Home About us Contact
|
Home About us Contact | ||
|
|
||
Diverse Functions (diverse + function)
Selected AbstractsDiverse Functions and Molecular Properties Emerging for CAX Cation/H+ Exchangers in PlantsPLANT BIOLOGY, Issue 4 2006T. Shigaki Abstract: Steep concentration gradients of many ions are actively maintained, with lower concentrations typically located in the cytosol, and higher concentrations in organelles and outside the cell. The vacuole is an important storage organelle for many ions. The concentration gradient of cations is established across the plant tonoplast, in part, by high-capacity cation/H+ (CAX) exchange activity. While plants may not be green yeast, analysis of CAX regulation and substrate specificity has been greatly aided by utilizing yeast as an experimental tool. The basic CAX biology in Arabidopsis has immediate relevance toward understanding the functional interplay between diverse transport processes. The long-range applied goals are to identify novel transporters and express them in crop plants in order to "mine" nutrients out of the soil and into plants. In doing so, this could boost the levels of essential nutrients in plants. [source] Mass spectrometric analysis of microtubule co-sedimented proteins from rat brainGENES TO CELLS, Issue 4 2008Tatsuhiko Sakamoto Microtubules (MTs) play crucial roles in a variety of cell functions, such as mitosis, vesicle transport and cell motility. MTs also compose specialized structures, such as centrosomes, spindles and cilia. However, molecular mechanisms of these MT-based functions and structures are not fully understood. Here, we analyzed MT co-sedimented proteins from rat brain by tandem mass spectrometry (MS) upon ion exchange column chromatography. We identified a total of 391 proteins. These proteins were grouped into 12 categories: 57 MT cytoskeletal proteins, including MT-associated proteins (MAPs) and motor proteins; 66 other cytoskeletal proteins; 4 centrosomal proteins; 10 chaperons; 5 Golgi proteins; 7 mitochondrial proteins; 62 nucleic acid-binding proteins; 14 nuclear proteins; 13 ribosomal proteins; 28 vesicle transport proteins; 83 proteins with diverse function and/or localization; and 42 uncharacterized proteins. Of these uncharacterized proteins, six proteins were expressed in cultured cells, resulting in the identification of three novel components of centrosomes and cilia. Our present method is not specific for MAPs, but is useful for identifying low abundant novel MAPs and components of MT-based structures. Our analysis provides an extensive list of potential candidates for future study of the molecular mechanisms of MT-based functions and structures. [source] AAA+ superfamily ATPases: common structure,diverse functionGENES TO CELLS, Issue 7 2001Teru Ogura The AAA+ superfamily of ATPases, which contain a homologous ATPase module, are found in all kingdoms of living organisms where they participate in diverse cellular processes including membrane fusion, proteolysis and DNA replication. Recent structural studies have revealed that they usually form ring-shaped oligomers, which are crucial for their ATPase activities and mechanisms of action. These ring-shaped oligomeric complexes are versatile in their mode of action, which collectively seem to involve some form of disruption of molecular or macromolecular structure; unfolding of proteins, disassembly of protein complexes, unwinding of DNA, or alteration of the state of DNA,protein complexes. Thus, the AAA+ proteins represent a novel type of molecular chaperone. Comparative analyses have also revealed significant similarities and differences in structure and molecular mechanism between AAA+ ATPases and other ring-shaped ATPases. [source] A survey of H2 gene sequences, including new wild-derived genesINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 1 2007N. A. Mitchison Summary A comprehensive collection of mouse major histocompatibility complex (MHC) promoter and exon 2 sequences is here presented and analysed. It covers the three best known class II genes and one class I gene, and includes new wild mouse sequences from the ,w' back-cross strains and from the Jackson collection. All sequences are in GenBank, and the new exon sequences largely confirm previous typing by serology and immune function. As in human leucocyte antigen (HLA), the overall nucleotide diversity is higher in the class II genes, in keeping with their more diverse function. Diversity along the promoters is highest in the region of known transcription factor binding, most notably in and around the CRE and rCAAT sequences. This distribution parallels that of maximum single nucleotide polymorphism impact previously obtained with reporter constructs. Taking into account the low nucleotide diversity of the CIITA promoter, we conclude that MHC promoters are likely to have diversified through co-evolution with their exons, while themselves also directly subject to natural selection. The H2Ebp alleles form a distinct group, associated with their lack of the recombination hot spot located between exon 2 and exon 3. The collection is expected to prove useful in guiding functional and evolutionary studies. [source] Six cadm/synCAM genes are expressed in the nervous system of developing zebrafishDEVELOPMENTAL DYNAMICS, Issue 1 2008Thomas Pietri Abstract The Cadm (cell adhesion molecule) family of cell adhesion molecules (also known as IGSF4, SynCAM, Necl and TSLC) has been implicated in a multitude of physiological and pathological processes, such as spermatogenesis, synapse formation