Deduced Aa Sequence Research Articles

Spatial and temporal expression patterns of diverse Pin-II proteinase inhibitor genes in Capsicum annuum Linn

Pin-II type proteinase inhibitor (PI) genes were cloned from fruit and stem tissues of Capsicum annuum L. var Phule Jyoti using primers designed from reported CanPI gene sequence ( AF039398). In total, 21 novel CanPIs, members of the Pin-II PI family, were identified in the study, with three isoforms of 1-inhibitory repeat domain (IRD), eight isoforms of 2-IRD, three isoforms of 3-IRD, five isoforms of 4-IRD and two partial CanPI sequences. Most of the sequences showed variation (2 to 20%) in the deduced AA sequences which were pronounced close to the reactive site loop. Expression patterns of CanPIs in the fruit and stem tissues of mature C. annuum plants were shown to vary qualitatively and quantitatively using semi-quantitative RT-PCR expression analysis. In the fruit tissue, CanPIs with different IRDs (from 1 to 4) were expressed simultaneously. In stem tissue, 1- and 2-IRD CanPIs were strongly expressed along moderate expression of 3- and 4-IRD genes. Analysis of CanPI protein activity showed a range of active forms across the tissues. CanPI expression was differentially up-regulated upon wounding and insect attack. Although infestation by aphids ( Myzus persicae) and lepidopteran pests ( Spodoptera litura) specifically induced 4-IRD CanPIs, virus-infected leaves did not affect CanPI expression. Analysis of CanPI protein activity indicated that the up-regulation in CanPI expression was not always correlated with increase in PI activity. Our results demonstrated that CanPI expression is regulated spatially, temporally as well as qualitatively and quantitatively.

CDNA cloning of Japanese flounder stanniocalcin 2 and its mRNA expression in a variety of tissues

Stanniocalcin 1 (STC1) is a glycoprotein hormone important in the maintenance of calcium and phosphate homeostasis in both fishes and mammals. Although two related STC genes, STC1 and STC2, were found to be expressed in multiple tissues as paracrine regulators in mammals, spatial expression pattern of stc2 mRNA has not been elucidated in fishes in contrast to that of clearly described stc1. In the present study, we have cloned and characterized a full-length stc2 cDNA from Japanese flounder ( Paralichyhus olivaceus) ovary and analyzed expression pattern of stc2 in both sexes. The flounder stc2 cDNA (1501 nucleotides) encoded a putative prehormone of 286 amino acids (aa) with a signal peptide of 20 aa and a mature protein of 266 aa. The deduced aa sequence of flounder stc2 showed high sequence identity with those of pufferfish, zebrafish, and human (57.7–89.0%), whereas it showed less identity with that of flounder stc1 (24.3%). RT-PCR analysis revealed that the flounder stc2 gene is expressed in all examined tissues including the pituitary, brain, heart, kidney, gills, stomach, spleen, skin, dorsal fin, skeletal muscle, liver, corpuscles of Stannius, intestine, ovary and testis. Our data indicate that fish stc2 gene, like stc1, is expressed in a wide variety of tissues.

Porcine sirtuin 1 gene clone, expression pattern, and regulation by resveratrol1

Sirtuin1 (Sirt1) is a NAD-dependent deacetylase that plays important roles in a variety of biological processes. In the current study, we examined tissue-specific and different expression pattern of porcine Sirt1 and the effect of resveratrol (RES) on expression of Sirt1 in porcine adipocytes. The full-length complementary DNA sequence of porcine Sirt1 was 4,024 bp (GenBank accession no: EU030283), with a 2,226-bp open reading frame encoding a 742-AA protein (a predicted molecular mass of 80.9 kDa; GenBank accession no. ABS29571). Comparison of the deduced AA sequence with the corresponding sequences of human, dog, cattle, and mouse Sirt1 showed 82 to 92% similarity. Furthermore, the porcine Sirt1 was highly expressed in porcine brain, to a lesser degree in spleen and white adipose tissue, and had low but detectable expression in liver. In subcutaneous adipose tissue and omental adipose tissue, expression of the porcine Sirt1 mRNA was greater in adult pigs than in young pigs (P < 0.01). In vitro, exposure of cultured adipocytes to 40 and 80 micro M RES for 24 h increased mRNA levels of porcine Sirt1 by 47.86% (P < 0.01) and 91.04% (P < 0.01), respectively. Accordingly, lipid accumulation and NEFA release were decreased (P < 0.05), respectively. After cultures were treated with RES for 48 h, the mRNA level of porcine Sirt1 was increased by 103.84% (P < 0.01) and 148.79% (P < 0.01), respectively. Lipid accumulation was decreased and NEFA release was increased (P < 0.05), respectively. These results provide information needed for manipulating Sirt1 expression in regulating fat deposition in pigs.

