[Show abstract][Hide abstract] ABSTRACT: Acetyl-CoA carboxylase α (ACC1), the major regulatory enzyme of fatty acid biosynthesis, catalyzes the conversion of acetyl-CoA to malonyl-CoA. The full-length cDNA coding ACC1 isoform was cloned from liver of grass carp. The cDNA obtained was 7515bp with a 7173bp open reading frame encoding 2389 amino acids. The ACC1 protein has a calculated molecular weight of 269.2kDa and isoelectric point of 6.23. Tissue distribution of ACC1 mRNA in brain, mesenteric adipose, spleen, white muscle and liver of grass carp was analyzed by real-time PCR method using β-actin as an internal control for cDNA normalization. The results showed that the expressions of ACC1 mRNA were detected in all examined tissues. Relative expression profile of ACC1 mRNA in liver normalized with β-actin level was 15, 92, 135 and 165-fold compared with the level in brain, white muscle, mesenteric adipose and spleen, respectively. In addition, we present evidence for the presence of two isoforms of ACC1 (265.7kDa and 267.2kDa) in grass carp liver that differ from the 269.2kDa ACC1 by the absence of 34 and 15 amino acids. In conclusion, the liver is one of the main ACC1 producing tissues in grass carp and ACC1 gene was highly homologous to that of mammals.
[Show abstract][Hide abstract] ABSTRACT: Over the past decades, inference of phylogenetic relationship and population diversity of metazoan species based on mitochondrial genome sequences has become popular. Tunicates, also known as urochordates, are members of the subphylum Tunicata or Urochordata, a group of underwater saclike filter feeders that is classified within the phylum Chordata. In this paper, a comprehensive bioinformatics analysis based on 12 tunicates mitochondrial genomes has been done, including the basic characteristics of the mitochondrial genome, protein coding genes, phylogenetic relationships and genetic different loci and so on. The length of 12 tunicates mitochondrial genomes are between 13, 648 bp and 16, 351 bp. The numbers of protein coding genes and transfer RNA genes of 12 mitochondrial genomes are slight different. Gene order is extremely rearranged among 12 tunicates mitochondrial genomes. The ratio of Ka/Ks of 12 protein-coding genes (atp8 gene was excluded) from 2 Ciona mitochondrial genomes is less than 1 (between 0.0927 and 0.6752), indicating a strong purification (negative) selection. The phylogenetic trees based on mitochondrial genomes showed that the subphylum Tunicata is divided into two clades: the class Thaliacea and the class Ascidiacea (BPP=100, BPM=100). In the internal of class Ascidiacea, two families (Pyuridae and Styelidae) clustered as a clade (BPP=100, BPM=100). Meanwhile three families (Polyclinidae, Didemnidae and Clavelinidae) clustered as a clade (BPP=100, BPM=100). The genetic variation analysis of main genes among tunicates showed that nad5, nad4 and cox1 genes are ideal molecular markers in tunicates population genetics studies, which can be applied in the analysis of genetic diversity within different groups.
[Show abstract][Hide abstract] ABSTRACT: Coelomactra antiquata is an economic shellfish which is famous feast food with a very high medical value. The protein samples of digestive tract tissues (stomach and intestine) were extracted by crushing, cracking, centrifugation and other extraction methods. The Bradford proteir quantitative kit was used for protein quantification. IEF electrophoresis and SDS-PAGE electrophoresis were carried out. The obtained gel was stained by coomassie brilliant blue R350 and the protein profile was scanned using ImageScanner III scanner to obtain the gel image. It is the first time to get the two-dimensional gel electrophoresis profile and initially construct the two-dimensional gel electrophoresis system on the proteome of C. antiquata stomach and intestine. The map analysis showed that the obtained protein spots of stomach and intestine distributed between pH=4 and pH=7, and the majority of proteins were acidic proteins. The number of extreme molecular weight or high pH proteins is relatively small. This study has provided a foundation for. the further exploration about the physiological and biochemical mechanisms on digestive tract tissues proteome of C. antiquata.
[Show abstract][Hide abstract] ABSTRACT: Sea urchins belong to the phylum Echinodermata and the class Echinoidea, which are economic marine organisms that have higher nutritious, medicinal, ecological and scientific value. In this paper, a comprehensive bioinformatics analysis based on 6 sea urchins mitochondrial genomes has been done, including the basic characteristics of the mitochondrial genome, protein-coding genes, gene order and genetic variation and so on. The length of 6 sea urchins mitochondrial genomes are between 15, 650 bp and 15, 767 bp. All 6 mitochondrial genomes are coding metazoan 37 standard genes. The gene orders are identical for 6 sea urchins mitochondrial genomes. The basic holothuroids and sea urchins mitochondrial gene orders are identical and the gene arrangement shared by sea urchins and basic holothuroids is the echinoderm ground pattern. Except for the atp8 gene, Ka/Ks ratio of the rest 12 mitochondrial protein-coding genes is much lower than 1 (between 0 and 0.1997), indicating a strong purifying selection (negative selection). However, the atp8 gene of Strongylocentrotus mitochondrial genomes encounter positive selection (Darwin selection), which is the first time reported in the mitochondrial genomes of marine invertebrates. The genetic variation analysis of 15 main genes (13 protein coding genes and 2 ribosomal RNA genes) among 6 sea urchins and 3 Strongylocentrotus showed that nad5, nad4 and cox1 genes are ideal molecular markers in sea urchin population genetics studies and can be applied in the analysis of genetic diversity within different groups, which providing a reference for the conservation of sea urchins biological diversity and use of the biological resources rationally.