and lung cancer. The precise mechanisms by which these adhesion molecules mediate these diverse functions remain unknown. To investigate mechanisms of action of these molecules during development, we have identified zebrafish orthologs of Cadm family members and have examined their expression patterns during development and in the adult. Zebrafish possess six cadm genes. Sequence comparisons and phylogenetic analysis suggest that four of the zebrafish cadm genes represent duplicates of two tetrapod Cadm genes, whereas the other two cadm genes are single orthologs of tetrapod Cadm genes. All six zebrafish cadms are expressed throughout the nervous system both during development and in the adult. The spatial and temporal patterns of expression suggest multiple roles for Cadms during nervous system development. Developmental Dynamics 237:233,246, 2008. © 2007 Wiley-Liss, Inc. [source] Drosophila neuromuscular synapse assembly and function require the TGF-, type I receptor saxophone and the transcription factor MadDEVELOPMENTAL NEUROBIOLOGY, Issue 2 2003Joel M. Rawson Abstract Transforming growth factor-,s (TGF-,) comprise a superfamily of secreted proteins with diverse functions in patterning and cell division control. TGF-, signaling has been implicated in synapse assembly and plasticity in both vertebrate and invertebrate systems. Recently, wishful thinking, a Drosophila gene that encodes a protein related to BMP type II receptors, has been shown to be required for the normal function and development of the neuromuscular junction (NMJ). These findings suggest that a TGF-,-related ligand activates a signaling cascade involving type I and II receptors and the Smad family of transcription factors to orchestrate the assembly of the NMJ. Here we demonstrate that the TGF-, type I receptor Saxophone and the downstream transcription factor Mothers against dpp (Mad) are essential for the normal structural and functional development of the Drosophila NMJ, a synapse that displays activity-dependent plasticity. © 2003 Wiley Periodicals, Inc. J Neurobiol 55: 134,150, 2003 [source] Electrochemical Nitric Oxide Sensors for Biological Samples , Principle, Selected Examples and ApplicationsELECTROANALYSIS, Issue 1 2003Fethi Bedioui Abstract The discoveries made in the 1980s that NO could be synthesized by mammalian cells and could act as physiological messenger and cytotoxic agent had elevated the importance of its detection. The numerous properties of NO, that enable it to carry out its diverse functions, also present considerable problems when attempting its detection and quantification in biological systems. Indeed, its total free concentration in physiological conditions has been established to be in nanomolar range. Thus, detection of nitric oxide remains a challenge, pointing out the difficult dual requirements for specificity and sensitivity. Exception made for the electrochemical techniques, most of the approaches (namely UV-visible spectroscopy, fluorescence, electron paramagnetic resonance spectroscopy) use indirect methods for estimating endogenous NO, relying on measurements of secondary species such as nitrite and nitrate or NO-adducts. They also suffer from allowing only ex situ measurements. So, the only strategies that allow a direct and in vivo detection of NO are those based on the use of ultramicroelectrodes. The reality is that surface electrode modification is needed to make the ultramicroelectrode material selective for NO. Therefore, the design of modified electrode surfaces using organized layers is very attractive and provides the ideal strategy. This review addresses a global description of the various approaches that have involved chemically modified microelectrodes specially designed for the electrochemical detection of NO in biological media. Selected significant examples of applications in biological tissues are also reported in order to highlight the importance of this approach in having new insights into the modulatory role of NO in physiology and pathophysiology. [source] Revisiting the specificity of the MHC class,II transactivator CIITA in vivoEUROPEAN JOURNAL OF IMMUNOLOGY, Issue 6 2006Abstract CIITA is a master regulatory factor for the expression of MHC class,II (MHC-II) and accessory genes involved in Ag presentation. It has recently been suggested that CIITA also regulates numerous other genes having diverse functions within and outside the immune system. To determine whether these genes are indeed relevant targets of CIITA in vivo, we studied their expression in CIITA-transgenic and CIITA-deficient mice. In contrast to the decisive control of MHC-II and related genes by CIITA, nine putative non-MHC target genes (Eif3s2, Kpna6, Tap1, Yars, Col1a2, Ctse, Ptprr, Tnfsf6 and Plxna1) were found to be CIITA independent in all cell types examined. Two other target genes, encoding IL-4 and IFN-,, were indeed found to be up- and down-regulated, respectively, in CIITA-transgenic CD4+ T,cells. However, there was no correlation between MHC-II expression and this Th2 bias at the level of individual transgenic T,cells, indicating an indirect control by CIITA. These results show that MHC-II-restricted Ag presentation, and its indirect influences on T,cells, remains the only pathway under direct control by CIITA in vivo. They also imply that precisely regulated MHC-II expression is essential for maintaining a proper Th1-Th2 balance. [source] Two conserved domains in regulatory B subunits mediate binding to the A subunit of protein phosphatase 2AFEBS JOURNAL, Issue 2 2002Xinghai