UMLS:C0009443 - FACTA Search

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Large-scale single-pass sequencing of cDNA libraries and microarray analysis have proven to be useful tools for discovering new genes and studying gene expression. As a first step in elucidating the defense mechanisms in hot pepper plants, a total of 8,525 expressed sequence tags (ESTs) were generated and analyzed in silico. The cDNA microarray analysis identified 613 hot pepper genes that were transcriptionally responsive to the non-host soybean pustule pathogen Xanthomonas axonopodis pv. glycines ( Xag). Several functional types of genes, including those involved in cell wall modification/biosynthesis, transport, signaling pathways and divergent defense reactions, were induced at the early stage of Xag infiltration. In contrast, genes encoding proteins that are involved in photosynthesis, carbohydrate metabolism and the synthesis of chloroplast biogenetic proteins were down-regulated at the late stage of Xag infiltration. These expression profiles share common features with the expression profiles elicited by other stresses, such as fungal challenge, wounding, cold, drought and high salinity. However, we also identified several novel transcription factors that may be specifically involved in the defense reaction of the hot pepper. We also found that the defense reaction of the hot pepper may involve the deactivation of gibberellin. Furthermore, many genes encoding proteins with unknown function were identified. Functional analysis of these genes may broaden our understanding of non-host resistance. This study is the first report of large-scale sequencing and non-host defense transcriptome analysis of the hot pepper plant species. (The sequence data in this paper have been submitted to the dbEST and GenBank database under the codes 10227604-10236595 and BM059564-BM068555, respectively. Additional information is available at http://plant.pdrc.re.kr/ks200201/pepper.html).
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PMID:EST and microarray analyses of pathogen-responsive genes in hot pepper (Capsicum annuum L.) non-host resistance against soybean pustule pathogen (Xanthomonas axonopodis pv. glycines). 1476 May 38

On the basis of acquired thermotolerance and cryotolerance, the optimal heat shock and cold shock temperatures have been determined for Deinococcus radiodurans. A heat shock at 42 degrees C maximized survival at the lethal temperature of 52 degrees C and a cold shock at 20 degrees C maximized survival after repeated freeze-thawing. Enhanced survival from heat shock was found to be strongly dependent on growth stage, with its greatest effect shortly after phase. Increased synthesis of a total of 67 proteins during heat shock and 42 proteins during cold shock were observed by two-dimensional polyacrylamide gel electrophoresis (2D PAGE) and autoradiography. Eight of the most highly induced heat shock proteins shown by 2D PAGE were identified by MALDI-MS as Hsp20, GroEL, DnaK, SodA, Csp, Protease I, and two proteins of unknown function.
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PMID:Heat shock and cold shock in Deinococcus radiodurans. 1521 Oct 28

The AID/APOBEC family (comprising AID, APOBEC1, APOBEC2, and APOBEC3 subgroups) contains members that can deaminate cytidine in RNA and/or DNA and exhibit diverse physiological functions (AID and APOBEC3 deaminating DNA to trigger pathways in adaptive and innate immunity; APOBEC1 mediating apolipoprotein B RNA editing). The founder member APOBEC1, which has been used as a paradigm, is an RNA-editing enzyme with proposed antecedents in yeast. Here, we have undertaken phylogenetic analysis to glean insight into the primary physiological function of the AID/APOBEC family. We find that although the family forms part of a larger superfamily of deaminases distributed throughout the biological world, the AID/APOBEC family itself is restricted to vertebrates with homologs of AID (a DNA deaminase that triggers antibody gene diversification) and of APOBEC2 (unknown function) identifiable in sequence databases from bony fish, birds, amphibians, and mammals. The cloning of an AID homolog from dogfish reveals that AID extends at least as far back as cartilaginous fish. Like mammalian AID, the pufferfish AID homolog can trigger deoxycytidine deamination in DNA but, consistent with its cold-blooded origin, is thermolabile. The fine specificity of its mutator activity and the biased codon usage in pufferfish IgV genes appear broadly similar to that of their mammalian counterparts, consistent with a coevolution of the antibody mutator and its substrate for the optimal targeting of somatic mutation during antibody maturation. By contrast, APOBEC1 and APOBEC3 are later evolutionary arrivals with orthologs not found in pufferfish (although synteny with mammals is maintained in respect of the flanking loci). We conclude that AID and APOBEC2 are likely to be the ancestral members of the AID/APOBEC family (going back to the beginning of vertebrate speciation) with both APOBEC1 and APOBEC3 being mammal-specific derivatives of AID and a complex set of domain shuffling underpinning the expansion and evolution of the primate APOBEC3s.
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PMID:Evolution of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases. 1549 50

