Home About us Contact
|
Home About us Contact | ||
|
|
||
Molecular Function (molecular + function)
Selected AbstractsAn adipocentric view of signaling and intracellular traffickingDIABETES/METABOLISM: RESEARCH AND REVIEWS, Issue 5 2002Silvia Mora Abstract Adipocytes have traditionally been considered to be the primary site for whole body energy storage mainly in the form of triglycerides and fatty acids. This occurs through the ability of insulin to markedly stimulate both glucose uptake and lipogenesis. Conventional wisdom held that defects in fuel partitioning into adipocytes either because of increased adipose tissue mass and/or increased lipolysis and circulating free fatty acids resulted in dyslipidemia, obesity, insulin resistance and perhaps diabetes. However, it has become increasingly apparent that loss of adipose tissue (lipodystrophies) in both animal models and humans also leads to metabolic disorders that result in severe states of insulin resistance and potential diabetes. These apparently opposite functions can be resolved by the establishment of adipocytes not only as a fuel storage depot but also as a critical endocrine organ that secretes a variety of signaling molecules into the circulation. Although the molecular function of these adipocyte-derived signals are poorly understood, they play a central role in the maintenance of energy homeostasis by regulating insulin secretion, insulin action, glucose and lipid metabolism, energy balance, host defense and reproduction. The diversity of these secretory factors include enzymes (lipoprotein lipase (LPL) and adipsin), growth factors [vascular endothelial growth factor (VEGF)], cytokines (tumor necrosis factor-,, interleukin 6) and several other hormones involved in fatty acid and glucose metabolism (leptin, Acrp30, resistin and acylation stimulation protein). Despite the large number of molecules secreted by adipocytes, our understanding of the pathways and mechanisms controlling intracellular trafficking and exocytosis in adipocytes is poorly understood. In this article, we will review the current knowledge of the trafficking and secretion processes that take place in adipocytes, focusing our attention on two of the best characterized adipokine molecules (leptin and adiponectin) and on one of the most intensively studied regulated membrane proteins, the GLUT4 glucose transporter. Copyright © 2002 John Wiley & Sons, Ltd. [source] Development of microreactor array chip-based measurement system for massively parallel analysis of enzymatic activityELECTRONICS & COMMUNICATIONS IN JAPAN, Issue 4 2009Yosuke Hosoi Abstract Microarray chip technology such as DNA chips, peptide chips, and protein chips is one of the promising approaches for achieving high-throughput screening (HTS) of biomolecule function since it has great advantages in feasibility of automated information processing due to one-to-one indexing between array position and molecular function as well as massively parallel sample analysis as a benefit of downsizing and large-scale integration. Mostly, however, the function that can be evaluated by such microarray chips is limited to affinity of target molecules. In this paper, we propose a new HTS system and enzymatic activity based on microreactor array chip technology. A prototype of the automated and massively parallel measurement system for fluorometric assay of enzymatic reactions was developed by the combination of microreactor array chips and a highly sensitive fluorescence microscope. Design strategy of microreactor array chips and an optical measurement platform for the high-throughput enzyme assay are discussed. © 2009 Wiley Periodicals, Inc. Electron Comm Jpn, 92(4): 35,41, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecj.10056 [source] INTEGRATING EVOLUTIONARY AND FUNCTIONAL APPROACHES TO INFER ADAPTATION AT SPECIFIC LOCIEVOLUTION, Issue 9 2010Jay F. Storz Inferences about adaptation at specific loci are often exclusively based on the static analysis of DNA sequence variation. Ideally, population-genetic evidence for positive selection serves as a stepping-off point for experimental studies to elucidate the functional significance of the putatively adaptive variation. We argue that inferences about adaptation at specific loci are best achieved by integrating the indirect, retrospective insights provided by population-genetic analyses with the more direct, mechanistic insights provided by functional experiments. Integrative studies of adaptive genetic variation may sometimes be motivated by experimental insights into molecular function, which then provide the impetus to perform population genetic tests to evaluate whether the functional variation is of adaptive significance. In other cases, studies may be initiated by genome scans of DNA variation to identify candidate loci for recent adaptation. Results of such analyses can then motivate experimental efforts to test whether the identified candidate loci do in fact contribute to functional variation in some fitness-related phenotype. Functional studies can provide corroborative evidence for positive selection at particular loci, and can potentially reveal specific molecular mechanisms of adaptation. [source] Cloning of Xenopus orthologs of Ctf7/Eco1 acetyltransferase and initial characterization of XEco2FEBS