Li Protein phosphatase 2A (PP2A) is an abundant heterotrimeric serine/threonine phosphatase containing highly conserved structural (A) and catalytic (C) subunits. Its diverse functions in the cell are determined by its association with a highly variable regulatory and targeting B subunit. At least three distinct gene families encoding B subunits are known: B/B55/CDC55, B,/B56/RTS1 and B,/PR72/130. No homology has been identified among the B families, and little is known about how these B subunits interact with the PP2A A and C subunits. In vitro expression of a series of B56, fragments identified two distinct domains that bound independently to the A subunit. Sequence alignment of these A subunit binding domains (ASBD) identified conserved residues in B/B55 and PR72 family members. The alignment successfully predicted domains in B55 and PR72 subunits that similarly bound to the PP2A A subunit. These results suggest that these B subunits share a common core structure and mode of interaction with the PP2A holoenzyme. [source] Microbial aldo-keto reductasesFEMS MICROBIOLOGY LETTERS, Issue 2 2002Elizabeth M Ellis Abstract The aldo-keto reductases (AKR) are a superfamily of enzymes with diverse functions in the reduction of aldehydes and ketones. AKR enzymes are found in a wide range of microorganisms, and many open reading frames encoding related putative enzymes have been identified through genome sequencing projects. Established microbial members of the superfamily include the xylose reductases, 2,5-diketo- d -gluconic acid reductases and ,-keto ester reductases. The AKR enzymes share a common (,/,)8 structure, and conserved catalytic mechanism, although there is considerable variation in the substrate-binding pocket. The physiological function of many of these enzymes is unknown, but a variety of methods including gene disruptions, heterologous expression systems and expression profiling are being employed to deduce the roles of these enzymes in cell metabolism. Several microbial AKR are already being exploited in biotransformation reactions and there is potential for other novel members of this important superfamily to be identified, studied and utilized in this way. [source] Neuronal p38 MAPK signalling: an emerging regulator of cell fate and function in the nervous systemGENES TO CELLS, Issue 11 2002Kohsuke Takeda p38 mitogen-activated protein kinases (MAPKs), together with extracellular signal-regulated kinases (ERKs) and c-Jun N-terminal kinases (JNKs), constitute the MAPK family. Multiple intracellular signalling pathways that converge on MAPKs exist in all eukaryotic cells and play pivotal roles in a wide variety of cellular functions. p38 MAPKs and JNKs, also termed stress-activated protein kinases (SAPKs), are preferentially activated by various cytotoxic stresses and cytokines and appear to be potent regulators of stress-induced apoptosis. Whereas JNKs have been shown to play pivotal roles in the regulation of neuronal apoptosis, the role of p38 MAPKs in the nervous system is poorly understood. However, accumulating evidence from mammalian cell culture systems and the strong genetic tool C. elegans suggests that neuronal p38 signalling has diverse functions beyond the control of cell death and survival. This review focuses on possible roles for the p38 pathway in the nervous system, with principal emphasis placed on the roles in neuronal cell fate decision and function. [source] Genetic and molecular aspects of Alzheimer's disease shed light on new mechanisms of transcriptional regulationGENES, BRAIN AND BEHAVIOR, Issue 3 2005P. Marambaud Rapid advances made in biological research aimed at understanding the molecular basis of the pathogenesis of Alzheimer's disease have led to the characterization of a novel catalytic activity termed ,-secretase. First described for its ,-amyloid-producing function, ,-secretase is now actively studied for its role in a novel signal transduction paradigm, which implicates cell-surface receptor proteolysis and direct surface-to-nucleus signal transduction. ,-Secretase targets numerous type I protein receptors involved in diverse functions ranging from normal development to neurodegeneration. In this Review we discuss how the study of the genetic and molecular aspects of Alzheimer's disease has revealed a dual role of ,-secretase in transcriptional regulation and in the pathogenesis of familial Alzheimer's disease. [source] Second chromosome genes required for heart development in Drosophila melanogasterGENESIS: THE JOURNAL OF GENETICS AND DEVELOPMENT, Issue 10 2007Ye Tao Abstract Heart development is an evolutionarily conserved process. The cardiac organ of Drosophila melanogaster is the dorsal vessel, a linear contractile tissue with cellular and morphogenetic similarities to the primitive heart tube formed at an early stage of vertebrate heart formation. Abundant evidence shows comparable intercellular signaling pathways and transcription factor networks are utilized in Drosophila and vertebrates, to specify cardiac progenitor cells and instruct their differentiation and function in forming the mature heart. With this proven conservation in mind, we screened the second chromosome of Drosophila for genetic intervals that harbor additional loci required for normal dorsal vessel morphogenesis. Our studies identified numerous regions, that when deleted, culminated in dorsal vessels with abnormal cell numbers and/or structural properties. Certain of the deficiency intervals were further characterized to identify individual genes essential for proper