Molecular cloning, sequence identification and expression analysis of novel caprine MYLPF gene

Skeletal muscle genes are important potentially functional candidate genes for livestock production and meat quality. Myosin regulatory light chain (MLC) regulates myofilament activation via phosphorylation by Ca²⁺ dependent myosin light chain kinase. The cDNA of the myosin light chain, phosphorylatable, fast skeletal muscle (MYLPF) gene from the longissimus dorsi of Tianfu goat was cloned and sequenced. The results showed that MYLPF full-length coding sequence consists of 513 bp and encodes 170 amino acids with a molecular mass of 19.0 kD. Two EF-hand superfamily domain of MYLPF gene conserved between caprine and other animals. The deduced amino acid sequence of MYLPF shared significant identity with the MYLPF from other mammals. A phylogenetic tree analysis revealed that the caprine MYLPF protein has a close genetic relationship and evolutional distance with MYLPF in other mammals. Analysis by RT-PCR showed that the MYLPF mRNA was detected in heart, liver, spleen, lung, kidney, gastrocnemius, abdominal muscle and longissimus dorsi. In particular, high expression levels of MYLPF mRNA were detected in the longissimus dorsi, gastrocnemius and abdominal muscle, and low level of expressions were observed in liver, spleen, lung and kidney. In addition, the temporal expression analysis further showed MYLPF expression decreased gradually with age in the skeletal muscle. This may be important as muscle growth occurs mainly in young age in goats. Western blotting results detected the MYLPF protein in four of the tissues in which MYLPF was shown to be expressed; the four exceptions were liver, spleen, lung and kidney.     

Gene cloning and expression analysis of IRF1 in half-smooth tongue sole (Cynoglossus semilaevis)

Interferon regulatory factor 1 (IRF1) was known to play key roles in antiviral defense in several species, and some other important biological processes. In this report, full length cDNA of IRF1 from Cynoglossus semilaevis (CsIRF1) was identified. It was of 1,455 bp, containing a 5′ UTR of 104 bp, a 3′ UTR of 541 bp with a poly (A) tail and an ORF of 810 bp encoding a putative protein of 269 amino acids. The putative CsIRF1protein contained one conserved IRF domain (1–113aa), and two low complexity regions (140–158aa and 230–242aa, respectively). Phylogenetic analysis showed that CsIRF1 was conserved in the teleost evolutionary branch, which was independent of mammalian, birds and amphibians. Additionally, CsIRF1 had the 96 % homology with marine fishes, while 66 % with freshwater fishes. The expression profiles of CsIRF1was analyzed by quantitative real-time PCR in healthy tissues and in immune tissues challenged with different pathogens [Vibrio anguillarum and Lymphocystis disease virus (LCDV)], respectively. CsIRF1 was widely expressed in healthy tissues of Cynoglossus semilaevis and with the highest expression in blood, as much as 19 times of that in liver. V. anguillarum and LCDV both induced the CsIRF1 gene expression distinctly in liver, with the peak value reached to 98-fold at 6 h and 25-fold at 24 h, respectively. The bacteria induced CsIRF1 suddenly up-expression in each detected tissues. However, at the initial stage of the challenge of virus LCDV, the CsIRF1 expression in blood and spleen were up regulated; on the contrary, its expression in liver and head kidney were down regulated, 0.3 and 0.4-fold 6 h post virus injection, respectively. These results suggested that CsIRF1 gene might involve in not only antiviral activity but also antibacterial procedure, indicating its vital role in Cynoglossus semilaevis innate defense system.     

Neurexophilin 1 Gene Polymorphism in Chickens and Its Variation Among Species

Neurexophilin 1 (nxph1) has been considered a potential candidate marker for sperm storage in chicken sperm storage tubules. In this work, one mutation of chicken nxph1 was detected. We analyzed 18 nxph1 gene sequences from 18 species. The coding sequence length of the zebra fish nxph1 gene is 819 bp; that of the other species is 816 bp. Amino acid alignment analysis revealed that the gene product is a conserved protein, especially in mammals. The sequences of mammals are highly conserved. We found 202 conserved amino acids (70–271), and there were only eight mutations in the remaining 69 amino acids. That level of conservation could be due to the nxph1 gene having been subjected to substantial constraints or strong purifying selection during millions of years of evolution.     

