OBJECTIVETo deduce all potential ligands undiscovered experimentally by searching all the proteins containing same C-termini, which can bind a certain PDZ domain.

METHODSWe developed a JAVA program for searching short exact sequence matches at C-terminus. According to the known C-termini, which PDZ domains recognized experimentally, Swissprot database has been searched by this program for all potential ligands.

RESULTSSome PDZ domains may have more potential ligand proteins, which are undiscovered yet experimentally. These bioinformatic results also provide clues for studying functions of hypothetical proteins and PDZ domains' protein interactions in many different organisms.

CONCLUSIONThe results may provide useful clues for discovering potential functions of hypothetical proteins and new functions of known proteins.

Amino Acid Sequence ; Binding Sites ; Conserved Sequence ; Ligands ; Protein Binding ; Proteins ; chemistry ; metabolism ; Software

Cysteine-rich secretory protein-1 (CRISP-1) is a glycoprotein secreted by the epididymal epithelium. It is a member of a large family of proteins characterized by two conserved domains and a set of 16 conserved cysteine residues. In mammals, CRISP-1 inhibits sperm-egg fusion and can suppress sperm capacitation. The molecular mechanism of action of the mammalian CRISP proteins remains unknown, but certain non-mammalian CRISP proteins can block ion channels. In the rat, CRISP-1 comprises two forms referred to as Proteins D and E. Recent work in our laboratory demonstrates that the D form of CRISP-1 associates transiently with the sperm surface, whereas the E form binds tightly. When the spermatozoa are washed, the E form of CRISP-1 persists on the sperm surface after all D form has dissociated. Cross-linking studies demonstrate different protein-protein interaction patterns for D and E, although no binding partners for either protein have yet been identified. Mass spectrometric analyses revealed a potential post-translational modification on the E form that is not present on the D form. This is the only discernable difference between Proteins D and E, and presumably is responsible for the difference in behavior of these two forms of rat CRISP-1. These studies demonstrate that the more abundant D form interacts with spermatozoa transiently, possibly with a specific receptor on the sperm surface, consistent with a capacitation-suppressing function during sperm transit and storage in the epididymis, and also confirm a tightly bound population of the E form that could act in the female reproductive tract.
Amino Acid Sequence ; Animals ; Conserved Sequence ; Humans ; Male ; Mammals ; Membrane Glycoproteins ; genetics ; metabolism ; Molecular Sequence Data ; Rats ; Spermatozoa ; physiology

MicroRNAs (miRNAs) act as regulators of gene expression by binding to the 3’ untranslated region (UTR) of target genes. They perform important biological functions in the various species. Among many miRNAs, miR-21-3p is known to serve vital functions in development and apoptosis in olive flounder. Using genomic and bioinformatic tools, evolutionary conservation of miR-21-3p was examined in various species, and expression pattern was analyzed in olive flounder. Conserved sequences (5’-CAGUCG-3’) in numerous species were detected through the stem-loop structure of miR-21-3p. Thus, we analyzed target genes of miR-21-3p. Among them, 3’ UTR region of PPIL2 gene indicated the highest binding affinity with miR-21-3p based on the minimum free energy value. The PPIL2 gene showed high expression levels in testis tissue of the olive flounder, whereas miR-21-3p showed rather ubiquitous expression patterns except in testis tissue, indicating that miR-21-3p seems to control the PPIL2 gene expression in a complementary repression manner in various tissues of olive flounder. Taken together, this current study contributes to infer the target gene candidates for the miR-21-3p using bioinformatics tools. Furthermore, our data offers important information on the relationship between miR-21-3p and target gene for further functional study.
Apoptosis ; Computational Biology ; Conserved Sequence ; Flounder* ; Gene Expression ; MicroRNAs ; Olea* ; Repression, Psychology ; Testis ; Untranslated Regions

