Biomedical subjects

Shicui Zhang

Publications and source records attributed to Shicui Zhang.

33 records · Page 2Linked to original sources

PubMed2005

Characterization and expression profile of AmphiCD63 encoding a novel member of TM4SF proteins from amphioxus Branchiostoma belcheri tsingtauense.

The study on CD antigen genes remains lacking in the cephalochordate amphioxus to date. In this report, the cDNA encoding CD63 was identified for the first time from the gut cDNA library of amphioxus Branchiostoma belcheri tsingtauense. Primary structural examination showed that the protein encoded by the cDNA contained four potential transmembrane domains characteristic of transmembrane 4 superfamily (TM4SF) proteins and a conserved CCG motif in the putative major extracellular loop. BLAST search revealed that the cDNA is closely associated with other known CD63 antigen genes, and it was thus designated AmphiCD63. Phylogenetic analysis indicated that AmphiCD63 is extremely close to vertebrate CD63, CD151 and CD53, suggesting they may have been evolved from a common ancestral gene. RT-PCR analysis exhibited that AmphiCD63 mRNA was abundant in muscle, ovary, foregut including hepatic caecum and hindgut, while it was present at considerably lower levels in notochord and gill and absent in testis.

Amino Acid Sequence↗

PubMed2004

Prediction of the interaction site on the surface of an isolated protein structure by analysis of side chain energy scores.

We show that residues at the interfaces of protein-protein complexes have higher side-chain energy than other surface residues. Eight different sets of protein complexes were analyzed. For each protein pair, the complex structure was used to identify the interface residues in the unbound monomer structures. Side-chain energy was calculated for each surface residue in the unbound monomer using our previously developed scoring function.1 The mean energy was calculated for the interface residues and the other surface residues. In 15 of the 16 monomers, the mean energy of the interface residues was higher than that of other surface residues. By decomposing the scoring function, we found that the energy term of the buried surface area of non-hydrogen-bonded hydrophilic atoms is the most important factor contributing to the high energy of the interface regions. In spite of lacking hydrophilic residues, the interface regions were found to be rich in buried non-hydrogen-bonded hydrophilic atoms. Although the calculation results could be affected by the inaccuracy of the scoring function, patch analysis of side-chain energy on the surface of an isolated protein may be helpful in identifying the possible protein-protein interface. A patch was defined as 20 residues surrounding the central residue on the protein surface, and patch energy was calculated as the mean value of the side-chain energy of all residues in the patch. In 12 of the studied monomers, the patch with the highest energy overlaps with the observed interface. The results are more remarkable when only three residues with the highest energy in a patch are averaged to derive the patch energy. All three highest-energy residues of the top energy patch belong to interfacial residues in four of the eight small protomers. We also found that the residue with the highest energy score on the surface of a small protomer is very possibly the key interaction residue.

Amino Acids↗

PubMed2004

Two classic cadherin-related molecules with no cadherin extracellular repeats in the cephalochordate amphioxus: distinct adhesive specificities and possible involvement in the development of multicell-layered structures.

We previously reported the existence of Bb-cadherin, a molecule related to classic cadherin, in the cephalochordate amphioxus (Branchiostoma belcheri). The structure of Bb-cadherin is unique in that it lacks the cadherin extracellular repeats, although its cytoplasmic domain shows close similarities to those of typical classic cadherins. The extracellular region of Bb-cadherin consists of laminin globular domains and a cysteine-rich EGF-like domain that are similar to domains in nonchordate classic cadherins. In this study, we identified a second amphioxus cadherin. It was designated Bb2-cadherin (Bb2C) while the previously reported cadherin has been renamed Bb1-cadherin (Bb1C). Bb2C is very similar to Bb1C in its overall structure and amino acid sequence. Genomic BLAST searches and phylogenetic analyses suggested that these two amphioxus genes have been generated through a gene duplication that occurred after separation of the cephalochordates from the other animals. They also bear distinct adhesive specificities. Immunohistochemical analyses showed that Bb1C and Bb2C, together with beta-catenin, appear to function as adherens junction constituents in the epithelia of different germ layers of the amphioxus embryo. Differential expression of the two cadherins was also observed in the developing, multicell-layered notochord. These observations suggest that, despite their unique structures, the functions and developmental roles of Bb1C and Bb2C are comparable to those of the classic cadherins characterized to date in other animal groups, such as the vertebrate E- and N-cadherins and the Drosophila DE- and DN-cadherins. The possible involvement of Bb1C and Bb2C in the development of multicell-layered structures characteristic of the cephalochordate body plan is presented.