Molecular Characterization and Expression Analysis of Heat Shock Cognate 70 After Heat Stress and Lipopolysaccharide Challenge in Sea Cucumber (Apostichopus japonicus)

A gene encoding hsc70 was cloned from the sea cucumber Apostichopus japonicus and named AjHsc70. The full-length cDNA sequence was 2,508 bp, containing a 5′-UTR of 77 bp, an ORF of 2,010 bp encoding 670 amino acids, and a 3′-UTR of 421 bp. Quantitative RT-PCR analysis revealed that AjHsc70 was expressed constitutively in all of the tested tissues with respiratory tree tissue showing the highest expression level. AjHsc70 expression was significantly induced by lipopolysaccharide, and the expression levels peaked at different sampling times in the body wall (24 h), coelomocytes (12 h), and intestine and respiratory tree tissues (6 h). After heat stress, AjHsc70 expression in intestine, coelomocytes, and body wall decreased acutely at first and then increased slightly. AjHsc70 expression patterns indicated that hsc70 plays an important role in mediating the responses of A. japonicus to bacterial challenge and heat stress.     

Molecular characterization and expression analysis of <Emphasis Type="Italic">Hsp90</Emphasis> in <Emphasis Type="Italic">Schizothorax prenanti</Emphasis>

Aquatic animals suffer from various environmental stresses because the aquatic environment is a very complex system. To monitor the health status of fish, Hsp90 a potential early warning marker was determined in Schizothorax prenanti after infection with a bacterium. In this study, we cloned Hsp90 from S. prenanti for the first time. The full-length cDNA sequence of SpHsp90 was 2663 bp, contains an open reading frame of 2181 bp, and has a gene encoding 726 amino acids, an estimated molecular mass of 83.38 kDa, and a theoretical isoelectric point of 4.91. The SpHsp90 amino acid sequence has five conserved HSP90 family signatures and shares 87.0–95.5 % identity with other vertebrates. Phylogenetic analysis and structure comparison indicated that SpHsp90 should be a β isoform of the HSP90 family. SpHsp90 was ubiquitously expressed in all examined tissues, and the highest level of expression was in the kidney. After Streptococcus agalactiae infection, the level of SpHsp90 expression had significant changes (P < 0.05) in the hepatopancreas, spleen, kidney, and blood. The expression increased to the highest level at 6 h in the blood and at 24 h in the hepatopancreas, spleen, and kidney. The results suggested that the SpHsp90 gene could be induced by S. agalactiae in S. prenanti and that SpHsp90 may be involved in resistance to bacterial infection and provide an early warning information. The kidney is the most suitable for detecting SpHsp90 after bacterial infection.     

Analysis on DNA sequence of <Emphasis Type="Italic">TSHB</Emphasis> gene and its association with reproductive seasonality in goats

Thyroid stimulating hormone beta chain (TSHB) is mainly expressed in pituitary and its expression is closely related to photoperiodic control of seasonal reproduction in animals. In the present study, ten primer pairs have been used to clone the DNA sequence and to detect genetic mutations of goat TSHB gene. Two DNA fragments of goat TSHB gene were obtained, which were 2,614 and 1,031 bp in length, respectively. They comprised about 2.5 kb 5′ regulatory region, all of the three exons and two introns. Goat TSHB gene has a coding region of 417 bp, encoding 138 amino acids which was predicted to be a secretory protein with a signal peptide of 16 amino acids. The sequence of TSHB gene is highly conserved among mammals. In addition, five mutations (C53A, 3 bp Indel at the 287–289 locus, 34 bp Indel at the 584–617 locus, A1819C and E2_72TA) were found in goat TSHB gene and they were shown to be in strong linkage disequilibrium. Interestingly, the genotype distributions for both single locus and haplotype have shown to be significant different between seasonal and nonseasonal goat breeds. And haplotype H2 and diplotype H2/H4 may be related to year-round estrus. We preliminarily presumed that the five closely linked mutations of goat TSHB gene may be part of the causal sources for the diversities of reproductive seasonality in goats. Our study may provide a possible efficient genetic way to decrease seasonality in goats.     

Isolation and Characterization of the PKAr Gene From a Plant Pathogen,Curvularia lunata

By using EST database from a full-length cDNA library of Curvularia lunata, we have isolated a 2.9 kb cDNA, termed PKAr. An ORF of 1,383 bp encoding a polypeptide of 460 amino acids with molecular weight 50.1 kDa, (GeneBank Acc. No. KF675744) was cloned. The deduced amino acid sequence of the PKAr shows 90 and 88 % identity with cAMP-dependent protein kinase A regulatory subunit from Alternaria alternate and Pyrenophora tritici-repentis Pt-1C-BFP, respectively. Database analysis revealed that the deduced amino acid sequence of PKAr shares considerable similarity with that of PKA regulatory subunits in other organisms, particularly in the conserved regions. No introns were identified within the 1,383 bp of ORF compared with PKAr genomic DNA sequence. Southern blot indicated that PKAr existed as a single copy per genome. The mRNA expression level of PKAr in different development stages were demonstrated using real-time quantitative PCR. The results showed that the level of PKAr expression was highest in vegetative growth mycelium, which indicated it might play an important role in the vegetative growth of C. lunata. These results provided a fundamental supporting research on the function of PKAr in plant pathogen, C. lunata.     