Sequence analysis of C18L gene of buffalopox virus: PCR strategy for specific detection and differentiation of buffalopox from orthopoxviruses

The C18L gene of buffalopox virus (BPXV), a homologue of Vaccinia virus (VACV), which encodes the ankyrin repeat protein was sequenced and analyzed to elucidate its genetic relationship with VACVs and also to devise a PCR strategy for the diagnosis of buffalopox. PCR amplification and sequencing of the C18L gene of BPXV-BP4 revealed the truncated ankyrin protein with a coding region consisting of only 50 amino acids (aa) as against a 150-aa-long peptide expressed by VACV (Copenhagen strain). BPXV-specific primers were designed and employed for sequence determination of six Indian BPXV isolates. Comparative sequence analyses of the C18L gene of BPXV isolates with that of published data of the genus orthopox viruses (OPXVs) revealed 71.2–77.3% homology at the nucleotide (nt) and 35.5–67.1% at the aa levels with VACVs. Phylogenetic analyses based on deduced aa sequences of all BPXVs showed clustering in a single group which is distinct from VACVs. Furthermore, PCR performed on the C18L gene (conventional and TaqMan) and duplex PCR based on C18L and DNA polymerase genes were developed using purified viral DNA for the specific detection and differentiation of BPXV from other OPXVs. This resulted in a specific amplicon of 368 bp from the C18L gene of BPXV. Duplex PCR resulted in 96 and 368 bp products from DNA Pol and C18L genes of BPXV and only a 96-bp amplicon of the DNA pol gene in other OPXVs. These assays were employed successfully for the differentiation of BPXV from Orthopox, Capripox and Parapox viruses as it was found to be specific only for BPXV. The authenticity of the amplicons was confirmed based on their size in agarose gel electrophoresis and sequence analysis. In contrast to the conventional PCR, the TaqMan assay was found to be rapid, specific and 100 times more sensitive with a detection limit as low as 5 pg of viral DNA. In addition, the assays were evaluated with DNA extracted from suspected clinical scab materials obtained from buffaloes, cows and human beings.

Molecular characterization and gene expression analysis of a pattern recognition protein from disk abalone, Haliotis discus discus

Pattern recognition molecules play an important role in innate immunity by recognizing common epitopes on the surface of invading microorganism. A pattern recognition protein (PRP) was isolated from a disk abalone, Haliotis discus discus, normalized cDNA library. It encodes 420 amino acids (aa) including a 20 aa signal peptide sequence. The mature protein has an estimated molecular mass of 45 kDa and predicted pI of 5.0. The deduced aa sequence showed greatest homology (50%) with a beta-glucan recognition protein (BGRP) of the freshwater snail Biomphalaria glabrata. Characteristic potential polysaccharide binding, cell adhesion, and glucanase motifs, similar to invertebrate PRP motifs were also found in HdPRP. Reverse transcription-polymerase chain reaction (RT-PCR) results showed that the HdPRP was constitutively expressed in the gill, mantle, digestive tract, hepatopancreas and hemocytes, suggesting an innate immune role in these tissues. Animals injected with Vibrio alginolyticus bacteria showed that the mRNA expression was increased at 12 h post-injection in the gill and continued until 48 h. Abalone CuZn superoxide dismutase (HdCuZnSOD) gene expression was analyzed to detect any oxidative stress after exposure to different pathogen-associated molecular patterns (PAMP). This analysis showed that mRNA expression was significantly increased in Vibrio, lipopolysaccharides (LPS) and beta-1,3-glucan-injected animals compared to controls. Abalone PRP can recognize different PAMP and may activate different genes involved in the defence against these pathogens. It acts as an acute inducible protein that could play an important role in the abalone immune defence mechanism.

