Home About us Contact
|
Home About us Contact | ||
|
|
||
Frame Encoding (frame + encoding)
Kinds of Frame Encoding Selected AbstractsIdentification of the ornithine decarboxylase gene in the putrescine-producer Oenococcus oeni BIFI-83FEMS MICROBIOLOGY LETTERS, Issue 2 2004Angela Marcobal Abstract We report here the identification of an ornithine decarboxylase (ODC) gene in the putrescine-producer Oenococcus oeni BIFI-83 strain. The gene contains a 2,235-nucleotide open reading frame encoding a 745-amino acid residues protein with a deduced molecular mass of 81 kDa. The primary structure of the ODC deduced from the nucleotide sequence has a consensus sequence containing the pyridoxal-5-phosphate (PLP) binding domain, and the critical amino acids residues involved in enzymatic activity are also conserved. As determined by BLAST analysis, the deduced amino acid sequence of the odc gene shares a 67% identity with the ODC protein from Lactobacillus 30a. The odc gene appears to be rarely present in the genome of O. oeni, since in a screening for the presence of this gene in 42 oenococcal strains none of the strains possessed an odc gene copy. [source] CANu1, a novel nucleolar protein, accumulated on centromere in response to DNA damageGENES TO CELLS, Issue 8 2008Choong-Ryoul Sihn Single nucleotide polymorphism is known to be an ideal marker to detect human diseases. We isolated a novel human gene, to be called as CANu1, by the large-scale genome-wide association analysis to screen specific Single nucleotide polymorphisms in colon cancer. It is mapped to chromosome 14q11.2 and its transcript contains a 948-nt open reading frame encoding a protein of 315 aa. Here, we observed that green fluorescence protein (GFP)-fused CANu1 protein was localized to nucleoli and the C-termini of CANu1 protein were essential for its localization. Moreover, the silencing of the CANu1 gene by siRNA caused ribosomal stress leading to G1 cell cycle arrest, the induction of p53 protein, and the translocation of B23 protein. In addition, CANu1 protein was translocated from nucleolus to nuclear foci in response to UV damage. Interestingly, the mobility of a GFP-CANu1 protein in the UV damaged cells was two times faster than non-irradiated cells. Taken together, we report that a novel nucleolar protein, CANu1, is essential to maintain ribosomal structure and responsive upon UV damage. [source] Molecular cloning of two prophenoloxidase genes from the mosquito Aedes aegyptiINSECT MOLECULAR BIOLOGY, Issue 1 2001A. S. Taft Abstract The biosynthesis of melanotic materials is an important process in the life of a mosquito. Melanin production is critical for many diverse processes such as egg chorion tanning, cuticular sclerotization, and melanotic encapsulation of metazoan parasites. Prophenoloxidase plays a critical role in this biochemical cascade. Two cDNAs, one full length and one partial clone, and two genomic clones encoding prophenoloxidase (pro-PO) were isolated from the yellow fever mosquito, Aedes aegypti. The full-length cDNA, pAaProPO1, is 2286 bp long with a 2055 bp open reading frame encoding a 685 amino acid protein that shares 89% identity with Armigeres subalbatus pro - PO. It contains two putative copper binding domains (amino acids 197,243 and 346,423) that are homologous to other insect pro-POs. AaProPO1 messenger RNA (mRNA) was detected by reverse transcription polymerase chain reaction (RT-PCR) only from third-stage larvae and not in adult mosquitoes after blood feeding, during the melanotic encapsulation of Dirofilaria immitis microfilariae or following exposure to bacteria. A 750 bp fragment of the second cDNA (pAaProPO2) was cloned using RT-PCR from mRNA obtained from 14-day postovipostional eggs. AaProPO2 mRNA was not found in any other life stages, and may be in low abundance or transiently expressed. AaProPO2 and AaProPO1 each contain three introns that are 60, 68 and 58 bp and 61, 69 and 59 bp long, respectively, and the intron sequences of these two genes are not similar. [source] cDNA of an arylphorin-type storage protein from Pieris rapae with parasitism inducible expression by the endoparasitoid wasp Pteromalus puparumINSECT SCIENCE, Issue 3 2009Jia-Ying Zhu Abstract, This report presents the cDNA cloning of a storage protein, PraAry, from Pieris rapae and investigates its expression regulated by parasitism of an endoparasitoid wasp Pteromalus puparum. The full-length cDNA of PraAry is 2 270 nucleotides and contains a 2 121 nucleotide open reading frame encoding 707 amino acids with calculated molecular weights of approximately 83 kDa. Analysis of the primary protein sequence revealed that it possesses a signal peptide of 16 amino acids at the N-terminus and contains two highly conserved storage protein signature motifs. According to both phylogenetic analysis and the criteria for amino acid composition, PraAry belongs to the subfamily of arylphorin-type storage protein (1.42% methionine and 18.82% aromatic amino acids). Reverse transcription , polymerase chain reaction analysis indicated that the transcriptional level of PraAry mRNA in P. rapae pupae fat body is inducible in response to parasitism by P. puparum. [source] Characterization and heterologous expression of a novel lysophospholipase gene from Antrodia cinnamomeaJOURNAL OF APPLIED MICROBIOLOGY, Issue 5 2010K.