cardiac organ formation. Our analyses identified eight genes of diverse functions that are needed for dorsal vessel development. Several of these sequences have known vertebrate homologues, further supporting a conserved genetic basis for heart formation in Drosophila and higher eukaryotes. genesis 45:607,617, 2007. © 2007 Wiley-Liss, Inc. [source] Roles of nuclear factor-,B in postischemic liverHEPATOLOGY RESEARCH, Issue 5 2008Thomas Shin Hepatic ischemia/reperfusion (I/R) results in a chain of events that culminate in liver dysfunction and injury. I/R injury is characterized by early oxidant stress followed by an intense acute inflammatory response that involves the transcription factor nuclear factor (NF)-,B. In addition to being a primary regulator of pro-inflammatory gene expression, NF-,B may play other roles in the hepatic response to I/R, such as mediating the expression of anti-apoptotic genes, preventing the accumulation of damaging reactive oxygen species, facilitating liver regeneration, and mediating the protective effects of ischemic preconditioning. In the present study, we review the diverse functions of NF-,B during hepatic I/R injury. [source] The Complementary Membranes Forming the Blood-Brain BarrierIUBMB LIFE, Issue 3 2002Richard A. Hawkins Abstract Brain capillary endothelial cells form the blood-brain barrier. They are connected by extensive tight junctions, and are polarized into luminal (blood-facing) and abluminal (brain-facing) plasma membrane domains. The polar distribution of transport proteins allows for active regulation of brain extracellular fluid. Experiments on isolated membrane vesicles from capillary endothelial cells of bovine brain demonstrated the polar arrangement of amino acid and glucose transporters, and the utility of such arrangements have been proposed. For instance, passive carriers for glutamine and glutamate have been found only in the luminal membrane of blood-brain barrier cells, while Na-dependent secondary active transporters are at the abluminal membrane. This organization could promote the net removal of nitrogen-rich amino acids from brain, and account for the low level of glutamate penetration into the central nervous system. Furthermore, the presence of a ,-glutamyl cycle at the luminal membrane and Na-dependent amino acid transporters at the abluminal membrane may serve to modulate movement of amino acids from blood-to-brain. Passive carriers facilitate amino acid transport into brain. However, activation of the ,-glutamyl cycle by increased plasma amino acids is expected to generate oxoproline within the blood-brain barrier. Oxoproline stimulates secondary active amino acid transporters (Systems A and B o,+ ) at the abluminal membrane, thereby reducing net influx of amino acids to brain. Finally, passive glucose transporters are present in both the luminal and abluminal membranes of the blood-brain barrier. Interestingly, a high affinity Na-dependent glucose carrier has been described only in the abluminal membrane. This raises the question whether glucose entry may be regulated to some extent. Immunoblotting studies suggest more than one type of passive glucose transporter exist in the blood-brain barrier, each with an asymmetrical distribution. In conclusion, it is now clear that the blood-brain barrier participates in the active regulation of brain extracellular fluid, and that the diverse functions of each plasma membrane domain contributes to these regulatory functions. [source] Expression profile of genes identified in human spermatogonial stem cell-like cells using suppression subtractive hybridizationJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 3 2010Jung Ki Yoo Abstract Spermatogenesis is the process by which testicular spermatogonial stem cells (SSCs) self-renew and differentiate into mature sperm in the testis. Maintaining healthy spermatogenesis requires proper proliferation of SSCs. In this study, we sought to identify factors that regulate the proliferation of SSCs. Human SSC (hSSC)-like cells were isolated from azoospermic patients by a modified culture method and propagated in vitro. After four to five passages, the SSC-like cells spontaneously ceased proliferating in vitro, so we collected proliferating (P)-hSSC-like cells at passage two and senescent (S)-hSSC-like cells at passage five. Suppression subtractive hybridization (SSH) was used to identify genes that were differentially expressed between the P-hSSC-like and S-hSSC-like cells. We selected positive clones up-regulated in P-hSSC-like cells using SSH and functionally characterized them by reference to public databases using NCBI BLAST tools. Expression levels of genes corresponding to subtracted clones were analyzed using RT-PCR. Finally, we confirmed the differential expression of 128 genes in positive clones of P-hSSC-like cells compared with S-hSSC-like cells and selected 23 known and 39 unknown clones for further study. Known genes were associated with diverse functions; 22% were related to metabolism. Fifteen of the known genes and two of the unknown genes were down-regulated after senescence of hSSC-like cells. A comparison with previous reports further suggests that known genes selected, SPP1, may be related to germ cell biogenesis and cellular proliferation. Our findings identify several potential novel candidate biomarkers of proliferating- and senescencet-hSSCs, and they provide potentially important insights into the function and characteristics of human SSCs. J. Cell. Biochem. 