon mutation, T-1762 and A-1764 substitutions in the core promoter region, and pre-S2 start codon mutations. Cells transfected with variants from mother and child, compared with wild-type virus, synthesized and released a similar number or fewer HBV DNA-containing particles. In conclusion, no particular HBV strain emerged during neonatal FHB. In this case, a de novo infection with variants showing a defect in HBe antigen and pre-S2 protein synthesis but not a high replication competence probably contributed to the fulminant disease course.

Adult↗
PubMed2005

Functional analysis of MRG-1: the ortholog of human MRG15 in Caenorhabditis elegans.

Mortality Factor on Chromosome 4 (MORF4) induces senescence in several immortal human cell lines. MORF-related gene on chromosome 15 (MRG15), another expressed family member, is highly conserved and expressed in yeast to humans. To determine the biological functions of human MRG15 (hMRG15) we used RNA-mediated interference (RNAi) to silence mrg-1, the Caenorhabditis elegans ortholog, and its closest homolog Y37D8A.11. Expression of mrg-1 RNAi resulted in sterility, body wall defects, vulval protrusion, and posterior developmental defects in worms. We expressed mrg-1 under its own and the cytomegalovirus promoter in human cells. Both constructs were expressed, indicating that C. elegans promoter elements are functional in mammalian cells. Overexpression from the cytomegalovirus promoter eventually resulted in cell death, possibly due to competition with hMRG15 in endogenous nucleoprotein complexes. Recent data indicate a role for yeast and human MRG15 in transcriptional regulation via chromatin remodeling. Here we demonstrate the importance of mrg-1 in development and reproduction in C. elegans and discuss its potential to impact the aging process.

Aging↗
PubMed2005

Functional analysis of EspB from enterohaemorrhagic Escherichia coli.

In enterohaemorrhagic Escherichia coli (EHEC), the type III secretion protein EspB is translocated into the host cells and plays an important role in adherence, pore formation and effector translocation during infection. The secretion domain of EspB has been mapped previously. To define the other functional determinants of EspB, several plasmids encoding different fragments of EspB were created and analysed to see which of them lost the functions of the full-length molecule. One finding was that residues 118-190 of EspB were required for both efficient translocation of EspB and interaction of EspB with EspA. Additionally, the segment consisting of residues 217-312 was necessary for bacterial adherence. Furthermore, a predicted transmembrane domain (residues 99-118) was found to be critical for EHEC to cause red blood cell haemolysis, presumably by forming pores in the cell membrane. The same segment was also important for actin accumulation induced beneath the bacterial-attachment site. Taken together, these data indicate that the EspB protein (312 residues in total) has functions associated with its different regions. These regions may interact with each other or with other components of the type III system to orchestrate the intricate actions of EHEC during infection.

Bacterial Adhesion↗
PubMed1979

Structural and functional analysis of cloned DNA segments containing the replication and incompatibility regions of a miniplasmid derived from a copy number mutant of NR1.

A 1.45-megadalton segment of DNA cloned from a miniplasmid derived in vivo from a copy number mutant of the R plasmid NR1 has been shown to contain all functions essential for incompatibility and autonomous plasmid replication in Escherichia coli. Specific endonuclease cleavage sites within this DNA segment that localize functions required for replication have been mapped. A 0.45-megadalton fragment that specifies the FII incompatibility of NR1 has been identified within the replication region, and DNA fragments containing this incompatibility region, but lacking other functions required for replication, have been cloned.

DNA Replication↗
PubMed1988

Structural and functional analysis of CR2/EBV receptor by means of monoclonal antibodies and limited tryptic digestion.