Using a molecular approach based on PCR, RT-PCR and northern blot analysis, a new member of the small heat shock family of wine, Lactobacillus plantarum, was cloned and characterized. The protein sequence deduced from the isolated gene had a calculated molecular mass of 18.548 kDa and was therefore named HSP 18.55. The gene codes for a protein homologous to the previously characterized HSP 19.3 and HSP 18.5 and is co-transcribed with an upstream gene of unknown function. Analysis of the 5' flanking region of the hsp 18.55 gene revealed the presence of putative cis elements able to bind alternative sigma factor sigma(B). Based on its structure, the gene was classified as belonging to class II of the heat shock genes according to Bacillus subtilis nomenclature for shock-responsive genes. Expression of the newly identified small heat shock gene, analyzed by RT-PCR and northern blot analysis, was induced by a wide range of abiotic stresses including heat, cold and ethanol, suggesting that the small family of heat shock genes is probably involved in the general stress response in wine L. plantarum. Moreover, the expression of hsp 18.5, hsp 18.55 and hsp 19.3 genes, analyzed over a complete culture cycle, revealed that early growing cells contained substantial amounts of hsp 18.5, hsp 18.55 and hsp 19.3 mRNAs, which rapidly declined upon entry into stationary phase.
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PMID:Cloning and characterization of the hsp 18.55 gene, a new member of the small heat shock gene family isolated from wine Lactobacillus plantarum. 1574 87

Using proteomic analysis, an investigation aimed at a better understanding of the molecular adaptation mechanisms of cold stress was carried out in rice (Oryza sativa). The seedlings were exposed to a progressively low temperature stress treatment from normal temperature to 15, 10, and 5 degrees C. Proteins were extracted from the leaves collected from both control and stressed seedlings. By fractionation, approximately 1700 protein spots were separated and visualized on CBB-stained 2-D gels. Sixty protein spots were found to be up-regulated in responding to the progressively low temperature stress and displayed different dynamic patterns. As an initial work, 41 of these proteins were identified using MALDI-TOF MS or ESI/MS/MS. These cold responsive proteins, besides two proteins of unknown function, include four factors of protein biosynthesis, four molecular chaperones, two proteases, and eight enzymes involved in biosynthesis of cell wall components, seven antioxidative/detoxifying enzymes, and proteins linked to energy pathway, as well as a protein involved in signal transduction. The functional proteomes illuminate the facts, at least in plant cell, that protein quality control mediated by chaperones and proteases and enhancement of cell wall components play important roles in tolerance to cold stress. Using TargetP program, the subcellular localization of the identified proteins was analyzed. Proteins (43.9%) were predicted to be located in the chloroplasts, implying that chloroplast proteome is virtually subjective to cold stress. The physiological implications, revealed from the experimental data, are discussed in context of a complex metabolic network in plant cells responsive to cold stress.
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PMID:A proteomic analysis of cold stress responses in rice seedlings. 1607 85

To further increase our understanding of responses in potato to abiotic stress and the potato transcriptome in general, we generated 20 756 expressed sequence tags (ESTs) from a cDNA library constructed by pooling mRNA from heat-, cold-, salt-, and drought-stressed potato leaves and roots. These ESTs were clustered and assembled into a collection of 5240 unique sequences with 3344 contigs and 1896 singleton ESTs. Assignment of gene ontology terms (GOSlim/Plant) to the sequences revealed that 8101 assignments could be made with a total of 3863 molecular function assignments. Alignment to a set of 78 825 ESTs from other potato cDNA libraries derived from root, leaf, stolon, tuber, germinating eye, and callus tissues revealed 1476 sequences unique to abiotic stressed potato leaf and root tissue. Sequences present within the 5240 sequence set had similarity to genes known to be involved in abiotic stress responses in other plant species such as transcription factors, stress response genes, and signal transduction processes. In addition, we identified a number of genes unique to the abiotic stress library with unknown function, providing new candidate genes for investigation of abiotic stress responses in potato.
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PMID:Analyzing the potato abiotic stress transcriptome using expressed sequence tags. 1609 26

Polyphosphate (polyP) is a linear polymer consisting of tens to hundreds of phosphate molecules joined together by high-energy anhydride bonds. These polymers are found in virtually all prokaryotic and eukaryotic cells and perform many functions; prominent among them are the responses to many stresses. Polyphosphate is synthesized by polyP kinase (PPK), using the terminal phosphate of ATP as the substrate, and degraded to inorganic phosphate by both endo- and exopolyphosphatases. Here we report the crystal structure and analysis of the polyphosphate phosphatase PPX from Escherichia coli O157:H7 refined at 2.2 Angstroms resolution. PPX is made of four domains. Domains I and II display structural similarity with one another and share the ribonuclease-H-like fold. Domain III bears structural similarity to the N-terminal, HD domain of SpoT. Domain IV, the smallest domain, has structural counterparts in cold-shock associated RNA-binding proteins but is of unknown function in PPX. The putative PPX active site is located at the interface between domains I and II. In the crystal structure of PPX these two domains are close together and represent the "closed" state. Comparison with the crystal structure of PPX/GPPA from Aquifex aeolicus reveals close structural similarity between domains I and II of the two enzymes, with the PPX/GPPA representing an "open" state. A striking feature of the dimer is a deep S-shaped canyon extending along the dimer interface and lined with positively charged residues. The active site region opens to this canyon. We postulate that this is a likely site of polyP binding.
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PMID:The structure of the exopolyphosphatase (PPX) from Escherichia coli O157:H7 suggests a binding mode for long polyphosphate chains. 1667 53