JOURNAL, Issue 24 2008Masatoshi Takagi Sister chromatid cohesion is important for the correct alignment and segregation of chromosomes during cell division. Although the cohesin complex has been shown to play a physical role in holding sister chromatids together, its loading onto chromatin is not sufficient for the establishment of sister chromatid cohesion. The activity of the cohesin complex must be turned on by Ctf7/Eco1 acetyltransferase at the replication forks as the result of a specific mechanism. To dissect this mechanism in the well established in vitro system based on the use of Xenopus egg extracts, we cloned two Xenopus orthologs of Ctf7/Eco1 acetyltransferase, XEco1 and XEco2. Both proteins share a domain structure with known members of Ctf7/Eco1 family proteins. Moreover, biochemical analysis showed that XEco2 exhibited acetyltransferase activity. We raised a specific antibody against XEco2 and used it to further characterize XEco2. In tissue culture cells, XEco2 gradually accumulated in nuclei through the S phase. In nuclei formed in egg extract, XEco2 was loaded into the chromatin at a constant level in a manner sensitive to geminin, an inhibitor of the pre-replication complex assembly, but insensitive to aphidicolin, an inhibitor of DNA polymerases. In both systems, no specific localization was observed during mitosis. In XEco2-depleted egg extracts, DNA replication occurred with normal kinetics and efficiency, and the condensation and sister chromatid cohesion of subsequently formed mitotic chromosomes was unaffected. These observations will serve as a platform for elucidating the molecular function of Ctf7/Eco1 acetyltransferase in the establishment of sister chromatid cohesion in future studies, in which XEco1 and XEco2 should be dissected in parallel. [source] Ubiquitination of E3 ubiquitin ligase TRIM5, and its potential roleFEBS JOURNAL, Issue 7 2008Keiko Yamauchi HIV-1 efficiently infects susceptible cells and causes AIDS in humans. Although HIV can also enter the cells of Old World monkeys, it encounters a block before reverse transcription. Data have shown that this species-specific restriction is mediated by tripartite motif (TRIM)5,, whose molecular function is still undefined. Here, we show that TRIM5, functions as a RING-finger-type E3 ubiquitin ligase both in vitro and in vivo and ubiquitinates itself in cooperation with the E2 ubiquitin-conjugating enzyme UbcH5B. In addition to the self-ubiquitination, we show that TRIM5, is ubiquitinated by another E3 ubiquitin ligase, Ro52, and deubiquitinated by YopJ, one of the pathogenic proteins derived from Yersinia species. Thus, the ubiquitination of TRIM5, is catalyzed by itself and Ro52 and downregulated by YopJ. Unexpectedly, although TRIM5, is ubiquitinated, our results have revealed that the proteasome inhibitors MG115 and MG132 do not stabilize it in HeLa cells, suggesting that the ubiquitination of TRIM5, does not lead to proteasomal degradation. Importantly, TRIM5, is clearly conjugated by a single ubiquitin molecule (monoubiquitination). Our monoubiquitin-fusion assay suggests that monoubiquitination is a signal for TRIM5, to translocate from cytoplasmic bodies to the cytoplasm. [source] A member of the YER057c/yjgf/Uk114 family links isoleucine biosynthesis and intact mitochondria maintenance in Saccharomyces cerevisiaeGENES TO CELLS, Issue 6 2001Jong-Myong Kim Background Two paralogs, YIL051c and YER057c, in the Saccharomyces cerevisiae genome are members of the YER057c/Yigf/Uk114 family, which is highly conserved among Eubacteria, Archaea and Eukarya. Although the molecular function of this protein family is not clear, previous studies suggest that it plays a role in the regulation of metabolic pathways and cell differentiation. Results Yil051cp is 70% identical in amino acid sequence to Yer057cp, and differs in that the former is longer by 16 amino acids containing, in part, the mitochondrial targeting signal at the N-terminus of the protein. An HA-tagged protein of Yil051cp is localized strictly in mitochondria, while that of Yer057cp is found in both cytoplasm and nucleus. Disruption of YIL051c (yil051c,) resulted in severe growth retardation in glucose medium due to isoleucine auxotroph, and no growth in glycerol medium due to the loss of mitochondria. An extract prepared from yil051c, cells showed no transaminase activity for isoleucine, while that for valine or leucine was intact. Haploid yil051c, cells newly isolated from the YIL051c/yil051c, hetero-diploids gradually lost mitochondrial DNA within 24 h in the absence of, but not in the presence of, an isoleucine. Mutants either requiring leucine (leu2,112) or isoleucine-valine (bat1,, bat2,) in a YIL051c background showed no changes in mitochondrial DNA maintenance in the absence of requirements. Conclusions Based on these results, we named Yil051c as Ibm1 (Isoleucine Biosynthesis and Mitochondria maintenance1) and concluded that: (i) Ibm1p determines the specificity of isoleucine biosynthesis, probably at the transamination step, (ii) Ibm1p is required for the maintenance of mitochondrial DNA when isoleucine is deficient, and (iii) Isoleucine compensates for the lack of Ibm1p. Taken together, Ibm1p may act as a sensor for isoleucine deficiency as well as a regulator determining the specificity for branched