-H. Hsu Abstract Aims:, A novel lysophospholipase (LysoPL) from the basidiomycetous fungi Antrodia cinnamomea named ACLysoPL was cloned, heteroexpressed in Escherichia coli and characterized. Methods and Results:, The gene encoding ACLysoPL was obtained from expressed sequence tags from A. cinnamomea. The full length of this gene has a 945 -bp open reading frame encoding 314 amino acids with a molecular weight of 35·5 kDa. ACLysoPL contains a lipase consensus sequence (GXSXG) motif and a Ser,His,Asp catalytic triad. A putative peroxisomal targeting signal type 1 was found in the C-terminal. Heterologous expression of ACLysoPL in E. coli showed that the enzyme preferentially hydrolyses long-chain acyl esterases at pH 7 and 30°C. ACLysoPL is a psychrophilic enzyme about 40% of whose maximum activity remained at 4°C. The LysoPL activities with lysophospholipids as substrate were analysed by gas chromatography/mass spectrometry. Conclusion:, We have identified and characterized a gene named ACLysoPL encoding a protein performing LysoPL and esterase activities. Significance and Impact of the Study:, This is the first LysoPL of A. cinnamomea identified and characterized at the molecular level. [source] A New Farnesyl Diphosphate Synthase Gene from Taxus media Rehder: Cloning, Characterization and Functional ComplementationJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 6 2006Zhi-Hua Liao Abstract Farnesyl diphosphate synthase (FPS; EC 2.5.1.10) catalyzes the production of 15-carbon farnesyl diphosphate which is a branch-point intermediate for many terpenoids. This reaction is considered to be a rate-limiting step in terpenoid biosynthesis. Here we report for the first time the cloning of a new full-length cDNA encoding farnesyl diphosphate synthase from a gymnosperm plant species, Taxus media Rehder, designated as TmFPS1. The full-length cDNA of TmFPS1 (GenBank accession number: AY461811) was 1 464 bp with a 1 056-bp open reading frame encoding a 351-amino acid polypeptide with a calculated molecular weight of 40.3 kDa and a theoretical pI of 5.07. Bioinformatic analysis revealed that TmFPS1 contained all five conserved domains of prenyltransferases, and showed homology to other FPSs of plant origin. Phylogenetic analysis showed that farnesyl diphosphate synthases can be divided into two groups: one of prokaryotic origin and the other of eukaryotic origin. TmFPS1 was grouped with FPSs of plant origin. Homology-based structural modeling showed that TmFPS1 had the typical spatial structure of FPS, whose most prominent structural feature is the arrangement of 13 core helices around a large central cavity in which the catalytic reaction takes place. Our bioinformatic analysis strongly suggests that TmFPS1 is a functional gene. Southern blot analysis revealed that TmFPS1 belongs to a small FPS gene family in T. media. Northern blot analysis indicated that TmFPS1 is expressed in all tested tissues, including the needles, stems and roots of T. media. Subsequently, functional complementation with TmFPS1 in a FPS-deficient mutant yeast demonstrated that TmFPS1 did encode farnesyl diphosphate synthase, which rescued the yeast mutant. This study will be helpful in future investigations aiming at understanding the detailed role of FPS in terpenoid biosynthesis flux control at the molecular genetic level. (Managing editor: Wei Wang) [source] Research note: Characterization of a cDNA encoding glutamine synthetase II from Gelidium crinale (Rhodophyta)PHYCOLOGICAL RESEARCH, Issue 1 2002D. Wilson Freshwater SUMMARY A cDNA encoding glutamine synthetase (GS) was characterized from the red alga, Gelidium crinale (Turner) Gaillon, using reverse-transcriptase polymerase chain reaction and the 5,- and 3,-rapid amplification of cDNA ends. Sequence analysis of a 1231-bp GS cDNA transcript included both 5, and 3, untranslated regions and a 1056-bp open reading frame encoding a 352 amino acid polypeptide. Comparison with GS sequences from other organisms revealed that the G. crinale cDNA encodes a type-II GS, and the absence of a N-terminal plastid signal sequence suggests that it is a cytosolic isoenzyme. Phylogenetic