Molecular Cloning ofStanniocalcin 1and Its Extracorpuscular Regulation by Salinity and Ca2+in the Japanese Flounder

Stanniocalcin 1 (Stc1) was originally identified as an anti-hypercalcemic hormone produced by the corpuscles of Stannius (CS) associated with the kidney in teleosts. While the stc1 gene is expressed in various tissues in fishes, its role and regulation in extra-CS tissues are unexplored. In the present study, we characterized a cDNA of stc1 in a euryhaline fish, the Japanese flounder (Paralichyhus olivaceus), and examined its expression in peripheral tissues in response to different salinities and Ca2+ ion concentrations. The Japanese flounder stc1 cDNA (1331 bp) encodes a preprohormone of 251 amino acids (aa), with a signal peptide of 17 aa and a pro-sequence peptide of 15 aa followed by the mature protein of 219 aa. The deduced aa sequence of Japanese flounder stc1 showed highest sequence identity (94.0%) with the European flounder Stc1 among fish and mammalian species, but lower identity to zebrafish, pufferfish, and human STC2 (23.1-25.4%). Lowered environmental salinity resulted in a decrease in stc1 mRNA expression in vivo in the gills, kidney, intestine, and CS glands of the Japanese flounder. Furthermore, we found that extracellular Ca2+ increased steady-state stc1 mRNA levels in gill and kidney cells as well as in the CS cells. Our findings suggest that Stc1 synthesis in the ionregulatory tissues is responsive to environmental salinity and Ca2+ level.

Molecular characterization of a calcium-binding protein SjCa8 from Schistosoma japonicum

A full-length cDNA encoding a cercarial stage-specifically expressed 8-kDa calcium-binding protein (SjCa8) was isolated from Schistosoma japonicum cercarial cDNA library using microarray screen. The putative gene coding for SjCa8 is of 371 bp with an open reading frame of 69 amino acid (aa). The deduced aa sequence showed 83% identity with the Schistosoma mansoni 8-kDa CaBP, 47% identity with Clonorchis sinensis calcium-binding protein, and 38% identity with Fasciola hepatica putative calcium-binding protein. Also, it shares more than 30% identity with the calmodulin of many different species, while the most significant similarity between them lies around the two calcium-binding loop regions. There are two potential sites for phosphorylation and one potential site for N-myristoylation in the sequence. The SjCa8 has also been predicted to contain a single pair of EF-hand Ca2+-binding domain. The recombinant SjCa8 (rSjCa8) protein expressed and purified from E. coli has been demonstrated to possess the calcium-binding activity. Immune serum from UV-attenuated S. japonicum cercariae-immunized rabbit detected rSjCa8 by Western blot assay, while the sera from S. japonicum naturally infected rabbit and normal rabbit could not. These findings may contribute to the development of an effective vaccine against schistosomiasis.

Application of bioinformatics-coupled experimental analysis reveals a new transport-competent nuclear localization signal in the nucleoprotein of Influenza A virus strain

BackgroundTwo nuclear localization sequences (NLS) in influenza A virus nucleoprotein (NP) have been demonstrated to be critical for nuclear import of NP and viral ribonucleoprotein complexes. However, a deletion mutant lacking these two signals was still able to localize to the nucleus suggesting the presence of yet another (a third) potential NLS in the NP protein. In order to identify the nature of this potential NLS signal in the NP of a WS/33L influenza virus A strain, we utilized the tools of bioinformatics coupled with functional experimental analyses in the present study.ResultsComparison of the deduced aa sequence of NP of WS/33L strain with the published WS/33 NP sequences revealed that a single amino acid (aa) change (Met to Arg) at position 105 results in converting the flanking regions (between aa position 90–121, a 32-residue stretch) into two classical overlapping bipartite NLS (obpNLS). GenBank search revealed that 9 out of 500 published NP sequences contain a similar Arg at position 105 (instead of Met) with a 100% homology to the obpNLS region. Various NP-green fluorescent protein (GFP) fusion constructs with and without the signal (obpNLS-Arg105) were utilized to understand the functional nature of this signal. We analyzed the transport competency of the expressed chimeric proteins in terms of their cellular localization by confocal immunofluorescence assay. Our analysis revealed that all NP-GFP constructs containing the wild-type (R105) sequence localized predominantly to the nucleus. Constructs lacking the obpNLS or constructs with reverse mutation (R105 to M105) on the other hand exhibited predominant cytoplasmic localization pattern. Interestingly, when the 32 aa obpNLS was fused with an unrelated viral protein (rotavirus NSP6) that has been known to be cytoplasmic protein, the chimeric protein (obpNLS-NSP6) was efficiently transported into the nucleus, indicating an efficient nuclear transport function of the 32-residue obpNLS in the NP of WS/33L strain of influenza A virus.ConclusionThis report while not only establishing a new NLS in the influenza A virus strain, it also reinforces the idea that proper application of bioinformatics-coupled experimental analysis serves as a powerful tool in identifying new functional signals in proteins of interest.