amino acid transaminase. [source] The utility of behavioral models and modules in molecular analyses of social behaviorGENES, BRAIN AND BEHAVIOR, Issue 3 2008Andrew B. Barron It is extremely difficult to trace the causal pathway relating gene products or molecular pathways to the expression of behavior. This is especially true for social behavior, which being dependent on interactions and communication between individuals is even further removed from molecular-level events. In this review, we discuss how behavioral models can aid molecular analyses of social behavior. Various models of behavior exist, each of which suggest strategies to dissect complex behavior into simpler behavioral ,modules.' The resulting modules are easier to relate to neural processes and thus suggest hypotheses for neural and molecular function. Here we discuss how three different models of behavior have facilitated understanding the molecular bases of aspects of social behavior. We discuss the response threshold model and two different approaches to modeling motivation, the state space model and models of reinforcement and reward processing. The examples we have chosen illustrate how models can generate testable hypotheses for neural and molecular function and also how molecular analyses probe the validity of a model of behavior. We do not champion one model over another; rather, our examples illustrate how modeling and molecular analyses can be synergistic in exploring the molecular bases of social behavior. [source] Glutamate Receptor Subunit ,2 Is Highly Expressed in a Novel Population of Glial-Like Cells in Rat Pineal Glands in CultureJOURNAL OF NEUROCHEMISTRY, Issue 3 2000Shouki Yatsushiro Abstract: The mammalian pineal gland uses L-glutamate as an intercellular chemical transmitter to regulate negatively melatonin synthesis. To receive glutamate signals, pinealocytes express at least three kinds of glutamate receptors: metabotropic receptor types 3 and 5 and an ionotropic receptor, GluR1. In this study, we examined whether or not the fourth class of ionotropic receptor, ,, which is known for its nondefinitive molecular function and its unique expression pattern in brain, is expressed in pineal gland. RT-PCR analyses with specific probes indicated the expression of mRNA of ,2 but not that of ,1 in pineal gland and cultured pineal cells. Western blotting analysis with polyclonal antibodies specific to the carboxyl-terminal region of the ,2 receptor recognized a single 110-kDa polypeptide of cerebellar membranes and specifically immunostained Purkinje cells. The ,2 antibodies recognized a 110-kDa polypeptide of pineal membranes and specifically immunostained huge glial-like cells with the occasional presence of several long, branching processes in a pineal cell culture. ,2 is not uniformly distributed throughout the cells and is relatively abundant at the periphery of the cell bodies and long processes, where the terminals of synaptophysin-positive processes of pinealocytes, a site for glutamate secretion, are frequently present. The ,2-positive cells constitute a very minor population among total pineal cells (,0.03%). Double immunolabeling with ,2 antibodies and antibodies against marker proteins for pineal interstitial cells clearly distinguishes ,2-positive pineal cells and other known interstitial cells, including glial fibrillary acidic protein- or vimentin-positive glial-like cells. These results indicated that the ,2 glutamate receptor is expressed in a novel subpopulation of pineal glial-like cells in culture and suggest the presence of a glutamate-mediated intercellular signal transduction mechanism between pinealocytes and ,2-expressing cells. The pineal cells may provide a good experimental system for studies on the function of glutamate receptor ,2. [source] Mss11p is a transcription factor regulating pseudohyphal differentiation, invasive growth and starch metabolism in Saccharomyces cerevisiae in response to nutrient availabilityMOLECULAR MICROBIOLOGY, Issue 1 2003Marco Gagiano Summary In Saccharomyces cerevisiae, the cell surface protein, Muc1p, was shown to be critical for invasive growth and pseudohyphal differentiation. The transcription of MUC1 and of the co-regulated STA2 glucoamylase gene is controlled by the interplay of a multitude of regulators, including Ste12p, Tec1p, Flo8p, Msn1p and Mss11p. Genetic analysis suggests that Mss11p plays an essential role in this regulatory process and that it functions at the convergence of at least two signalling cascades, the filamentous growth MAPK cascade and the cAMP-PKA pathway. Despite this central role in the control of filamentous growth and starch metabolism, the exact molecular function of Mss11p is unknown. We subjected Mss11p to a detailed molecular analysis and report here on its role in transcriptional regulation, as well as on the identification of specific domains required to confer transcriptional activation in response to nutritional signals. We show that Mss11p contains two independent transactivation domains, one of which is a highly conserved sequence that is found in several proteins with unidentified function in mammalian and invertebrate organisms. We also identify conserved amino acids that are required for the activation function. [source] Gq-coupled Rhodopsin Subfamily Composed