[Show abstract][Hide abstract] ABSTRACT: The basic characteristics of loaches mitochondrial genomes were fully revealed by comprehensive bioinformatics analyses of 9 loaches mitochondrial genomes. Loaches mitochondrial genomes contain 37 standard metazoan genes and their gene order is identical. The Ka/Ks ratio of the Cobitis and Misgurnus 13 mitochondrial protein-coding genes is lower than (between 0.0021 and 0.5322), indicating a strong purifying selection (negative selection). The phylogenetic trees based on mitochondrial genomes showed that the family Cobitidae is divided into two clades: the subfamily Botiinae and the subfamily Cobitinae. In the internal of subfamily Cobitinae, the genus Cobitis and the genus Misgurnus clusted as a clade, meanwhile the genus Acantopsis and the genus Pangio clusted as another clade. As for the three species from the genus Cobitis, the relationship between C. striata and C. choii is closer than C. sinensis. The genetic variation analysis of main genes (13 protein coding genes and 2 ribosomal RNA genes) among loaches species showed that nad5, nad4 and cox 1 genes are ideal molecular markers, which can be used to analysis the genetic diversity among different groups and provide more protection for rational use of its biological resources.
[Show abstract][Hide abstract] ABSTRACT: A full-length cDNA coding lipoprotein lipase (LPL) was cloned from liver of adult common carp (Cyprinus carpio Var. Jian) by RT-PCR and rapid amplification of cDNA ends (RACE) approaches. The cDNA obtained was 2,411 bp long with a 1,524 bp open reading frame (ORF) encoding 507 amino acids. This amino acid sequence contains two structural regions: N-terminus (24-354 residues) and C-terminus (355-507 residues). Before N-terminus, 1-23 residues is signal peptide, 6-23 residues is transmembrance helix. At N-terminus, some conversed functional sites were found, including two N-linked glycosylation sites Asn(41) and Asn(88); one catalytic triad Ser(174), Asp(198) and His(283); one conserved heparin-binding site Arg(321) to Arg(324) (RKNR); eight cysteines residues Cys(69) and Cys(82), Cys(258) and Cys(281), Cys(306) and Cys(325), Cys(317) and Cys(320) which are involved in four disulfide bridges; one polypeptide "lid" that participates in substrate specificity. At C-terminus, Asn(401) is another N-linked glycosylation site, and Trp(434) and Trp(435) (WW) is lipid-binding site. The amino acid sequence has a high similarity, and shows similar structural features to LPL of other species. Tissue distribution of LPL mRNA in liver, head kidney, mesenteric adipose tissue, heart and white muscle of common carp was analyzed by semi-quantitative RT-PCR method using beta-actin gene as internal control. The result showed that the expressions of LPL mRNA were detected in all examined tissues of common carp. The expression levels of LPL in the mesenteric adipose tissue was highest among these tissues, following in liver and head kidney, and the lowest expression was found in heart and white muscle.
[Show abstract][Hide abstract] ABSTRACT: A full-length cDNA coding lipoprotein lipase (LPL) was cloned from liver of adult Pengze crucian carp (Carassius auratus var. Pengze) by RT-PCR and rapid amplification of cDNA ends (RACE) approaches. The cDNA obtained was 1877 bp long with a 1524 bp open reading frame (ORF) encoding 507 amino acids, including a putative signal peptide of 23 amino acids long. The deduced amino acid sequence has a high similarity and shows similar structural features to LPL of other species. The LPL protein has a calculated molecular mass of 57.7 kDa and isolectric point of 7.85. Tissue distribution of LPL mRNA in mesenteric adipose tissue, liver, heart, head kidney and white muscle of adult Pengze crucian carp was analyzed by semi-quantitative RT-PCR method using beta-actin gene as internal control, the result showed that this gene was ubiquitously expressed in all tissues tested with the highest abundance in mesenteric adipose tissue, following in head kidney and liver, and the lowest expression was found in heart and white muscle.
Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology 03/2009; 153(1):109-15. DOI:10.1016/j.cbpb.2009.02.006 · 1.55 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The first and second internal transcribed spacer (ITS1 and ITS2) regions of the ribosomal DNA from four species, Meretrix meretrix L., Cyclina sinensis G., Mercenaria mercenaria L., and Protothaca jedoensis L., belonging to the family Veneridae were amplified by PCR and sequenced. The size of the ITS1 PCR amplification product ranged from 663 bp to 978 bp, with GC contents ranging from 60.78% to 64.97%. The size of the ITS1 sequence ranged from 585 bp to 900 bp, which is the largest range reported thus far in bivalve species, with GC contents ranging from 61.03% to 65.62%. The size of the ITS2 PCR amplification product ranged from 513 bp to 644 bp, with GC contents ranging from 61.29% to 62.73%. The size of the ITS2 sequence ranged from 281 bp to 412 bp, with GC contents ranging from 65.21% to 67.87%. Extensive sequence variation and obvious length polymorphisms were noted for both regions in these species, and sequence similarity of ITS2 was higher than that of ITS1 across species. The complete sequences of 5.8S ribosomal RNA gene were obtained by assembling ITS1 and ITS2 sequences, and the sequence length in all species was 157 bp. The phylogenetic tree of Veneridae clams was reconstructed using ITS2-containing partial sequences of both 5.8S and 28S ribosomal DNA as markers and the corresponding sequence information in Arctica islandica as the outgroup. Tree topologies indicated that P. jedoensis shared a close relationship with M. mercenaria and C. sinensis, a distant relationship with other species.