Porcine adipose triglyceride lipase complementary deoxyribonucleic acid clone, expression pattern, and regulation by resveratrol1

Adipose triglyceride lipase (ATGL) was recently identified and described as a major novel triglyceride lipase in animals. In this study, we aimed to study the tissue-specific and developmental expression pattern of porcine ATGL (pATGL) and the effect of resveratrol (RES) on expression of pATGL in vitro. The full-length cDNA sequence of pATGL was 1,958 bp (accession no. EF583921), with a 1,458-bp open reading frame encoding a 486-AA protein (the predicted molecular mass of 53.2 kDa, accession no. ABS58651). Comparison of the deduced AA sequence with the bovine, mouse, rat, dog, and human adipose triglyceride lipase showed 87, 84, 83, 81, and 80% similarity, respectively. Furthermore, the pATGL was highly expressed in porcine adipose tissue, to a lesser degree in kidney, heart, and muscle, and least but detectable in brain. In s.c. adipose tissue, pATGL mRNA was low at birth (1 kg of BW) and then increased, reaching a maximal value at 20 kg of BW (approximately 8 wk old; P < 0.01). In peritoneal and omental adipose tissue, the greatest expression of pATGL was observed at 40 kg of BW (approximately 12 wk old). In vitro, exposure of cultured adipocytes to 40 and 80 muM RES for 24 h increased the mRNA levels of pATGL by 95.3% (P < 0.05) and 146.8% (P < 0.01), respectively. Accordingly, lipid accumulation was decreased by 25.7% (P < 0.05) and 60.8% (P < 0.01), respectively. When treated with RES for 48 h, the mRNA levels of pATGL were increased by 104.1% (P < 0.05) and 163.1% (P < 0.01), respectively. As expected, lipid accumulation was decreased by 9.7% (P > 0.05) and 29.0% (P < 0.05), respectively. These results add to our understanding of the role of pATGL in adipose tissue development and as a potential target for regulating fat deposition and meat quality.

Crustacean hyperglycemic hormone from the tropical land crab, Gecarcinus lateralis: Cloning, isoforms, and tissue expression

Crustacean hyperglycemic hormone (CHH) regulates carbohydrate metabolism, molting, and ion and water transport. cDNAs encoding four CHH isoforms (designated EG-CHH-A, -B, -C, and -D) were cloned from eyestalk ganglia (EG) from land crab, Gecarcinus lateralis. The isoforms differed in the 3′ region of the open reading frame and/or the length of the 3′ untranslated region. All encoded essentially identical preprohormones containing a 28-amino acid (aa) signal peptide, a 42-aa precursor related peptide and a 72-aa mature CHH. All deduced aa sequences had the six cysteines, two arginines, one aspartate, one phenylalanine, and one arginine originally identified as characteristic of this neuropeptide family. There was a single aa difference between the EG-CHH-D mature hormone and the other three isoforms. The EG-CHH isoforms were expressed in EG, hindgut, and thoracic ganglion. A fifth CHH isoform, designated pericardial organ (PO)-CHH, was similar to the PO-CHH isoform described in green crab, Carcinus maenas. It was expressed in hindgut and testis, but not in eyestalk ganglia; its expression in PO was not determined. The deduced aa sequence of the PO-CHH was identical to that of the EG-CHH isoforms through aa #40 of the mature peptide. The divergent aa sequence between positions #41 and #73 was encoded by an insertion of a 111-bp sequence absent in EG-CHH cDNAs. The data suggest that EG-CHH and PO-CHH isoforms are generated by alternative splicing of at least two CHH genes.