Cloning of Hsp21 gene and its expression in Chinese shrimp Fenneropenaeus chinensis in response to WSSV challenge

In the present study, a DNA sequence encoding a small heat shock protein gene (FcHsp21) in the Chinese shrimp, Fenneropenaeus chinensis, was cloned, and its expression was analyzed after white spot syndrome virus (WSSV) infection. The FcHsp21 gene contained an open reading frame (ORF) of 555 bp in length, encoding a 184 amino acid protein with a theoretical size of about 21 kDa and a predicted isoelectric point of 5.38. The mRNA of the Hsp21 had a long Poly(A) tail (748 bp) with six polyadenylation signals (AATAA) downstream from the terminator. In addition, the gene contained a relatively long intron (507 bp), which has not been described in shrimps. The intron contained a long compound type microsatellite repeat sequence. The analysis of the phylogenetics revealed that the Hsp21 was highly conserved among the genomes of animals. Our results show that the expression modes of FcHsp21 can be changed by different WSSV infection methods. The expression of FcHsp21 was inhibited by muscle-injecting WSSV, but induced by feeding WSSV.     

Transgenic tobacco plants expressing PicW gene from Picea wilsonii exhibit enhanced freezing tolerance

A cold-induced gene of 669 bp in length without introns, PicW, was cloned from Picea. wilsonii, a cold tolerant conifer species. Sequence analysis showed that it was a member of the dehydrin family because of its conserved amino acid constitution and protein secondary structure. The protein was rich in hydrophilic amino acids such as alanine, lysine, glutamic acid, glutamine and threonine, but devoid of two hydrophobic amino acids, cysteine and tryptophan. The PicW gene contained five repeated motifs homologous to the core K-segment in dehydrins. Protein secondary structure prediction showed that PicW comprised 29 % α-helix, mostly in the K-homologous segment, and random coils. The PicW gene was cloned into the expression vector PEZR(K)-LC under the 35S promoter and transformed into tobacco plants. After treatment at ?5 °C for 3 h, all of the tobacco plants were wilting. However, the transgenic plants showed better growth performance than wild-type plants. Further tests of physiological indexes including relative electrolyte leakage and malondialdehyde content, proline and soluble sugar content also revealed significant differences between the wild-type and transgenic tobacco plants. It was concluded that the PicW gene could be an important gene resource for freezing-tolerant plant breeding.     

Molecular cloning and expression of a C-type lectin gene from Venerupis philippinarum

C-type lectins have been demonstrated to play important roles in invertebrate innate immunity by mediating the recognition of pathogens and clearing the micro-invaders. In the present study, a C-type lectin gene (denoted as VpCTL) was identified from Venerupis philippinarum by expressed sequence tag and rapid amplification of cDNA ends approaches. The full-length cDNA of VpCTL consists of 904 nucleotides with an open-reading frame of 456 bp encoding a peptide of 151 amino acids. The deduced amino acid sequence of VpCTL shared high similarity with C-type lectins from other species. The C-type lectin domain and the characteristic EPN and WND motifs were found in VpCTL. The VpCTL mRNA was dominantly expressed in the haemocytes of the V. philippinarum. After Listonella anguillarum challenge, the temporal expression of VpCTL mRNA in haemocytes was increased by 97- and 84-fold at 48 and 96 h, respectively. With high expression level in haemocytes and hepatopancreas, and the up-regulated expression in haemocytes indicted that VpCTL was perhaps involved in the immune responses to L. anguillarum challenge.     