The receptor for the C3d fragment of the third component of complement, CR2, has recently been shown also to act as the receptor for the Epstein-Barr virus (EBV) and to be involved in the control of B-cell proliferation. In order to define functionally important domains on this molecule, we produced monoclonal antibodies to several distinct epitopes. CR2 was purified from a NP-40 lysate of human tonsils by a new method involving sequential chromatography on lentil lectin Sepharose 4B and DEAE-Sephadex and used to immunize mice. After fusion we obtained four stable hybridoma lines producing antibody to CR2. Specificity of these antibodies for CR2 was ascertained by immunofluorescence analysis on a panel of various cells known to possess CR2, by their reactivity in a recently described ELISA for C3 receptors, by Western blotting with purified CR2 and immunoprecipitation from 125I-labelled Raji cells. These four antibodies were found to recognize three distinct epitopes localized on the same fragments of 95,000, 72,000, 50,000, 32,000 and 28,000 MW obtained after mild tryptic digestion of CR2. The 72,000 MW fragment contains the binding site for C3d. Two monoclonal antibodies recognizing the same epitope did not inhibit the binding of C3d-coated sheep erythrocytes to Raji cells, whereas the other two antibodies against distinct epitopes did inhibit in the presence of a second antibody. All four monoclonal antibodies stimulated the proliferation of human peripheral blood B cells.

Antibodies, Monoclonal↗
PubMed2002

Functional analysis of human hematopoietic repopulating cells mobilized with granulocyte colony-stimulating factor alone versus granulocyte colony-stimulating factor in combination with stem cell factor.

Using in vitro progenitor assays, serum-free in vitro cultures, and the nonobese diabetic/severe combined immune-deficient (NOD/SCID) ecotropic murine virus knockout xenotransplantation model to detect human SCID repopulating cells (SRCs) with multilineage reconstituting function, we have characterized and compared purified subpopulations harvested from the peripheral blood (PB) of patients receiving granulocyte colony-stimulating factor (G-CSF) alone or in combination with stem cell factor (SCF). Mobilized G-CSF plus SCF PB showed a 2-fold increase in total mononuclear cell content and a 5-fold increase in CD34-expressing cells depleted for lineage-marker expression (CD34(+)Lin(-)) as compared with patients treated with G-CSF alone. Functionally, G-CSF plus SCF-mobilized CD34(+)CD38(-)Lin(-) cells contained a 2-fold enhancement in progenitor frequency as compared with G-CSF-mobilized subsets. Despite enhanced cellularity and progenitor capacity, G-CSF plus SCF mobilization did not increase the frequency of SRCs as determined by limiting dilution analysis by means of unfractionated PB cells. Purification of SRCs from these sources demonstrated that as few as 1000 CD34(+)CD38(-)Lin(-) cells from G-CSF-mobilized PB contained SRC capacity while G-CSF plus SCF-mobilized CD34(+)CD38(-)Lin(-) cells failed to repopulate at doses up to 500 000 cells. In addition, primitive CD34(-)CD38(-)AC133(+)Lin(-) cells derived from G-CSF plus SCF-mobilized PB were capable of differentiation into CD34-expressing cells, while the identical subfractions from G-CSF PB were unable to produce CD34(+) cells in serum-free cultures. Our study defines qualitative and quantitative distinctions among subsets of primitive cells mobilized by means of G-CSF plus SCF versus G-CSF alone, and therefore has implications for the utility of purified repopulating cells from these sources.

Animals↗
PubMed2003

Yeast functional analysis: identification of two essential genes involved in ER to Golgi trafficking.

We screened for genes potentially involved in the secretory and vacuolar pathways a collection of 61 yeast strains, each bearing an essential orphan gene regulated by the tetO7-CYC1 promoter that can be down-regulated by doxycycline. After down-regulating the expression of these genes, we performed systematic Western blot analysis for markers of the secretory and vacuolar pathways that undergo post-translational modifications in their intracellular trafficking. Accumulation of protein precursors, revealed by Western immunoblot analysis, indicates defects in the secretory pathway or in associated biochemical modifications. After screening the whole collection, we identified two genes involved in ER to Golgi trafficking: RER2, a cis-prenyl transferase, and USE1, the function of which was unknown. We demonstrated that repression of USE1 also leads to BiP secretion, and therefore likely affects retrograde, in addition to anterograde, ER to Golgi trafficking. The collection also includes two essential genes involved in intracellular trafficking that were conveniently repressed without resulting growth or trafficking defects.

Biological Transport↗
PubMed2002

Phylogenetic and functional analysis of the bacteriophage P1 single-stranded DNA-binding protein.