Isolation and characterization of a metagenome-derived and cold-active lipase with high stereospecificity for (R)-ibuprofen esters

We report on the isolation and biochemical characterization of a novel, cold-active and metagenome-derived lipase with a high stereo-selectivity for pharmaceutically important substrates. The respective gene was isolated from a cosmid library derived from oil contaminated soil and designated lipCE. The deduced aa sequence indicates that the protein belongs to the lipase family l.3, with high similarity to Pseudomonas fluorescens lipases containing a C-terminal secretion signal for ABC dependent transport together with possible motifs for Ca(2+)-binding sites. The overexpressed protein revealed a molecular weight of 53.2kDa and was purified by refolding from inclusion bodies after expression in Escherichia coli. The optimum temperature of LipCE was determined to be 30 degrees C. However, the enzyme still displayed 28% residual activity at 0 degrees C and 16% at -5 degrees C. Calcium ions strongly increased activity and thermal stability of the protein. Further detailed biochemical characterization of the recombinant enzyme showed an optimum pH of 7 and that it retained activity in the presence of a range of metal ions and solvents. A detailed analysis of the enzyme's substrate spectrum with more than 34 different substrates indicated that the enzyme was able to hydrolyze a wide variety of substrates including the conversion of long chain fatty acid substrates with maximum activity for pNP-caprate (C(10)). Furthermore LipCE was able to hydrolyze stereo-selectively ibuprofen-pNP ester with a high preference for the (R) enantiomer of >91% ee and it demonstrated selectivity for esters of primary alcohols, whereas esters of secondary or tertiary alcohols were nearly not converted.

RFamide Peptides Inhibit the Expression of Melanotropin and Growth Hormone Genes in the Pituitary of an Agnathan, the Sea Lamprey, Petromyzon marinus

Neuropeptides with the Arg-Phe-amide motif at their C termini (RFamide peptides) were identified in the brains of several vertebrates, and shown to have important physiological roles in neuroendocrine, behavioral, sensory, and autonomic functions. The present study identified RFamide peptides, which are teleost prolactin-releasing peptide (PrRP) homologs, in the sea lamprey, Petromyzon marinus and characterized their effect on the release of pituitary hormones in vitro. Two RFamide peptides (RFa-A and RFa-B) were isolated from an acid extract of sea lamprey brain, including hypothalamus by Sep-Pak C18 cartridge, affinity chromatography using anti-salmon PrRP serum, and reverse-phase HPLC on an ODS-120T column. Amino acid (aa) sequences and mass spectrometric analyses revealed that RFa-A and RFa-B consist of 25 and 20 aa, respectively, and have 75% sequence identity within the C-terminal 20 aa. The RFa-B cDNA encoding a preprohormone of 142 aa was cloned from the lamprey brain, and the deduced aa sequence from positions 48-67 was identical to the sequence of RFa-B. However, the preprohormone does not include an aa sequence similar to the RFa-A sequence. Cell bodies, which were immunoreactive to anti-salmon PrRP serum, were located in the periventricular arcuate nucleus, ventral part of the hypothalamus, and immunoreactive fibers were abundant from the hypothalamus to the brain. A small number of immunoreactive fibers were detected in the dorsal half of the rostral pars distalis of the pituitary, close to the GH-producing cells. In addition, anti-salmon PrRP immunoreactivities were observed in the pars intermedia, corresponding to melanotropin cells. Likewise, signal of RFa-B mRNA was detected not only in the brain but also in the pars intermedia. The synthetic RFa-A and -B inhibited GH mRNA expression in a dose-dependent fashion in vitro, which is comparable to the inhibitory effect of teleost PrRP on GH release. Both RFa-A and -B also inhibited the expression of proopiomelanotropin mRNA, but no effects were observed in the expression of proopiocortin and gonadotropin beta mRNAs. The results indicate that RFamide peptides, which are teleost PrRP homologs, are present in the hypothalamus and pituitary of sea lamprey, and may be physiologically involved in the inhibition of GH and melanotropin release in the sea lamprey pituitary.