of Invertebrate Visual Pigment and Melanopsin,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Mitsumasa Koyanagi Rhodopsins (rhodopsins and their related photopigments) are phylogenetically classified into at least seven subfamilies, which are also roughly discriminated by molecular function. The Gq-coupled rhodopsin subfamily, members of which activate the Gq type G protein upon light absorption, contains pigments which underlie both visual and nonvisual physiologic functions. Gq-coupled visual pigments have been found in the rhabdomeric photoreceptor cells of varied protostomes, and those of molluskans and arthropods have been extensively investigated. Recently, a novel photopigment, melanopsin, and its homologs have been identified in varied vertebrates. In mammals, melanopsin is localized in retinal ganglion cells and is involved in nonvisual systems, including circadian entrainment and pupillary light responses. More recently, we discovered a melanopsin homolog in amphioxus, the closest living invertebrate to vertebrates. Amphioxus melanopsin is localized in putative nonvisual photoreceptor cells with rhabdomeric morphology and exhibits molecular properties almost identical to those of invertebrate Gq-coupled visual pigments. The localization and properties of amphioxus melanopsin bridged the functional and evolutionary gap between invertebrate Gq-coupled visual pigments and vertebrate circadian photopigment melanopsins. Research into the Gq-coupled rhodopsin subfamily, especially invertebrate melanopsins, will provide an opportunity to investigate the evolution of various physiologic functions, based on orthologous genes, during animal evolution. [source] Functional analyses of the Physcomitrella patens phytochromes in regulating chloroplast avoidance movementTHE PLANT JOURNAL, Issue 6 2007Hidetoshi Uenaka Summary Red light-induced chloroplast movement in Physcomitrella patens (Pp) is mediated by dichroic phytochrome in the cytoplasm. To analyze the molecular function of the photoreceptor in the cytoplasm, we developed a protoplast system in which chloroplast photomovement was exclusively dependent on the expression of phytochrome cDNA constructs introduced by polyethylene glycol (PEG) transformation. YFP was fused to the phytochrome constructs and their expression was detected by fluorescence. The chloroplast avoidance response was induced in the protoplasts expressing a YFP fusion of PHY1,PHY3, but not of PHY4 or YFP alone. Phy::yfp fluorescence was detected in the cytoplasm. No change in the location of phy1::yfp or phy2::yfp was revealed before and after photomovement. When phy1::yfp and phy2::yfp were targeted to the nucleus by fusing a nuclear localization signal to the constructs, red light avoidance was not induced. To determine the domains of PHY2 essential for avoidance response, various partially-deleted PHY2::YFP constructs were tested. The N-terminal extension domain (NTE) was found to be necessary but the C-terminal histidine kinase-related domain (HKRD) was dispensable. An avoidance response was not induced under expression of phytochrome N-terminal half domain [deleting both the PAS (Per, Arnt, Sim)-related domain (PRD) and HKRD]. GUS fusion of this N-terminal half domain, reported to be fully functional in Arabidopsis for several phyA- and phyB-regulated responses was not effective in chloroplast avoidance movement. Domain requirement and GUS fusion effect were also confirmed in PHY1. These results indicate that Pp phy1,Pp phy3 in the cytoplasm mediate chloroplast avoidance movement, and that NTE and PRD, but not HKRD, are required for their function. [source] Differential gene expression profiles in the venom gland/sac of Orancistrocerus drewseni (Hymenoptera: Eumenidae)ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY (ELECTRONIC), Issue 4 2009Ji Hyeong Baek Abstract To determine differential gene expression profiles in the venom gland and sac (gland/sac) of a solitary hunting wasp species, Orancistrocerus drewseni Saussure (1857), a subtractive cDNA library was constructed by suppression subtractive hybridization. A total of 498 expressed sequence tags (EST) were clustered and assembled into 205 contigs (94 multiple sequences and 111 singletons). About 65% (134) of the contigs had matched BLASTx hits (E,10,4). Among these, 115 contigs had similarity to proteins with assigned molecular function in the Gene Ontology database, and most of them (112 contigs, 83%) were homologous to genes from Hymenoptera, particularly to Apis mellifera (98 contigs). The contigs encoding hyaluronidase and phospholipase A2, known to be main components of wasp venoms, were found in high frequencies (27 and 4%, respectively, as judged by the number of ESTs) in the gene ontology category of catalytic activity. Full-length open reading frames of hyaluronidase and phospholipase A2 were characterized and their abundance in the venom gland/sac was confirmed by quantitative real-time PCR. Several contigs encoding enzymes, including zinc-metallopeptidases that are likely involved in the processing and activation of venomous proteins or peptides, were also identified from the library. Discovery of venom gland/sac-specific genes should promote further studies on biologically active components in the venom of O. drewseni. © 2009 Wiley