110: 752,762, 2010. © 2010 Wiley-Liss, Inc. [source] The role of the disintegrin metalloproteinase ADAM15 in prostate cancer progressionJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 6 2009Neali Lucas Abstract The metalloproteinase ADAM15 is a multi-domain disintegrin protease that is upregulated in a variety of human cancers. ADAM15 mRNA and protein levels are increased in prostate cancer and its expression is significantly increased during metastatic progression. It is likely that ADAM15 supports disease progression differentially through the action of its various functional domains. ADAM15 may downregulate adhesion of tumor cells to the extracellular matrix, reduce cell,cell adhesion, and promote metastasis through the activity of its disintegrin and metalloproteinase domains. Additionally, ADAM15 can influence cell signaling by shedding membrane-bound growth factors and other proteins that interact with receptor tyrosine kinases, leading to receptor activation. There is also evidence supporting a role for ADAM15 in angiogenesis and angioinvasion of tumor cells, which are critical for unrestrained tumor growth and metastatic spread. Given its diverse functions, ADAM15 may represent a pivotal regulatory component of tumor progression, an important target for therapeutic intervention, or emerge as a biomarker of disease progression. J. Cell. Biochem. 106: 967,974, 2009. © 2009 Wiley-Liss, Inc. [source] Paradoxical roles for lysyl oxidases in cancer,A prospectJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 6 2007Stacey L. Payne Abstract Lysyl oxidase (LOX) is an extracellular matrix (ECM) enzyme that catalyzes the cross-linking of collagens or elastin in the extracellular compartment, thereby regulating the tensile strength of tissues. However, recent reports have demonstrated novel roles for LOX, including the ability to regulate gene transcription, motility/migration, and cell adhesion. These diverse functions have led researchers to hypothesize that LOX may have multiple roles affecting both extra- and intracellular cell function(s). Particularly noteworthy is aberrant LOX expression and activity that have been observed in various cancerous tissues and neoplastic cell lines. Both down and upregulation of LOX in tumor tissues and cancer cell lines have been described, suggesting a dual role for LOX as a tumor suppressor, as well as a metastasis promoter gene,creating a conundrum within the LOX research field. Here, we review the body of evidence on LOX gene expression, regulation, and function(s) in various cancer cell types and tissues, as well as stromal,tumor cell interactions. Lastly, we will examine putative mechanisms in which LOX facilitates breast cancer invasion and metastasis. Taken together, the literature demonstrates the increasingly important role(s) that LOX may play in regulating tumor progression and the necessity to elucidate its myriad mechanisms of action in order to identify potentially novel therapeutics. J. Cell. Biochem. 101: 1338,1354, 2007. © 2007 Wiley-Liss, Inc. [source] Heavy chain of cytoplasmic dynein is a major component of the postsynaptic density fractionJOURNAL OF NEUROSCIENCE RESEARCH, Issue 2 2006Huei-Hsuan Cheng Abstract A protein with an apparent molecular size of 490 kDa was found in the postsynaptic density (PSD) fraction isolated from porcine cerebral cortices and rat forebrains, and this 490 kDa protein accounted for ,3% of the total protein of these samples. Matrix-assisted laser desorption ionization-time of flight mass spectrometric and Western blotting analyses consistently indicated that this 490 kDa protein consisted primarily of the heavy chain of cytoplasmic dynein (cDHC). Immunocytochemical analyses showed that cDHC was found in 92% and 89% of the phalloidin-positive protrusions that were themselves associated with discrete clusters of synaptophysin, a presynaptic terminal marker, and PSD-95, a postsynaptic marker, on neuronal processes, respectively. Quantitative Western blotting analyses of various subcellular fractions isolated from porcine cerebral cortices and rat forebrains further showed that not only the heavy but also the intermediate chains of dynein are enriched in the PSD fraction. Cytoplasmic dynein is a microtubule-associated motor protein complex that drives the movement of various cargos toward the minus ends of microtubules and plays many other diverse functions in the cell. Our results that cDHC is a major component of the PSD fraction, that both dynein heavy and intermediate chains are enriched in the PSD fraction and that cDHC is present in dendritic spines raise the possibilities that cytoplasmic dynein may play structural and functional roles in the postsynaptic terminal. © 2006 Wiley-Liss, Inc. [source] Osteopontin expression correlates with prognostic variables and survival in clear cell renal cell carcinomaJOURNAL OF SURGICAL ONCOLOGY, Issue 4 2006Koviljka Matusan MD Abstract Background and Objectives Osteopontin (OPN) is a phosphorylated glycoprotein with diverse functions including tumorigenesis and tumor cell metastasis. Recently, it has been detected in a growing number of human tumors, and assessed as a potential prognostic marker. The aim of this study was to analyze the expression of OPN in normal renal tissue and clear cell renal cell carcinomas (CRCCs), and to assess its prognostic significance. Methods The expression of OPN protein was immunohistochemically analyzed in 171 CRCCs and compared to usual clinicopathological parameters such as tumor size, nuclear grade, pathological stage, Ki-67 proliferation index, and cancer-specific survival. Results In normal renal parenchyma, the expression of OPN was seen in distal tubular epithelial cells, calcifications, and some stromal cells. The upregulation of OPN was observed in 61 CRCCs (35.7%) in the form of cytoplasmic granular staining of various intensities. Statistical analysis showed correlation of the OPN expression with tumor size (P,<,0.001), Fuhrman nuclear grade (P,<,0.001), pathological stage (P,=,0.011), and Ki-67 proliferation index (P,<,0.001). Moreover, patients with OPN-positive tumors had significantly worse prognosis in comparison to patients with tumors lacking OPN protein (P,=,0.004). Conclusion Our results suggest that overexpression of OPN is involved in the progression of CRCC. J. Surg. Oncol. 