Differential expression of Paragonimus westermani eggshell proteins during the developmental stages

Eggs of trematode parasites are comprised of numerous vitelline cells and one fertilized ovum, and are encapsulated within a protein shell provided by the vitellocytes. In this study, we isolated two full-length cDNA clones that showed substantial levels of sequence identity with trematode-specific eggshell precursor proteins from the human lung fluke, Paragonimus westermani. These cDNAs, designated Pw-Vit20 (868-bp-long) and Pw-Vit36 (883-bp-long), shared a 76% identity with one another at the nucleotide level, and each encoded a 261-amino acid (aa) polypeptide. The deduced aa sequences contained a N-terminal hydrophobic segment, as well as a sequence motif of Gly-Gly-Gly-Tyr-Asp-Asn/Thr-Tyr-Gly-Lys/Gln, which is highly homologous with the eggshell proteins of Fasciola hepatica. With the high frequencies of tyrosine, glycine and lysine, the positions occupied by tyrosine, which has been proved to be converted into dihydroxyphenylalanine, were well preserved. Pw-Vit20 and Pw-Vit36 were found to be monoexonic genes with variably diverged variants scattered into multiple genomic loci. Their protein products were localized in the vitelline follicles and eggshells. Expression of Pw-Vit20 was restricted to the egg and adult stages, thus suggesting a critical involvement of Pw-Vit20 in the parasite’s fecundity activity. Conversely, Pw-Vit36 was constitutively expressed in the metacercariae and juvenile stages in the vitelline follicles and ducts, which suggested that the prepositioning of stem or primordial vitelline cells within the juveniles prior to sexual maturation. Pw-Vit36 might acquire a unique or additional function relevant to the maturation and/or development of the vitelline cells/follicles during the evolutionary period of P. westermani. Differential biological implications of multiple eggshell precursor proteins may provide insight into the molecular mechanism of eggshell formation and the developmental process of the vitelline follicles in the parasitic trematode.

Correlation of amino acid variations within nonstructural 4B protein with initial viral kinetics during interferon‐alpha‐based therapy in HCV‐1b‐infected patients

Chronic hepatitis C is a major cause of liver cirrhosis leading to chronic liver failure and hepatocellular carcinoma. Different hepatitis C virus (HCV) proteins have been associated with resistance to interferon-alpha-based therapy. However, the exact mechanisms of virus-mediated interferon resistance are not completely understood. The importance of amino acid (aa) variations within the HCV nonstructural (NS)4B protein for replication efficiency and viral decline during the therapy is unknown. We investigated pretreatment sera from 42 patients with known outcome to interferon-based therapy. The complete NS4B gene was amplified and sequenced. Mutational analyses of predicted conformational, functional, structural and phylogenetic properties of the deduced aa sequences were performed. The complete NS4B protein was highly conserved with a median frequency of 0.015 +/- 0.009 aa exchanges (median +/- SD, 4.00 +/- 2.31). Especially within the predicted transmembranous domains of the NS4B protein, the mean number of aa variations was low (median frequency, 0.013 +/- 0.013). Neither the number of aa variations nor specific aa exchanges were correlated with HCV RNA serum concentration at baseline. A rapid initial HCV RNA decline of >/=1.5 log(10) IU/mL at week 2 of interferon-based therapy was associated with a higher frequency of nonconservative aa exchanges within the complete NS4B protein in comparison with patients with a nonrapid HCV RNA decline (median frequency, 0.011 +/- 0.005 vs 0.004 +/- 0.003, P = 0.006). Overall, the aa sequence of the NS4B protein was highly conserved, indicating an important role for replication in vivo. Amino acid variations with relevant changes of physicochemical properties may influence replication efficiency, associated with a rapid early virological response.