Amino Acid Sequence↗

PubMed2004

Evolution and expression of the amphioxus AmphiHMGB gene encoding an HMG-box protein.

Amphioxus HMGB gene, AmphiHMGB, encoding a high mobility group (HMG) protein was identified from the gut cDNA library of Branchiostoma belcheri tsingtauense. Primary structural examination indicates that it is a member of HMGB family. Molecular phylogenetic analysis suggests that AmphiHMGB represents the archetype of chordate HMGB genes including HMGB1, HMGB2 and HMGB3 although it may have lost its C-terminal domain during evolution. Northern blotting revealed that AmphiHMGB expression was restricted mainly to guts in the adult, and AmphiHMGB transcripts were in greater abundance in gastrula and neurula though they were markedly low in 1-day larva.

Amino Acid Sequence↗

PubMed2004

Macrophage migration inhibitory factor (MIF) in chinese amphioxus as a molecular marker of immune evolution during the transition of invertebrate/vertebrate.

Macrophage migration inhibitory factor (MIF) is an important cytokine related to host defenses and autoimmune diseases. Here, we reported two full-length cDNA clones isolated from Chinese amphioxus (Branchiostoma belcheri tsingtaunese). Amino acid sequences analysis and structure prediction of these two molecules, called Bbt-MIF-I and Bbt-MIF-II, respectively, indicated that several conservative domains existed in the two amphioxus MIFs and their sequences were highly homologous to their counterparts of other species. Intriguingly, the Bbt-MIFs gene is present in multi-copy per haploid genome, which is very unusual compared with vertebrate's MIF gene given the known genome duplication theory. The genomic copy number, expression pattern of MIF gene and phylogenetic analysis of MIF proteins all suggested that a leap forward happened for MIF gene during the evolution from invertebrate to vertebrate. Considering the crucial role of MIF in innate immunity, MIF might serve as one of key molecular markers of evolution of immune system.

Amino Acid Sequence↗

PubMed2004

The development of the lymphoid organs of flounder, Paralichthys olivaceus, from hatching to 13 months.

The growth of the lymphoid organs, such as head kidney, spleen and thymus were studied in flounder, Paralichthys olivaceus Temminck & Schlegel, from hatching to 13 months of age. Except for the thymus, all organs grew as the fish grew. By 2 months of age the lymphoid organs attained their maximum relative weight. The organ weight showed a closer correlation to body weight than they did to age. The total number of leucocytes in the lymphoid organs increased with age, but the number per milligram of lymphoid organ remained constant. A micro and ultrastructural study of the lymphoid organs showed that the full development of the lymphoid organs was not achieved until the juvenile stage. The spleen and head kidney had mixed populations of "red" and "white" cells. The head kidney was more lymphoid than the spleen. The thymus involuted quickly during the first 6 months. The blood components had no obvious relationship with age or season during the period studied.

Age Factors↗

PubMed2004

Presence of prophenoloxidase in the humoral fluid of amphioxus Branchiostoma belcheri tsingtauense.

The presence of phenoloxidase (PO) activity in the humoral fluid of amphioxus Branchiostoma belcheri tsingtauense was electrophoretically and spectrophotometrically studied. The enzyme was present in the humoral fluid predominantly as an inactive proenzyme, prophenoloxidase (proPO). The optimum temperature for activation of the proPO ranged from 30 degrees C to 35 degrees C, and the enzyme exhibited optimum activity at pH between 7.0 and 7.5. ProPO in the humoral fluid was readily activated to active form PO by exogenous elicitors such as trypsin, zymosan and LPS. The activation of the proPO by exogenous elicitors was significantly enhanced in the presence of 10 mM Ca2+, but was susceptible to serine protease inhibitors like soybean trypsin inhibitor and p-nitrophenyl-p'-guanidinobenzoate. PAGE revealed a single band of PO activity in the humoral fluid with an apparent molecular mass of 150 kDa, which was resolved to three bands with molecular masses of 44, 46 and 72 kDa, respectively, after SDS-PAGE. This is the first report on the presence of the enzyme PO in amphioxus humoral fluid.

Animals↗

PubMed2004

C-banding pattern and nucleolar organizer regions of amphioxus Branchiostoma belcheri tsingtauense Tchang et Koo, 1936.