Bacteriophage P1 encodes a single-stranded DNA-binding protein (SSB-P1), which shows 66% amino acid sequence identity to the SSB protein of the host bacterium Escherichia coli. A phylogenetic analysis indicated that the P1 ssb gene coexists with its E. coli counterpart as an independent unit and does not represent a recent acquisition of the phage. The P1 and E. coli SSB proteins are fully functionally interchangeable. SSB-P1 is nonessential for phage growth in an exponentially growing E. coli host, and it is sufficient to promote bacterial growth in the absence of the E. coli SSB protein. Expression studies showed that the P1 ssb gene is transcribed only, in an rpoS-independent fashion, during stationary-phase growth in E. coli. Mixed infection experiments demonstrated that a wild-type phage has a selective advantage over an ssb-null mutant when exposed to a bacterial host in the stationary phase. These results reconciled the observed evolutionary conservation with the seemingly redundant presence of ssb genes in many bacteriophages and conjugative plasmids.

Bacteriophage P1↗
PubMedDate not supplied

Surgical reduction of the renal mass in rats: morphologic and functional analysis on the remnant kidney.

PURPOSE: This study has analyzed the biochemical and morphological effects on the remnant kidney in rats which were submitted to progressive surgical ablation of renal mass. METHODS: Sixty Wistar male rats, weighing between 210 and 380g, were used and they were distributed in 3 groups of 20 animals each. The rats from the groups called 1, 2 and 3 were submitted to the surgical removal of renal tissue equivalent to 1/2, 2/3 and 5/6 of the whole renal mass, respectively. Then the groups were subdivided into 2 subgroups and they were operated again within 24 hours (subgroups 1B, 2B and 3B) and within 8 weeks (subgroups 1C, 2C and 3C) for the removal of the remnant kidney. 24-hour urine and blood were collected to analyze serum creatinine, clearance of creatinine and proteinuria in the first surgical intervention and at the time of the re-operation. The remnant kidney was submitted to a macroscopic evaluation for the degree of hypertrophy and to the analysis of histology. RESULTS: There was a significant increase of the volume of the remnant kidney (164%) and glomerular sclerosis was present in 40% of the animals submitted to the ablation of 5/6 of renal mass. Functional alterations characterized by the increase of urinary excretion of proteins (50% in group 3), rise in the serum creatinine (261% subgroup 2B; 371% subgroup 3B, 118% subgroup 3C) and a significant reduction of the clearance of creatinine (control x subgroup 3C = 2,88 x 1,15 ml/min: p<0,05 were also observed. CONCLUSION: The compensatory renal hypertrophy, as well as the glomerular injury translated in the form of proteinuria and sclerosis, are closed related to the volume of the remnant kidney, thus they are more evident when a greater fraction of the renal tissue is excised.

Adaptation, Physiological↗
PubMed2005

Molecular profile and partial functional analysis of novel endothelial cell-derived growth factors that regulate hematopoiesis.

Recent progress has been made in the identification of the osteoblastic cellular niche for hematopoietic stem cells (HSCs) within the bone marrow (BM). Attempts to identify the soluble factors that regulate HSC self-renewal have been less successful. We have demonstrated that primary human brain endothelial cells (HUBECs) support the ex vivo amplification of primitive human BM and cord blood cells capable of repopulating non-obese diabetic/severe combined immunodeficient repopulating (SCID) mice (SCID repopulating cells [SRCs]). In this study, we sought to characterize the soluble hematopoietic activity produced by HUBECs and to identify the growth factors secreted by HUBECs that contribute to this HSC-supportive effect. Extended noncontact HUBEC cultures supported an eight-fold increase in SRCs when combined with thrombopoietin, stem cell factor, and Flt-3 ligand compared with input CD34(+) cells or cytokines alone. Gene expression analysis of HUBEC biological replicates identified 65 differentially expressed, nonredundant transcripts without annotated hematopoietic activity. Gene ontology studies of the HUBEC transcriptome revealed a high concentration of genes encoding extracellular proteins with cell-cell signaling function. Functional analyses demonstrated that adrenomedullin, a vasodilatory hormone, synergized with stem cell factor and Flt-3 ligand to induce the proliferation of primitive human CD34(+)CD38(-)lin(-) cells and promoted the expansion of CD34(+) progenitors in culture. These data demonstrate the potential of primary HUBECs as a reservoir for the discovery of novel secreted proteins that regulate human hematopoiesis.