Asf1 Is Required for Viability and Chromatin Assembly during DNA Replication in Vertebrate Cells

Asf1 (anti-silencing function 1), a well conserved protein from yeast to humans, acts as a histone chaperone and is predicted to participate in a variety of chromatin-mediated cellular processes. To investigate the physiological role of vertebrate Asf1 in vivo, we generated a conditional Asf1-deficient mutant from chicken DT40 cells. Induction of Asf1 depletion resulted in the accumulation of cells in S phase with decreased DNA replication and increased mitotic aberrancy forming multipolar spindles, leading to cell death. In addition, nascent chromatin in Asf1-depleted cells showed increased nuclease sensitivity, indicating impaired nucleosome assembly during DNA replication. Complementation analyses revealed that the functional domain of Asf1 for cell viability was confined to the N-terminal core domain (amino acids 1-155) that is a binding platform for histones H3/H4, CAF-1p60, and HIRA, whereas Asf1 mutant proteins, abolishing binding abilities with both p60 and HIRA, exhibit no effect on viability. These results together indicate that the vertebrate Asf1 plays a crucial role in replication-coupled chromatin assembly, cell cycle progression, and cellular viability and provide a clue of a possible role in a CAF-1- and HIRA-independent chromatin-modulating process for cell proliferation.

Comparative sequence analysis of envelope protein genes of Indian buffalopox virus isolates

Buffalopox virus (BPXV) is considered to be a close variant of vaccinia virus (VACV), the prototype member of the genus Orthopoxvirus. In the present study, we have analyzed the sequences of H3L, A27L, and D8L gene-homologues of VACV in BPXV to elucidate its genetic relationship to VACV and other orthopoxviruses (OPVs). Products of these genes have been shown to be important in attachment of VACV to host cell surface receptors during viral entry. Additionally, the A27L gene is also responsible for cell fusion during infection, while the H3L gene is required for synthesis of the highly immunogenic major envelope protein p35. Full-length nucleotide sequences of H3L, A27L, and D8L genes of three BPXV isolates were determined by PCR amplification, cloning, and sequencing. The nucleotide (nt) sequence and the deduced amino acid (aa) sequences were compared with published sequences from other members of the genus Orthopoxvirus. Comparative sequence analysis of all the three genes revealed high sequence identity of BPXV isolates with VACV (close to 99% sequence identity) at both the nt and aa level. Phylogenetic analysis based on the deduced aa sequences of the H3L, A27L, and D8L genes also showed that BPXVs are more closely related to VACV than to any of the other OPVs.

Molecular characterization and expression analysis of stanniocalcin-1 in turbot ( Scophthalmus maximus)

Stanniocalcin-1 (STC-1) is an anti-hypercalcemic hormone that is produced by the corpuscles of Stannius (CS) in the teleost. The hormone is a homodimeric glycoprotein involved in the calcium and phosphate regulation in both teleost fish and mammals. In the present study, we have cloned and characterized a full-length cDNA of STC-1 from the turbot ( Scophthalmus maximus) CS and examined its expression pattern in various tissues. The turbot STC cDNA (1246 nucleotides) encodes a putative preprohormone of 248 amino acids (aa) with a signal peptide of 18 aa and a pro-sequence peptide of 14 aa followed by a mature protein of 216 aa. The deduced aa sequence of turbot STC-1 shows the highest sequence identity (86.3%) with that of European flounder STC-1 among the fish and mammalian STC-1. The aa sequence of turbot STC-1 showed moderate sequence identity with those of salmoniforms (chum salmon and rainbow trout), cypriniforms (zebrafish), ancient fish (gar and bowfin), and humans (43.7–66.9%), respectively, whereas it showed less identity with those of zebrafish and human STC-2 (23.8–25.4%). RT-PCR analysis revealed that the turbot STC-1 gene is expressed in the CS, pituitary, brain, kidney, liver, heart, muscle, and gonad. In a transient transfection of turbot STC-1 cDNA construct into human embryonic kidney 293T cells followed by Western blot analysis, a recombinant STC-1 secreted into a medium was detected as a single band of 28 kDa under reducing conditions and a 50 kDa protein under non-reducing conditions. Deglycosylation of the recombinant STC-1 led to a decrease in the molecular mass. Our data indicate that the turbot STC-1 gene is widely expressed and the secreted protein exists as a homodimeric glycoprotein.