2006;94:325,331. © 2006 Wiley-Liss, Inc. [source] Identification of Candida albicans genes induced during thrush offers insight into pathogenesisMOLECULAR MICROBIOLOGY, Issue 5 2003Shaoji Cheng Summary Candida albicans causes a wide spectrum of diseases, ranging from mucocutaneous infections like oral thrush to disseminated candidiasis. Screening for C. albicans genes expressed within infected hosts might advance understanding of candidal pathogenesis, but is impractical using existing techniques. In this study, we used an antibody-based strategy to identify C. albicans genes expressed during thrush. We adsorbed sera from HIV-infected patients with thrush against candidal cells grown in vitro and screened a C. albicans genomic expression library. We identified 10 genes encoding immunogenic antigens and used reverse transcription-polymerase chain reaction to verify that they were induced within thrush pseudomembranes recovered from a patient. The in vivo induced genes are involved in diverse functions, including regulation of yeast-hyphal morphogenesis, adhesion to host cells, nutrient uptake, phospholipid biosynthesis and amino acid catabolism. Four genes encode known virulence determinants (HWP1, CST20, CPP1 and RBF1). Another gene, LPD1, for which a role in candidal pathogenesis is unknown, encodes a protein homologous to a bacterial virulence determinant. Most importantly, disruption of CaNOT5, a newly identified gene, conferred defects in morphogenesis, decreased adherence to human buccal epithelial cells and attenuated mortality during murine disseminated candidiasis, proving that our strategy can identify genes encoding novel virulence determinants. [source] Repression of virulence genes by phosphorylation-dependent oligomerization ofCsrR at target promoters in S. pyogenesMOLECULAR MICROBIOLOGY, Issue 4 2001Alita A. Miller csrRS encodes a two-component regulatory system that represses the transcription of a number of virulence factors in Streptococcus pyogenes, including the hyaluronic acid capsule and pyrogenic exotoxin B. CsrRS-regulated virulence factors have diverse functions during pathogenesis and are differentially expressed throughout growth. This suggests that multiple signals induce CsrRS-mediated gene regulation, or that regulated genes respond differently to CsrR, or both. As a first step in dissecting the csrRS signal transduction pathway, we determined the mechanism by which CsrR mediates the repression of its target promoters. We found that phosphorylated CsrR binds directly to all but one of the promoters of its regulated genes, with different affinities. Phosphorylation of CsrR enhances both oligomerization and DNA binding. We defined the binding site of CsrR at each of the regulated promoters using DNase I and hydroxyl radical footprinting. Based on these results, we propose a model for differential regulation by CsrRS. [source] Multiple determinants influence root colonization and induction of induced systemic resistance by Pseudomonas chlororaphis O6MOLECULAR PLANT PATHOLOGY, Issue 6 2006SONG HEE HAN SUMMARY Colonization of the roots of tobacco by Pseudomonas chlororaphis O6 induces systemic resistance to the soft-rot pathogen, Erwinia carotovora ssp. carotovara SCC1. A screen of the transposon mutants of P. chlororaphis O6 showed mutants with about a fivefold reduction in ability to induce systemic resistance to the soft-rot disease. These mutations disrupted genes involved in diverse functions: a methyl-accepting chemotaxis protein, biosynthesis of purines, phospholipase C, transport of branched-chain amino acids and an ABC transporter. Additional mutations were detected in the intergenic spacer regions between genes encoding a GGDEF protein and fumarate dehydratase, and in genes of unknown function. The mutants in the ABC transporters did not display reduced root colonization. However, the other mutants had up to 100-fold reduced colonization levels. Generally the production of metabolites important for interactions in the rhizosphere, phenazines and siderophores, was not altered by the mutations. A reduced induction of systemic resistance by a purine biosynthesis mutant with a disrupted purM gene correlated with poor growth rate, lesser production of phenazines and siderophore and low levels of root colonization. These studies showed that multiple determinants are involved in the induction of systemic resistance, with there being a requirement for strong root colonization. [source] Identifying natural substrates for chaperonins using a sequence-based approachPROTEIN SCIENCE, Issue 1 2005George Stan Abstract The Escherichia coli chaperonin machinery, GroEL, assists the folding of a number of proteins. We describe a sequence-based approach to identify the natural substrate proteins (SPs) for GroEL. Our method is based on the hypothesis that natural