Adrenomedullin↗
PubMed2001

Functional analysis of the Arabidopsis thaliana mismatch repair gene MSH2.

The Arabidopsis thaliana MSH2 (AtMSH2) gene encodes a protein that belongs to a family of highly conserved proteins (MutS homologues (MSH)) involved in DNA mismatch repair. Sequence analysis strongly suggests that this single copy gene is indeed a homologue of MSH2, a gene known to play a central role in eukaryotic mismatch repair. In this report, we show that the AtMSH2 protein has functional attributes characteristic of previously described mismatch repair proteins. First, over-expression of this protein in Escherichia coli leads to a mutator phenotype similar to that reported previously for known functional homologues. Second, gel retardation assays revealed that the AtMSH2 protein has a 10-fold greater affinity for DNA containing a single pair of mismatched nucleotides versus perfectly matched DNA. These results provide experimental evidence that AtMSH2 is indeed a functional homologue of MutS.

Adenosine Triphosphatases↗
PubMed1999

Functional analysis of activation and repression domains of the rainbow trout aryl hydrocarbon receptor nuclear translocator (rtARNT) protein isoforms.

The aryl hydrocarbon receptor nuclear translocator (ARNT) protein is involved in many signaling pathways. Rainbow trout express isoforms of ARNT protein that are divergent in their C-terminal domains due to alternative RNA splicing. Rainbow trout ARNT(b) (rtARNT(b)) contains a C-terminal domain rich in glutamine and asparagine (QN), whereas the C-terminal domain of rtARNT(a) is rich in proline, serine, and threonine (PST). rtARNT(b) functions positively in AH receptor-mediated signaling, whereas rtARNT(a) functions negatively. Studies were performed to understand how changes in the C-terminal domains of the two rtARNT isoforms affect function. Deletion of the QN-rich C-terminal domain of rtARNT(b) did not affect function in aryl hydrocarbon receptor (AHR)-mediated signaling, whereas deletion of the PST-rich domain of rtARNT(a) restored function. Expression of the PST-rich domain on truncated rtARNT(b) or mouse ARNT (mARNT) reduced function of this protein by 50-80%. Gel shift assays revealed that the PST-rich domain affected AHR-mediated signaling by inhibiting DNA binding of the AHR*ARNT heterodimer. Gal4 transactivation assays revealed a potent transactivation domain in the QN-rich domain of rtARNT(b). In contrast, Gal4 proteins containing the PST-rich domain of rtARNT(a) did not transactivate because the proteins did not bind to DNA. Secondary structure analysis of the PST-rich domain revealed hydrophilic and hydrophobic regions. Truncation of the hydrophobic domain that spanned the final 20-40 amino acids of the rtARNT(a) restored function to the protein, suggesting that repressor function was related to protein misfolding or masking of the basic DNA binding domain. Functional diversity within the C-terminal domain is consistent with other negatively acting transcription factors and illustrates a common biological theme.

Animals↗
PubMed1993

Cloning and functional analysis of the mouse c-kit promoter.

The c-kit protooncogene encodes a tyrosine kinase receptor expressed during ontogeny and adult life by several important and developmentally distinct cell lineages. Mice carrying germ line c-kit mutations exhibit deficiencies in most of these lineages, demonstrating that c-kit function is necessary for their normal development. To facilitate the identification of cis-acting elements which regulate tissue-specific c-kit expression, we cloned and characterized a mouse c-kit promoter which is functional in different cell types. A major c-kit transcription initiation site (TIS), located 58 bp upstream from the translation initiation codon, is utilized in mouse mast cells and in c-kit-positive cells in the mouse cerebellum. The effects of deletions in the 5' flanking region on reporter gene activity identify three short regulatory regions which function in both mouse and human c-kit positive cell lines. The nucleotide sequence of this region does not include CCAAT or TATA boxes but contains consensus binding sites for Sp1, Ap-2 and several short GA-rich elements which resemble binding sites for the ETS-domain proteins.

Animals↗