Chromosome banding study remains lacking in amphioxus heretofore. This paper reports the C-band pattern of the metaphase chromosomes of amphioxus Branchiostoma belcheri tsingtauense, the first description of banded karyotype in cephalochordate. The C-banding showed that around 50% of the second chromosome pair examined was heteromorphic, while the remaining ones were homomorphic. In contrast, the other 17 pairs were all homomorphic. These broadly support our previous suggestion that the second chromosome pair is a pair of sex-chromosomes. The C-banding stained positively about 54.3% of the chromosome surface. Most of the centromeric and terminal regions in many chromosomes had positive C-bands, and some interstitial C-bands were also observed in some chromosomes. It seems clear that chromosomes of amphioxus are highly heterochromatinized. In addition, silver staining revealed a single pair of nucleolar organizer regions (NORs) located in the telomeric regions of medium-sized chromosomes. It is suggested that the number and location of NORs in amphioxus represent the primitive condition for chordates.

Animals↗

PubMed2004

G-banding patterns of the chromosomes of amphioxus Branchiostoma belcheri tsingtauense.

Chromosome banding study remains lacking in amphioxus heretofore. This paper reports the G-band patterns of the metaphase chromosomes of amphioxus Branchiostoma belcheri tsingtauense, the first description and numbering of the karyotyped bands in a cephalochordate. G-banding results show that four out of the ten second pair chromosomes examined are heteromorphic, while the remaining ones (6/10) are homomorphic. In contrast, the other 17 pair chromosomes are all homomorphic. These broadly support our previous suggestion that the chromosomes No. 2 are a pair of sex-chromosomes. G-banding method stains positively 65.5% of the chromosome surface, and a total of 149 G-bands (77 positive, 65 negative and 7 variable) has been recorded in the 17 autosomes and the dimorphic chromosomes 2A' and 2A.

Animals↗

PubMed2003

An ascidian RING finger gene is specifically expressed in a single cell of larval ocellus.

The ascidian nervous system is extremely simple, although the structure of it is comparable with the complex vertebrate nervous system. This simplicity makes the ascidian nervous system a good model to understand how the neuronal circuit is built up in the chordate nervous system. In order to study the formation of the neuronal circuit at the single cell level, molecular markers to characterize specific single cells are desired. In the present paper, we describe the gene expression pattern of CIGL: an ascidian homologue of Goliath, a Drosophila RING-finger gene. In the early embryonic stage, CiGl is expressed in the lateral part of the neural tube and in several peripheral nerve cells. Later in the larval stage, CiGl specifically marks ocellus: one of the pigment cells in the ascidian brain, which is involved in the photoreceptive system. CiGl will be useful to understand the differentiation mechanism of ocellus, and especially to test the model proposed by. In addition, the finding of this single cells specific gene expression pattern at a certain developmental stage encourages us to look for more genes which mark single cells, especially those that have not been well characterized.

Amino Acid Sequence↗

PubMed2003

Cloning and phylogenetic analysis of an amphioxus myogenic bHLH gene AmphiMDF.

In this study, a member of the MyoD gene family, AmphiMDF, was isolated from the embryos of amphioxus by degenerate PCR, followed by rapid amplification of cDNA ends (RACE). Southern blot analysis confirmed that only a single myogenic bHLH gene was present in the genome of amphioxus Branchiostoma belcheri tsingtauense. Sequence and phylogenetic analyses indicated that AmphiMDF falls at the base of its vertebrate homologs. The amino acid sequence of AmphiMDF was almost equally similar to those of the four clusters of the vertebrate MyoD family. This suggests that AmphiMDF is not only the sister but also the archetype of the vertebrate myogenic bHLH genes. The scenarios to explain the origin of the vertebrate MyoD gene family from the ancestral myogenic bHLH gene like AmphiMDF are also discussed.

Amino Acid Sequence↗

PubMed2003

Presence and characterization of complement-like activity in the amphioxus Branchiostoma belcheri tsingtauense.

The humoral fluid of Branchiostoma belcheri tsingtauense was examined for the presence of complement-like activity. The humoral fluid showed hemolytic activity for rabbit erythrocytes and those from species representing mammals, birds, amphibians and fish, but not sensitized sheep erythrocytes. There was no relationship between phylogeny of the target erythrocytes and degree of hemolysis. The hemolytic activity was optimally assayed at 20 degrees C, at pH 7.5, and in the presence of 10 mM Mg2+. The hemolytic activity was Mg2+-dependent and heat-sensitive, and was abrogated by treatment with rabbit anti-human C3 serum, zymosan, methylamine, hydrazine, and phenylmethylenesulfonyl fluoride. In addition, Western blotting and titration by turbidimetric immunoassay (TIA) revealed that amphioxus humoral fluid contained C3 component, and its concentration is about 1.17 mg/ml, which is comparable to C3 concentration in human or dog sera. These suggest that the hemolytic activities displayed by amphioxus humoral fluid appear to represent the vertebrate complement system probably operating via the alternative pathway.