Periodicals, Inc. [source] Structure of OsmC from Escherichia coli: a salt-shock-induced proteinACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2004Dong Hae Shin The crystal structure of an osmotically inducible protein (OsmC) from Escherichia coli has been determined at 2.4,Å resolution. OsmC is a representative protein of the OsmC sequence family, which is composed of three sequence subfamilies. The structure of OsmC provides a view of a salt-shock-induced protein. Two identical monomers form a cylindrically shaped dimer in which six helices are located on the inside and two six-stranded ,-sheets wrap around these helices. Structural comparison suggests that the OsmC sequence family has a peroxiredoxin function and has a unique structure compared with other peroxiredoxin families. A detailed analysis of structures and sequence comparisons in the OsmC sequence family revealed that each subfamily has unique motifs. In addition, the molecular function of the OsmC sequence family is discussed based on structural comparisons among the subfamily members. [source] Structure of the hypothetical protein AQ_1354 from Aquifex aeolicusACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2003Vaheh Oganesyan The crystal structure of a hypothetical protein AQ_1354 (gi 2983779) from the hyperthermophilic bacteria Aquifex aeolicus has been determined using X-ray crystallography. As found in many structural genomics studies, this protein is not associated with any known function based on its amino-acid sequence. PSI-BLAST analysis against a non-redundant sequence database gave 68 similar sequences referred to as `conserved hypothetical proteins' from the uncharacterized protein family UPF0054 (accession No. PF02310). Crystallographic analysis revealed that the overall fold of this protein consists of one central ,-helix surrounded by a four-stranded ,-sheet and four other ,-helices. Structure-based homology analysis with DALI revealed that the structure has a moderate to good resemblance to metal-dependent proteinases such as collagenases and gelatinases, thus suggesting its possible molecular function. However, experimental tests for collagenase and gelatinase-type function show no detectable activity under standard assay conditions. Therefore, we suggest either that the members of the UPF0054 family have a similar fold but different biochemical functions to those of collagenases and gelatinases or that they have a similar function but perform it under different conditions. [source] MraZ from Escherichia coli: cloning, purification, crystallization and preliminary X-ray analysisACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2005Melanie A. Adams The MraZ family of proteins, also referred to as the UPF0040 family, are highly conserved in bacteria and are thought to play a role in cell-wall biosynthesis and cell division. The murein region A (mra) gene cluster encodes MraZ proteins along with a number of other proteins involved in this complex process. To date, there has been no clear functional assignment provided for MraZ proteins and the structure of a homologue from Mycoplasma pneumoniae, MPN314, failed to suggest a molecular function. The b0081 gene from Escherichia coli that encodes the MraZ protein was cloned and the protein was overexpressed, purified and crystallized. This data is presented along with evidence that the E. coli homologue exists in a different oligomeric state to the MPN314 protein. [source] Genome dynamics in major bacterial pathogensFEMS MICROBIOLOGY REVIEWS, Issue 3 2009Ole Herman Ambur Abstract Pathogenic bacteria continuously encounter multiple forms of stress in their hostile environments, which leads to DNA damage. With the new insight into biology offered by genome sequences, the elucidation of the gene content encoding proteins provides clues toward understanding the microbial lifestyle related to habitat and niche. Campylobacter jejuni, Haemophilus influenzae, Helicobacter pylori, Mycobacterium tuberculosis, the pathogenic Neisseria, Streptococcus pneumoniae, Streptococcus pyogenes and Staphylococcus aureus are major human pathogens causing detrimental morbidity and mortality at a global scale. An algorithm for the clustering of orthologs was established in order to identify whether orthologs of selected genes were present or absent in the genomes of the pathogenic bacteria under study. Based on the known genes for the various functions and their orthologs in selected pathogenic bacteria, an overview of the presence of the different types of genes was created. In this context, we focus on selected processes enabling genome dynamics in these particular pathogens, namely DNA repair, recombination and horizontal gene transfer. An understanding of the precise molecular functions of the enzymes participating in DNA metabolism and their importance in the maintenance of bacterial genome integrity has also, in recent years, indicated a future role for these enzymes as targets for therapeutic intervention. [source] Missense mutations of human homeoboxes: A reviewHUMAN MUTATION, Issue 5 2001Angela V. D'Elia Abstract The homeodomain (encoded by the homeobox) is the DNA-binding domain of a large variety of transcriptional regulators involved in controlling cell fate decisions and development. Mutations of homeobox-containing genes cause