analyses of GSII amino acid sequences supports the multiple origin of cytosolic and plastid isoenzymes during eukaryotic evolution. [source] Porcine skeletal muscle differentially expressed gene CMYA1: isolation, characterization, mapping, expression and association analysis with carcass traitsANIMAL GENETICS, Issue 3 2009X. L. Xu Summary To investigate the differences in gene expression between some obese and lean pig breeds, differential display of mRNA was employed in our previous research. One differentially expressed EST (BI596262) was further identified as the porcine cardiomyopathy associated 1 (CMYA1) gene because of its homology to the human CMYA1 gene. The full-length DNA of the porcine CMYA1 gene encompasses 9379 bp, including a complete open reading frame encoding 1839 amino acid residues, a 158-bp 5,-untranslated region and a 630-bp 3,-untranslated region. The porcine CMYA1 gene was assigned to chromosome 13 by the radiation hybrid panel (IMpRH). The porcine CMYA1 gene was expressed only in the striated muscle. Single nucleotide polymorphism (SNP) scanning in the coding region identified one synonymous mutation (c.1053C>T) and three missense mutations, c.1394A>G (p.His465Arg), c.1751A>G (p.Asp582Gly) and c.3290C>A (p.Thr1097Asp). The allele frequencies were tested among about 200 unrelated pigs from several pig breeds. Linkage mapping was further conducted with the SNP c.1751A>G (p.Asp582Gly) in a Berkshire × Yorkshire resource family and this confirmed that porcine CMYA1 is closely linked with Sw344 (distance = 2 cM, LOD score is 129.47), an interesting region harbouring a QTL for back fat thickness. Association analysis in our experimental pig population showed that different genotypes of CMYA1 gene were associated with different back fat thicknesses (P < 0.05). Our results suggest that the porcine CMYA1 gene has effects on porcine back fat deposition and further investigation will be necessary to illustrate the underlying mechanisms. [source] Cloning and expression analysis of a cDNA encoding lipoprotein lipase from the liver of adult grass carp (Ctenopharyngodon idella)AQUACULTURE RESEARCH, Issue 16 2009Han-Liang Cheng Abstract A full-length cDNA coding lipoprotein lipase (LPL) was cloned from the liver of adult grass carp (Ctenopharyngodon idella) using reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends approaches. The cDNA obtained was 2414 bp long with a 1524 bp open reading frame encoding 507 amino acids, including a putative signal peptide 21 amino acids long. The LPL protein has a calculated molecular weight of 57.77 kDa and an isolectric point of 8.132. The main domains of LPL, such as catalytic site, disulphide bridge, N-linked glycosylation site, heparin-binding domain, lipid-binding site and site of dimer formation, are basically conserved between the grass carp and other vertebrates. The tissue distribution of LPL mRNA in the liver, head kidney, mesenteric adipose tissue, heart and white muscle of adult grass carp was analysed using the semi-quantitative RT-PCR method using ,-actin gene as an internal control; the result showed that the expressions of LPL mRNA were detected in all examined tissues of adult grass carp. The expression levels of LPL in the mesenteric adipose tissue were the highest among these tissues, followed by the liver and head kidney and the lowest expression was found in the heart and white muscle. [source] Hydrophobic peptides: novel regulators within bacterial membraneMOLECULAR MICROBIOLOGY, Issue 1 2009Eric Alix Summary Identification of short coding sequences is challenging, both experimentally and in silico, and functional natural peptides (< 50 amino acids) have to a large extent been overlooked in Gram-negative bacteria. Recent results have converged to highlight the role of hydrophobic peptides that form a novel class of active molecules in Escherichia coli and Salmonella enterica serovar Typhimurium. These peptides can play a regulatory role by interacting with protein partners at the inner membrane and by modulating protein partner activity or stability. Genome-wide analyses in both bacterial species have identified several conserved short open reading frames encoding a single transmembrane segment. We discuss the known and predicted membrane-associated peptides and the tools for their identification. Besides the identification of novel regulatory networks, characterization of peptides with a single transmembrane helix segment and proteins that interact with them provides a powerful opportunity to study interactions between alpha helices within biological membranes. In addition, some bioactive membrane peptides could provide a basis for engineering membrane protein antagonists. [source] | ||||||||||