Animals↗

PubMedDate not supplied

Characterization and expression of AmphiCL encoding cathepsin l proteinase from amphioxus Branchiostoma belcheri tsingtauense.

An amphioxus complementary DNA, AmphiCL, encoding cathepsin L proteinase was isolated from the gut cDNA library of Branchiostoma belcheri tsingtauense. It is 1480 bp long, and its longest open reading frame codes for a precursor protein, which consists of 327 amino acid residues including a signal peptide (preregion), a propeptide, and a mature proteinase. Northern blot showed that AmphiCL was expressed in the gill, testis, hepatic cecum, and hind-gut with a molecular size of about 1480 bp. AmphiCL was also expressed at low level in the muscle, notochord, and ovary as revealed by the more sensitive reverse transcriptase polymerase chain reaction techniques. Semiquantitative RT-PCR also showed that although AmphiCL expression in the gut was significantly downregulated by feeding Arthrospira platensis powder, a protein-rich food, its expression in the same tissue was upregulated by exposure to lipopolysaccharide, an integral component of the outer membrane of gram-negative bacteria. This suggests that although the involvement of AmphiCL in food digestion remains to be confirmed, AmphiCL may play a role in inflammatory reaction in amphioxus.

Amino Acid Sequence↗

PubMedDate not supplied

A novel amphioxus cadherin that localizes to epithelial adherens junctions has an unusual domain organization with implications for chordate phylogeny.

Although data are available from only vertebrates, urochordates, and three nonchordate animals, there are definite differences in the structures of classic cadherins between vertebrates plus urochordates and nonchordates. In this study we examined structural diversity of classic cadherins among bilaterian animals by obtaining new data from an amphioxus (Cephalochordata, Chordata), an acorn worm (Hemichordata), a sea star (Echinodermata), and an oyster (Mollusca). The structures of newly identified nonchordate cadherins are grouped together with those of the known sea urchin and Drosophila cadherins, whereas the structure of an amphioxus (Branchiostoma belcheri) cadherin, designated BbC, is differently categorized from those of other known chordate cadherins. BbC is identified as a cadherin by its cytoplasmic domain whose sequence is highly related to the cytoplasmic sequences of all known classic cadherins, but it lacks all of the five repeats constituting the extracellular homophilic-binding domain of other chordate cadherins. The ectodomains of BbC match the ectodomains found in nonchordate cadherins but not present in other chordate cadherins. We show that the BbC functions as a cell-cell adhesion molecule when expressed in Drosophila S2 cells and localizes to adherens junctions in the ectodermal epithelia in amphioxus embryos. We argue that BbC is the amphioxus homologue of the classic cadherins involved in the formation of epithelial adherens junctions. The structural relationships of the cadherin molecules allow us to propose a possibility that cephalochordates might be basal to the sister-groups vertebrates and urochordates.

Adherens Junctions↗

PubMedDate not supplied

Molecular evolution of fibrillar collagen in chordates, with implications for the evolution of vertebrate skeletons and chordate phylogeny.

Vertebrates have seven types of fibrillar collagens that are encoded by 11 genes. Types I, V, and XXIV collagens are components of mineralized bone, whereas types II, XI, and XXVII collagens are components of cartilage. In this study, we traced the molecular evolutionary history of chordate collagen genes and examined how gene duplications gave rise to the collagen genes used for skeletons. Our analyses of deuterostome collagen genes, including one amphioxus gene that we identified in this study, suggest that the common ancestors of deuterostomes possessed three fibrillar collagen genes. Expression analyses of chordate fibrillar collagen genes suggest that in the ancestors of chordates, fibrillar collagen was co-opted to the formation of the notochord sheath independently in three clades. Our results also imply that co-option of collagen genes to cartilage occurred in clade A (col2A1), clade B (col11A1, 11A2), and clade C (COL27A1). Similarly, some fibrillar collagen genes have been co-opted for mineralized bone independently from clade A genes (col1A1, 1A2, 5A2), clade B genes (col5A1), and clade C genes (COL24A1). These frequent co-options for notochord, cartilage, and mineralized bone must have been accompanied by the rapid evolution of cis-regulatory elements for transcription. In addition, we found that one of the ascidian fibrillar collagen genes possesses an amino acid insertion at the identical site of the C-terminal noncollagenous domain in vertebrate fibrillar collagen genes. This observation raises a suspicion about the relatively well-accepted phylogeny of the close relationship between amphioxus and vertebrates.

Amino Acid Sequence↗