several diseases in humans. A variety of missense mutations giving rise to human diseases have been described. These mutations are an excellent model to better understand homeodomain molecular functions. To this end, homeobox missense mutations giving rise to human diseases are reviewed. Seventy-four independent homeobox mutations have been observed in 17 different genes. In the same genes, 30 missense mutations outside the homeobox have been observed, indicating that the homeodomain is more easily affected by single amino acids changes than the rest of the protein. Most missense mutations have dominant effects. Several data indicate that dominance is mostly due to haploinsufficiency. Among proteins having the homeodomain as the only DNA-binding domain, three "hot spot" regions can be delineated: 1) at codon encoding for Arg5; 2) at codon encoding for Arg31; and 3) at codons encoding for amino acids of recognition helix. In the latter, mutations at codons encoding for Arg residues at positions 52 and 53 are prevalent. In the recognition helix, Arg residues at positions 52 and 53 establish contacts with phosphates in the DNA backbone. Missense mutations of amino acids that contribute to sequence discrimination (such as those at positions 50 and 54) are present only in a minority of cases. Similar data have been obtained when missense mutations of proteins possessing an additional DNA-binding domain have been analyzed. The only exception is observed in the POU1F1 (PIT1) homeodomain, in which Arg58 is a "hot spot" for mutations, but is not involved in DNA recognition. Hum Mutat 18:361,374, 2001. © 2001 Wiley-Liss, Inc. [source] Role of TIEG1 in biological processes and disease statesJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 3 2007Malayannan Subramaniam Abstract A novel TGF, Inducible Early Gene-1 (TIEG1) was discovered in human osteoblast (OB) cells by our laboratory. Over the past decade, a handful of laboratories have revealed a multitude of organismic, cellular, and molecular functions of this gene. TIEG1 is now classified as a member of the 3 zinc finger family of Krüppel-like transcription factors (KLF10). Other closely related factors [TIEG2 (KLF11) and TIEG3/TIEG2b] have been reported and are briefly compared. As described in this review, TIEG1 is shown to play a role in regulating estrogen and TGF, actions, the latter through the Smad signaling pathway. In both cases, TIEG1 acts as an inducer or repressor of gene transcription to enhance the TGF,/Smad pathway, as well at other signaling pathways, to regulate cell proliferation, differentiation, and apoptosis. This review outlines TIEG1's molecular functions and roles in skeletal disease (osteopenia/osteoporosis), heart disease (hypertrophic cardiomyopathy), and cancer (breast and prostate). J. Cell. Biochem. 102: 539,548, 2007. © 2007 Wiley-Liss, Inc. [source] Defining the membrane proteome of NK cellsJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 1 2010Dhimankrishna Ghosh Abstract The present study was initiated to define the composition of the membrane proteome of the Natural Killer (NK) like cell line YTS. Isolated membranes were treated with reagents that have been reported to remove peripheral membrane proteins. Additional steps involving trifluoroethanol (TFE) were introduced in an effort to remove remaining nonintegral membrane proteins. This treatment resulted in the release of a subset of proteins without any apparent disruption of membrane integrity. The membranes were solubilized and digested with trypsin in 25% TFE. The resulting peptides were separated using an off-line two-dimensional reversed phase LC technique at alkaline and acidic pHs. Mass spectrometric analysis identified 1843 proteins with high confidence scores. On the basis of the presence of transmembrane regions or evidence of posttranslational modifications and prediction algorithms, approximately 40% of the identified proteins were predicted as plausible membrane proteins. The remaining species were largely involved in cellular processes and molecular functions that could be predicted to be transiently associated with membranes. The analytical approaches presented in this study offer robust generic methods for the identification and characterization of membrane proteins. These observations highlight the fact that the membrane is a dynamic entity that is composed of integral and stably associated proteins. Copyright © 2009 John Wiley & Sons, Ltd. [source] Biochemical applications of mass spectrometry in pharmaceutical drug discoveryMASS SPECTROMETRY REVIEWS, Issue 3 2005Kieran F. Geoghegan Abstract Biochemical applications of mass spectrometry (MS) are important in the pharmaceutical industry. They comprise compositional analyses of biomolecules, especially proteins, and methods that measure molecular functions such as ligand binding. In early drug discovery, MS is used to characterize essential reagents and in structural biology. A number of MS-based methods have been proposed for use in high-throughput screening (HTS), but are unlikely to supplant established radiometric and fluorometric methods for this purpose. These methods, which include pulsed-ultrafiltration MS, frontal affinity chromatography-MS, and size-exclusion chromatography-MS, may ultimately be most successful in the post-screening