CDNA cloning and mRNA expression of growth hormone in Belontiidae (Anabantoidei suborder)

Complete cDNA encoding for the growth hormone (GH) of the Belontiidae fish family (Anabantoidei suborder) was cloned by RACE PCR using several sets of degenerate oligonu- cleotides. GH cDNA of the pearl gourami (Trichogaster leeri; pgGH), cloned from the pituitary, included the 5’ and 3’ noncoding sequences of 44 bp and 181 bp, respectively, and consisted of 840 bp that encoded for a prehormone of 204 amino acid (aa) residues. GH cDNA of the blue gourami (T. trichopterus; bgGH) and its deduced aa sequence had the same lengths as those of the pgGH, with nucleotide and aa identities of 97% and 99%, respectively. GH cDNA cloned from the dwarf gourami (Colisa lalia; dgGH) differed from both pgGH and bgGH. The identity of the dgGH cDNA nucleotides was 88%, compared to pgGH and bgGH. However, the identity of the deduced dgGH aa sequence was 97% when compared to bgGH and 96% when compared to pgGH. Nucleotides of GH cDNA of the fighting fish (Betta splendens; ffGH) had an identity of 82% to those of pgGH and bgGH, and 81% to the dwarf gourami. Higher identity was found among the aa sequences than among the nucleotide sequences. The identity of the cloned aa ffGH compared to bgGH, pgGH, and dgGH was 93%, 92%, and 91%, respectively. Higher levels of GH mRNA were found in females in immature, vitellogenic, and mature stages than in males in various stages of gonadal development. No significant differences in the GH transcription level were found between immature and mature females and males. However, the mRNA level decreased significantly during sexual behavior in males. GH sequence and expression may be used as systematic markers for Belontiidae fish and possibly other fish.

Stanniocalcin in the euryhaline flounder ( Platichthys flesus): Primary structure, tissue distribution, and response to altered salinity

Stanniocalcin (STC) is a homodimeric glycoprotein hormone that was first discovered in fish, where it is largely produced by a unique endocrine gland, the corpuscles of Stannius (CS). In bony fish, it is thought to be an important regulator of calcium and phosphate uptake from the aquatic environment. This report describes the molecular cloning of STC from euryhaline flounder ( Platichthys flesus) CS cDNA and genomic DNA. The flounder STC encodes a prehormone of 251 amino acids (aa) with a signal peptide of 17 aa, followed by another 15 aa sequence before the mature protein of 219 aa. The deduced aa sequence of flounder STC shows 62.9–89.0% similarity and 50.4–83.1% identity with other known fish STC sequences, but only 42.3% identity with mouse STC1, 24.4% identity with fugu and zebrafish STC2, and 22.3% identity with mouse STC2. Primary structural analysis demonstrated that flounder STC gene contains five exons in contrast to the four exons present in mammalian STC gene. RT-PCR revealed the expression of flounder STC mRNA to be widely spread in many tissues and organs, similar to the situation in mammals and other fish. Quantitative PCR (Q-PCR) was conducted to measure relative STC expression levels in the CS, which showed STC mRNA expression levels in seawater-adapted fish CS were about 3-fold higher than in freshwater-adapted fish CS.

RDM1, a Novel RNA Recognition Motif (RRM)-containing Protein Involved in the Cell Response to Cisplatin in Vertebrates

A variety of cellular proteins has the ability to recognize DNA lesions induced by the anti-cancer drug cisplatin, with diverse consequences on their repair and on the therapeutic effectiveness of this drug. We report a novel gene involved in the cell response to cisplatin in vertebrates. The RDM1 gene (for RAD52 Motif 1) was identified while searching databases for sequences showing similarities to RAD52, a protein involved in homologous recombination and DNA double-strand break repair. Ablation of RDM1 in the chicken B cell line DT40 led to a more than 3-fold increase in sensitivity to cisplatin. However, RDM1-/- cells were not hypersensitive to DNA damages caused by ionizing radiation, UV irradiation, or the alkylating agent methylmethane sulfonate. The RDM1 protein displays a nucleic acid binding domain of the RNA recognition motif (RRM) type. By using gel-shift assays and electron microscopy, we show that purified, recombinant chicken RDM1 protein interacts with single-stranded DNA as well as double-stranded DNA, on which it assembles filament-like structures. Notably, RDM1 recognizes DNA distortions induced by cisplatin-DNA adducts in vitro. Finally, human RDM1 transcripts are abundant in the testis, suggesting a possible role during spermatogenesis.