Recombinant β-1,3-1,4-glucanase from Theobroma cacao impairs Moniliophthora perniciosa mycelial growth

In this work, we identified a gene from Theobroma cacao L. genome and cDNA libraries, named TcGlu2, that encodes a β-1,3-1,4-glucanase. The TcGlu2 ORF was 720 bp in length and encoded a polypeptide of 239 amino acids with a molecular mass of 25.58 kDa. TcGlu2 contains a conserved domain characteristic of β-1,3-1,4-glucanases and presented high protein identity with β-1,3-1,4-glucanases from other plant species. Molecular modeling of TcGlu2 showed an active site of 13 amino acids typical of glucanase with β-1,3 and 1,4 action mode. The recombinant cDNA TcGlu2 obtained by heterologous expression in Escherichia coli and whose sequence was confirmed by mass spectrometry, has a molecular mass of about 22 kDa (with His-Tag) and showed antifungal activity against the fungus Moniliophthora perniciosa, causal agent of the witches’ broom disease in cacao. The integrity of the hyphae membranes of M. perniciosa, incubated with protein TcGlu2, was analyzed with propidium iodide. After 1 h of incubation, a strong fluorescence emitted by the hyphae indicating the hydrolysis of the membrane by TcGlu2, was observed. To our knowledge, this is the first study of a cacao β-1,3-1,4-glucanase expression in heterologous system and the first analysis showing the antifungal activity of a β-1,3-1,4-glucanase, in particular against M. perniciosa.     

Cloning and expression analysis of the gene encoding fibrinogen-like protein A,a novel regeneration-related protein from Apostichopus japonicus

Fibrinogen-like protein A (FGLA), a member of the fibrinogen-related protein superfamily, exists in different tissues of vertebrates and invertebrates. FGLA plays crucial roles including innate immune response, blood clotting and regeneration. In this study, the fibrinogen-like protein A (fglA) was cloned from Apostichopus japonicus using rapid amplification of cDNA ends PCR techniques. The cDNA sequence of fglA is 1,524 bp with a 849 bp open reading frame encoding a polypeptide of 282 amino acids, with an N-terminal signal peptide and a conserved C-terminal domain. Bioinformatic analysis revealed that the predicted molecular weight of the whole protein is 31.9 kDa and it has an isoelectric point of 5.64. In-situ hybridization demonstrated that fglA is widely distributed in body wall, intestines, longitudinal muscles and respiratory tree. The expression levels of fglA during different regeneration stages in the body wall, intestine and respiratory trees were analyzed by real-time PCR. The expression of fglA gradually increased within 1 h in body wall, and reached a plateau before decreasing to the basal level. This indicates that fglA is associated with the regeneration of Apostichopus japonicus.     

Characterization of Squalene synthase Gene from Chlorophytum borivilianum (Sant. and Fernand.)

Saponins are important group of secondary metabolites known for their pharmacological properties. Chlorophytum borivilianum contains high amount of saponins and is thus, recognized as an important medicinal plant with aphrodisiac properties. Though the plant is well known for its pharmaceutical properties, there is meager information available about the genes and enzymes responsible for biosynthesis of saponins from this plant. Squalene synthase (SqS) is the key enzyme of saponin biosynthesis pathway and here, we report cloning and characterization of SqS gene from C. borivilianum. A full-length CbSqS cDNA consisting of 1,760 bp was cloned which contained an open reading frame (ORF) of 1,233 bp, encoding a protein of 411 amino acids. Analysis of deduced amino acid sequence of CbSqS predicted the presence of conserved isoprenoid family domain and catalytic sites. Phylogenetic analysis revealed that CbSqS is closer to Glycine max and monocotyledonous plants. 3D structure prediction using various programs showed CbSqS structure to be similar to SqS from other species. C-terminus truncated recombinant squalene synthase (TruncCbSqS) was expressed in E. coli M15 cells with optimum expression induced with 1 mM IPTG at 37 °C. The gene expression level was analyzed through semi-quantitative RT-PCR and was found to be higher in leaves as compared to the roots.     

Molecular cloning, sequence characterization, SNP detection, and tissue expression analysis of duck FMO3 gene

Flavin-containing monooxygenase 3 (FMO3) is an important monooxygenase for catalytic oxygenation of many harmful xenobiotics. Mutations in the FMO3 gene have been identified as causing trimethylaminuria in human and fishy off-flavor in cow milk and chicken eggs. In this study, the full-length cDNA sequence of Pekin duck FMO3 gene was cloned, sequenced, and characterized. The full-length cDNA sequence consisted of 1,846 bp and contained a 1,599 bp open-reading frame encoding 532 amino acids. Duck FMO3 gene shared a similar nine exon–eight intron structure with chicken and human. The duck FMO3 putative protein sequence showed high identity with that of chicken (82 %), and relative low identity with those of mammals (61–66 %). We also found that the duck FMO3 gene was dramatically expressed in liver, lung, and kidney compared to that in other tissues in the ducks, indicating the possible roles the FMO3 gene could play in the three tissues. By bidirectional sequencing, we also found one nonsense mutation, 5 nonsynonymous, and 21 synonymous mutations in the coding region of the FMO3 gene in 11 duck breeds and some of them were predicted to be potentially associated with the activities of FMO3 protein.