lead development phase. In full development, MS is used heavily in the search for biomarkers that can be used to gauge disease progression and drug action. This review gives equal attention to the technical aspects of MS-based methods and to selective pressures present in the industrial environment that influence their chances of gaining wide application. © 2004 Wiley Periodicals, Inc., Mass Spec Rev 24:347,366, 2005 [source] Modeling the proteome of a Marek's disease transformed cell line: a natural animal model for CD30 overexpressing lymphomasPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 8 2007Joram J. Buza Dr. Abstract Marek's disease (MD) in the chicken, caused by the highly infectious MD ,-herpesvirus (MDV), is both commercially important and a unique, naturally occurring model for human T-cell lymphomas overexpressing the Hodgkin's disease antigen, CD30. Here, we used proteomics as a basis for modeling the molecular functions and biological processes involved in MDV-induced lymphomagenesis. Proteins were extracted from an MDV-transformed cell line and were then identified using 2-D LC-ESI-MS/MS. From the resulting 3870 cellular and 21 MDV proteins we confirm the existence of 3150 "predicted" and 12 "hypothetical" chicken proteins. The UA-01 proteome is proliferative, differentiated, angiogenic, pro-metastatic and pro-immune-escape but anti-programmed cell death, -anergy, -quiescence and -senescence and is consistent with a cancer phenotype. In particular, the pro-metastatic integrin signaling pathway and the ERK/MAPK signaling pathways were the two predominant signaling pathways represented. The cytokines, cytokine receptors, and their related proteins suggest that UA-01 has a regulatory T-cell phenotype. [source] Calcium/calmodulin-dependent serine protein kinase and mental retardation,ANNALS OF NEUROLOGY, Issue 4 2009Yi-Ping Hsueh PhD Calcium/calmodulin-dependent serine protein kinase (CASK) belongs to the membrane-associated guanylate kinase protein family. The members of this protein family function as multiple domain adaptor proteins originally identified at cell junctions and synapses. Insertional mutations or targeted disruption of the CASK gene in mice results in neonatal lethality, indicating an important role for CASK in development. Recently, several reports have also indicated that mutations in the human CASK gene result in X-linked malformations of the brain and mental retardation. At the molecular level, many studies indicate that CASK is critical for synapse formation at both presynaptic and postsynaptic junctions, and in the regulation of gene expression. The known molecular functions of CASK explain, at least partially, mental retardation and brain developmental defects in patients. In this review, recent findings about CASK are summarized and discussed. Ann Neurol 2009;66:438,443 [source] Phenotypic interactions of spinster with the genes encoding proteins for cell death control in Drosophila melanogasterARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY (ELECTRONIC), Issue 3 2010Akira Sakurai Abstract The spin gene was first identified by its mutant phenotype, which is characterized by extremely strong mate refusal by females in response to male courtship in Drosophila. Spin mutants are also known to be accompanied by a remarkable reduction in programmed cell death in the reproductive and nervous systems. To better understand the molecular functions of spin, we searched for its genetic modifiers. Forced expression of spin+ in somatic cells as driven by ptc-Gal4 in the testis resulted in the invasion of mature sperm into the anterior testes tip, which is otherwise occupied only by immature germ cells. To obtain genes that modulate spin's effect, the gain-of-function spin phenotype was observed in the presence of a chromosome harboring an EP or GS P-element insertion, which initiates transcription of the genomic sequence neighboring the insertion site. We isolated th and emc as suppressors of spin and atg8a as a gene that reproduces the spin phenotype on its own. th encodes Inhibitor of apoptosis-1, and mammalian Id genes homologous to emc are known to inhibit apoptosis. atg8a encodes a protein essential for autophagy. These results suggest that spin promotes cell death mechanisms that are regulated negatively by th and emc and positively by atg8a. © 2010 Wiley Periodicals, Inc. [source] Animal performance and stress: responses and tolerance limits at different levels of biological organisationBIOLOGICAL REVIEWS, Issue 2 2009Karin S. Kassahn ABSTRACT Recent advances in molecular biology and the use of DNA microarrays for gene expression profiling are providing new insights into the animal stress response, particularly the effects of stress on gene regulation. However, interpretation of the complex transcriptional changes that occur during stress still poses many challenges because the relationship between changes at the transcriptional level and other levels of biological organisation is not well understood. To confront these challenges, a conceptual model linking physiological and transcriptional responses to stress would be helpful. Here, we provide the basis for one such model by synthesising data from organismal, endocrine, cellular, molecular, and genomic studies. We show using available examples