SPs are those that contain patterns of residues similar to those found in either GroES mobile loop and/or strongly binding peptide in complex with GroEL. The method is validated by comparing the predicted results with experimentally determined natural SPs for GroEL. We have searched for such patterns in five genomes. In the E. coli genome, we identify 1422 (about one-third) sequences that are putative natural SPs. In Saccharomyces cerevisiae, 2885 (32%) of sequences can be natural substrates for Hsp60, which is the analog of GroEL. The precise number of natural SPs is shown to be a function of the number of contacts an SP makes with the apical domain (NC) and the number of binding sites (NB) in the oligomer with which it interacts. For known SPs for GroEL, we find ,4 < NC < 5 and 2 , NB , 4. A limited analysis of the predicted binding sequences shows that they do not adopt any preferred secondary structure. Our method also predicts the putative binding regions in the identified SPs. The results of our study show that a variety of SPs, associated with diverse functions, can interact with GroEL. [source] Plant-extract-induced changes in the proteome of the soil-borne pathogenic fungus Thielaviopsis basicolaPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 8 2010Joëlle V. F. Coumans Abstract Thielaviopsis basicola is a hemibiotroph fungus that causes black root rot disease in diverse plants with significant impact on cotton production in Australia. To elucidate how T. basicola growth and proteome are influenced by interactions with natural sources, this fungus was cultured in the presence of root extracts from non-host (wheat, hairy vetch) and susceptible host (cotton, lupin) plants. We found that T. basicola growth was significantly favored in the presence of host extracts, while hierarchical clustering analysis of 2-DE protein profiles of T. basicola showed plant species had a larger effect on the proteome than host/non-host status. Analysis by LC-MS/MS of unique and differentially expressed spots and identification using cross-species similarity searching and de novo sequencing allowed successful identification of 41 spots. These proteins were principally involved in primary metabolism with smaller numbers implicated in other diverse functions. Identification of several "morpho" proteins suggested morphological differences that were further microscopically investigated. Identification of several highly expressed spots suggested that vitamin B6 is important in the T. basicola response to components present in hairy vetch extract, and finally, three spots, induced in the presence of lupin extract, may correspond to malic enzyme and be involved in lipid accumulation. [source] Identification of in vitro phosphorylation sites in the Arabidopsis thaliana somatic embryogenesis receptor-like kinasesPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 2 2009Rumyana Karlova Abstract The Arabidopsis thaliana somatic embryogenesis receptor-like kinase (SERK) family consists of five leucine-rich repeat receptor-like kinases (LRR-RLKs) with diverse functions such as brassinosteroid insensitive 1 (BRI1)-mediated brassinosteroid perception, development and innate immunity. The autophosphorylation activity of the kinase domains of the five SERK proteins was compared and the phosphorylated residues were identified by LC-MS/MS. Differences in autophosphorylation that ranged from high activity of SERK1, intermediate activities for SERK2 and SERK3 to low activity for SERK5 were noted. In the SERK1 kinase the C-terminally located residue Ser-562 controls full autophosphorylation activity. Activation loop phosphorylation, including that of residue Thr-462 previously shown to be required for SERK1 kinase activity, was not affected. In vivo SERK1 phosphorylation was induced by brassinosteroids. Immunoprecipitation of CFP-tagged SERK1 from plant extracts followed by MS/MS identified Ser-303, Thr-337, Thr-459, Thr-462, Thr-463, Thr-468, and Ser-612 or Thr-613 or Tyr-614 as in vivo phosphorylation sites of SERK1. Transphosphorylation of SERK1 by the kinase domain of the main brassinosteroid receptor BRI1 occurred only on Ser-299 and Thr-462. This suggests both intra- and intermolecular control of SERK1 kinase activity. Conversely, BRI1 was transphosphorylated by the kinase domain of SERK1 on Ser-887. BRI1 kinase activity was not required for interaction with the SERK1 receptor in a pull down assay. [source] Immunocytochemical Localization of Caveolin-3 in the Synoviocytes of the Rat Temporomandibular Joint During DevelopmentTHE ANATOMICAL RECORD : ADVANCES IN INTEGRATIVE ANATOMY AND EVOLUTIONARY BIOLOGY, Issue 3 2008Masahiro Niwano Abstract Caveolins,caveolin-1, -2, -3 (Cav1, 2, 3),are major components of caveolae, which have diverse functions. Our recent study on the temporomandibular joint (TMJ) revealed expressions of Cav1 and muscle-specific Cav3 in some synovial fibroblast-like type B cells with well-developed caveolae. However, the involvement of Cav3 expression in the differentiation and maturation of type B cells remains unclear. The present study therefore examined the chronological alterations in the localization of Cav3 in the synovial lining cells of the rat TMJ during postnatal development by immunocytochemical techniques. Observations showed immature type B cells possessed a few caveolae with Cav1 but lacked Cav3 protein at postnatal day 5 (P5). At P14, Cav3-immunopositive type B cells first appeared in the synovial lining layer. They increased in number and immunointensity from P14 to P21 as