Genes involved in pathogenicity of several plant pathogens were shown to be induced at relatively cold temperatures. Loci from the fire blight pathogen Erwinia amylovora (Burrill) induced at 18 degrees C were identified using the miniTn5 transposon that contains the promoterless reporter gene gusA coding for beta-glucuronidase (GUS). Certain mutants (2.7%) expressed GUS predominantly at 18 degrees C on minimal medium plates, indicating that the transposon had been inserted downstream of a putatively thermoregulated promoter. Those mutants were further screened with a quantitative GUS fluorometric assay. A total of 21 mutants were selected: 19 mutants had a transposon insertion in temperature-dependent genetic loci, with a 2.2- to 6.3-fold induction of gusA gene expression at 18 degrees C, and two mutants with impaired growth at 18 degrees C. Some of these genetic loci encoded (i) proteins implicated in flagella biosynthesis, biotin biosynthesis, multi-drug efflux, and type II secretion protein, and (ii) proteins of unknown function.
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PMID:Identification of low-temperature-regulated genes in the fire blight pathogen Erwinia amylovora. 1669 72

The temperate japonica rice cultivar M202 is the predominant variety grown in California due to its tolerance to low temperature stress, good grain quality and high yield. Earlier analysis of a recombinant inbred line mapping population derived from a cross between M202 and IR50, an indica cultivar that is highly sensitive to cold stress, resulted in the identification of a number of QTL conferring tolerance to cold-induced wilting and necrosis. A major QTL, qCTS12, located on the short arm of chromosome 12, contributes over 40% of the phenotypic variance. To identify the gene(s) underlying qCTS12, we have undertaken the fine mapping of this locus. Saturating the short arm of chromosome 12 with microsatellite markers revealed that qCTS12 is closest to RM7003. Using RM5746 and RM3103, which are immediately outside of RM7003, we screened 1,954 F(5)-F(10) lines to find recombinants in the qCTS12 region. Additional microsatellite markers were identified from publicly available genomic sequence and used to fine map qCTS12 to a region of approximately 87 kb located on the BAC clone OSJNBb0071I17. This region contains ten open reading frames (ORFs) consisting of five hypothetical and expressed proteins of unknown function, a transposon protein, a putative NBS-LRR disease resistance protein, two zeta class glutathione S-transferases (OsGSTZ1 and OsGSTZ2), and a DAHP synthetase. Further fine mapping with markers developed from the ORFs delimited the QTL to a region of about 55 kb. The most likely candidates for the gene(s) underlying qCTS12 are OsGSTZ1 and OsGSTZ2.
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PMID:Fine mapping of the qCTS12 locus, a major QTL for seedling cold tolerance in rice. 1674 39

To improve knowledge about axonal membrane properties in nociceptive and non-nociceptive C fibres, we studied impulse-dependent velocity changes by in vivo microneurography in the rat sciatic nerve. Cutaneous C fibres were classified, based primarily on their activity-dependent slowing profile, as Type 1A (mechano-responsive nociceptors; CMR; n = 23), Type 1B (mechano-insensitive nociceptors; CMI; n = 24), Type 2 (cold units; n = 2), Type 3 units (unknown function; n = 4) or Type 4 (presumed sympathetics; n = 23) units. They were excited by single, double and triple electrical stimuli to the skin at mean rates of 0.25, 0.5, 1 and 2 Hz and with interstimulus intervals ranging from 2 to 1000 ms. All CMRs exhibited only postspike subnormality at 0.25 and 0.5 Hz. They gradually developed supernormality with higher stimulation rates, and 12/19 CMRs were supernormal at 1 Hz. The CMIs showed a greater tendency towards supernormality, with 10/21 already supernormal at 0.25 Hz, 17/24 at 0.5 Hz and all were supernormal at 1 Hz. In some CMIs but in none of the CMRs, the supernormal period was directly followed by a peak in late subnormality. Among non-nociceptive fibres, all Type 4 units exhibited long-lasting supernormality independent of the stimulation rate, whereas the cold units showed short-lived supernormality. In both, supernormality increased with higher stimulation rates. Regardless of fibre function or stimulation rate, a second conditioning stimulus always induced additional slowing, providing evidence for a passive origin of supernormality in all rat C fibre subtypes. However, the degree and time-course of extra slowing due to a preconditioning stimulus was highly dependent on fibre function and stimulation rate. These data indicate axonal membrane differences between different functional classes of C fibres, which resemble those previously described in human C fibres.
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PMID:Velocity recovery cycles of single C fibres innervating rat skin. 1702 8

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