from ectothermic vertebrates that reduced oxygen levels and oxidative stress are common to many stress conditions and that the responses to different types of stress, such as environmental, handling and confinement stress, often converge at the challenge of dealing with oxygen imbalance and oxidative stress. As a result, a common set of stress responses exists that is largely independent of the type of stressor applied. These common responses include the repair of DNA and protein damage, cell cycle arrest or apoptosis, changes in cellular metabolism that reflect the transition from a state of cellular growth to one of cellular repair, the release of stress hormones, changes in mitochondrial densities and properties, changes in oxygen transport capacities and changes in cardio-respiratory function. Changes at the transcriptional level recapitulate these common responses, with many stress-responsive genes functioning in cell cycle control, regulation of transcription, protein turnover, metabolism, and cellular repair. These common transcriptional responses to stress appear coordinated by only a limited number of stress-inducible and redox-sensitive transcription factors and signal transduction pathways, such as the immediate early genes c-fos and c-jun, the transcription factors NF,B and HIF - 1,, and the JNK and p38 kinase signalling pathways. As an example of environmental stress responses, we present temperature response curves at organismal, cellular and molecular levels. Acclimation and physiological adjustments that can shift the threshold temperatures for the onset of these responses are discussed and include, for example, adjustments of the oxygen delivery system, the heat shock response, cellular repair system, and transcriptome. Ultimately, however, an organism's ability to cope with environmental change is largely determined by its ability to maintain aerobic scope and to prevent loss in performance. These systemic constraints can determine an organism's long-term survival well before cellular and molecular functions are disturbed. The conceptual model we propose here discusses some of the crosslinks between responses at different levels of biological organisation and the central role of oxygen balance and oxidative stress in eliciting these responses with the aim to help the interpretation of environmental genomic data in the context of organismal function and performance. [source] Regulatory mechanisms and functions of intermediate filaments: A study using site- and phosphorylation state-specific antibodiesCANCER SCIENCE, Issue 3 2006Ichiro Izawa Intermediate filaments (IF) form the structural framework of the cytoskeleton. Although histopathological detection of IF proteins is utilized for examining cancer specimens as reliable markers, the molecular mechanisms by which IF are involved in the biology of cancer cells are still unclear. We found that site-specific phosphorylation of IF proteins induces the disassembly of filament structures. To further dissect the in vivo spatiotemporal dynamics of IF phosphorylation, we developed site- and phosphorylation state-specific antibodies. Using these antibodies, we detected kinase activities that specifically phosphorylate type III IF, including vimentin, glial fibrillary acidic protein and desmin, during mitosis. Cdk1 phosphorylates vimentin-Ser55 from prometaphase to metaphase, leading to the recruitment of Polo-like kinase 1 (Plk1) to vimentin. Upon binding to Phospho-Ser55 of vimentin, Plk1 is activated, and then phosphorylates vimentin-Ser82. During cytokinesis, Rho-kinase and Aurora-B specifically phosphorylate IF at the cleavage furrow. IF phosphorylation by Cdk1, Plk1, Rho-kinase and Aurora-B plays an important role in the local IF breakdown, and is essential for the efficient segregation of IF networks into daughter cells. As another part of our research on IF, we have set out to find the binding partners with simple epithelial keratin 8/18. We identified tumor necrosis factor receptor type 1-associated death domain protein (TRADD) as a keratin 18-binding protein. Together with data from other laboratories, it is proposed that simple epithelial keratins may play a role in modulating the response to some apoptotic signals. Elucidation of the precise molecular functions of IF is expected to improve our understanding of tumor development, invasion and metastasis. (Cancer Sci 2006; 97: 167,174) [source] Live cell fluorescence microscopy to study microbial pathogenesisCELLULAR MICROBIOLOGY, Issue 4 2009Adam D. Hoppe Summary Advances in microscopy and fluorescent probes provide new insight into the nanometer-scale biochemistry governing the interactions between eukaryotic cells and pathogens. When combined with mathematical modelling, these new technologies hold the promise of qualitative, quantitative and predictive descriptions of these pathways. Using the light microscope to study the spatial and temporal relationships between pathogens, host cells and their respective biochemical machinery requires an appreciation for how fluorescent probes and imaging devices function. This review summarizes how live cell fluorescence microscopy with common instruments can provide quantitative insight into the cellular and molecular functions of hosts and pathogens. [source] | |||||||||||||||||||||||||