occlusion became active. In immunoelectron microscopy and double immunolabeling with heat shock protein 25 (Hsp25) and Cav3, coexpressed type B cells developed rough endoplasmic reticulum and numerous caveolae, while the Cav3-immunonegative type B cell with Hsp25 immunoreaction possessed few of these. Results suggest that Cav3 expression, which is closely related to added functional stimuli, reflects the differentiation of the type B synoviocytes. Anat Rec, 291:233,241, 2008. © 2008 Wiley-Liss, Inc. [source] Genetics of atrioventricular conduction disease in humansTHE ANATOMICAL RECORD : ADVANCES IN INTEGRATIVE ANATOMY AND EVOLUTIONARY BIOLOGY, Issue 2 2004D. Woodrow Benson Abstract Atrioventricular (AV) conduction disease (block) describes impairment of the electrical continuity between the atria and ventricles. Classification of AV block has utilized biophysical characteristics, usually the extent (first, second, or third degree) and site of block (above or below His bundle recording site). The genetic significance of this classification is unknown. In young patients, AV block may result from injury or be the major cardiac manifestation of neuromuscular disease. However, in some cases, AV block has unknown or idiopathic cause. In such cases, familial clustering has been noted and published pedigrees show autosomal dominant inheritance; associated heart disease is common (e.g., congenital heart malformation, cardiomyopathy). The latter finding is not surprising given the common origin of working myocytes and specialized conduction system elements. Using genetic models incorporating reduced penetrance (disease absence in some individuals with disease gene), variable expressivity (individuals with disease gene have different phenotypes), and genetic heterogeneity (similar phenotypes, different genetic cause), molecular genetic causes of AV block are being identified. Mutations identified in genes with diverse functions (transcription, excitability, and energy homeostasis) for the first time provide the means to assess risk and offer insight into the molecular basis of this important clinical condition previously defined only by biophysical characteristics. © 2004 Wiley-Liss, Inc. [source] Characterization of a sub-family of Arabidopsis genes with the SPX domain reveals their diverse functions in plant tolerance to phosphorus starvationTHE PLANT JOURNAL, Issue 6 2008Ke Duan Summary Four genes of Arabidopsis (At5g20150, At2g26660, At2g45130 and At5g15330) encoding no conservative region other than an SPX domain (SYG1, Pho81 and XPR1) were named AtSPX1,AtSPX4. The various subcellular localizations of their GFP fusion proteins implied function variations for the four genes. Phosphate starvation strongly induced expression of AtSPX1 and AtSPX3 with distinct dynamic patterns, while AtSPX2 was weakly induced and AtSPX4 was suppressed. Expression of the four AtSPX genes was reduced to different extents in the Arabidopsis phr1 and siz1 mutants under phosphate starvation, indicating that they are part of the phosphate-signaling network that involves SIZ1/PHR1. Over-expression of AtSPX1 increased the transcript levels of ACP5, RNS1 and PAP2 under both phosphate-sufficient and phosphate-deficient conditions, suggesting a potential transcriptional regulation role of AtSPX1 in response to phosphate starvation. Partial repression of AtSPX3 by RNA interference led to aggravated phosphate-deficiency symptoms, altered P allocation and enhanced expression of a subset od phosphate-responsive genes including AtSPX1. Our results indicate that both AtSPX1 and AtSPX3 play positive roles in plant adaptation to phosphate starvation, and AtSPX3 may have a negative feedback regulatory role in AtSPX1 response to phosphate starvation. [source] Microarray analysis of chromatin-immunoprecipitated DNA identifies specific regions of tobacco genes associated with acetylated histonesTHE PLANT JOURNAL, Issue 6 2004Yii Leng Chua Summary The acetylation states of histones present on the upstream, promoter, coding or intronic regions of 88 tobacco genes were examined with chromatin immunoprecipitation (ChIP) experiments using antibodies that recognised acetylated histone H4. The DNA sequences enriched in the immunoprecipitates were amplified by ligation-mediated PCR, labelled with Cy-dUTP and hybridised to DNA microarrays. In green tobacco shoots, histone H4 acetylation was localised to 300,600-bp sequences in the promoters or coding regions of 31 genes, or occurred extensively over several kilobase-pair regions containing the upstream, promoter and/or coding regions of 25 genes. Genes associated with high histone H4 acetylation levels at promoters were actively expressed, whereas genes depleted in acetylated histone H4 were non-transcribed or expressed at very low levels, suggesting a correlation between histone H4 acetylation and gene activity. Trichostatin A (TA), an inhibitor of histone deacetylases (HDAs), did not alter histone H4 acetylation states globally but increased acetylation levels at specific tobacco sequences, suggesting that HDAs are targeted to particular nucleosomes. Genes that were upregulated by TA were associated with increased histone H4 acetylation at promoter or coding regions, indicating that acetylation of histones on coding regions may activate transcription. Increased histone H4 acetylation leading to elevated expression was observed on genes with diverse functions, suggesting that histone H4 acetylation is involved in regulation of many plant processes. [source] | ||||||||||||||||||||||||||||||||||