Hepatitis B is a serious infectious disease worldwide, and hepatitis B virus (HBV) is the direct cause of this disease. In recent years, as an essential part of its evolutionary process, HBV mutation has been extensively studied domestically and globally. However, the study on the conserved sequences in HBV sequences is still in its infancy. In this study, we applied multiple EM for motif elicitation (MEME) algorithm to discover HBV motif and proposed a new metric, conservative index (CI), to carry out phylogenetic analysis based on HBV sequences. Then, the constructed phylogenetic tree was subjected to reliability assessment. The results demonstrated that the new metric CI combined with the MEME algorithm can effectively help to discover motifs in HBV sequences and construct a phylogenetic tree based on them and to analyze the evolutionary relationship between HBV sequences; in addition, the possible ancestral sequences of samples may be obtained by conservative analysis. The proposed method is valuable for the exploratory study on large HBV sequence data sets.
Computational Biology ; Conserved Sequence ; Evolution, Molecular ; Hepatitis B virus ; genetics ; Humans ; Nucleotide Motifs ; Phylogeny ; Reproducibility of Results

The full-length genome of one human bocavirus (HBoV) and the VP1 sequences of nine HBoV were amplified from patients' samples by PCR, cloned into pGEM-T vector separately, and sequenced. In this study, the one full length gemome and nine VP1 sequences of HBoV were aligened with 14 sequences of Parvoviruses which were canonical exemplars in Parvovirinae. Phylogenetic analysis showed that HBoV capsid sequences positioned closely to B19 parvovirus, although they positioned far in phylogenetic tree based on full length genome. Many similarities were found between HBoV and B19 in capsid by alignment on secondary structural elements. Because both B19 and HBoV are the only Parvoviruses that infect mankind, so study on HBoV may be used for reference to B19 which had been studied for about 30 years. By analysis of mutational sites, HBoV capsid protein showed a highly conserved secondary structural elements, but highly active in VP1-U, leading end of VP2 and insertions between the strands of the betaG-H. This cued that HBoV inclined to immune evasion and infectant adaptive faculty.
Amino Acid Sequence ; Base Sequence ; Bocavirus ; classification ; genetics ; Capsid Proteins ; chemistry ; genetics ; Cloning, Molecular ; Conserved Sequence ; Genome, Viral ; Humans ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction

OBJECTIVETo clone farnesyl diphosphate synthase (FPS) gene from Eleutherococcus senticosus and analyze the bioinformatics and expression of the gene.

METHODThe FPS full length cDNA was cloned by rapid amplification of cDNA ends (RACE). The data was analyzed by bioinformatics method, the structure and function of FPS was deduced. The expression of FPS in different organ of E. senticosus was detected by RT-PCR.

RESULTThe full length of FPS cDNA was 1 499 bp containing a 1 029 bp ORF that encoded 342 amino acids. The deduced protein sequence exhibited two Asp riches conserved motifs (DDXXD). Without transmembrane domain, FPS was located in cytoplasm. RT-PCR result showed that FPS gene expressed in different organs of E. senticosus. The expression amounts of FPS in different organs were different significantly (P < 0.05).

CONCLUSIONThe FPS gene of E. senticosus was successfully cloned for the first time, and provided a stable foundation for studying on its effect and expression control on E. senticosus saponins biosynthesis.

Amino Acid Sequence ; Cloning, Molecular ; Computational Biology ; Conserved Sequence ; Eleutherococcus ; enzymology ; genetics ; Gene Expression Regulation, Plant ; Geranyltranstransferase ; chemistry ; genetics ; metabolism ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Conformation

Streptoverticillum caespitosus ATCC27422 is a producing strain of mitomycin A for cancer therapy. Taking the advantage of the conserved sequences of genes flanking the oriC of high G + C Gram-positive bacteria, a 1.3 kb DNA fragment containing oriC and its flanking region was cloned by PCR. Nuleotide sequence comparisons revealed that the cloned fragment is more than 80% identical to the same region of S. coelicolor. There are 22 DnaA-boxes in the oriC region, and the conserved sequence of DnaA-box is TTGTCCACA. The plasmid containing the oriC of S. caespitosus was constructed (pMJ9), and it was able to transform the protoplast of Streptomyces lividans ZX7 at the frequency of 3.2 x 10(2) transformants/micrograms plasmid DNA. The colony and mycelia's morphology of the transformants are normal. The constructed plasmid can exist stable in the host as a low copy extra-chromosome replicon. The high rate of the homology and the cross genus replication initiation activity suggests close relationship between Streptomyces and Streptoverticillum in the evolution. While the maximum likelihood phylogenetic tree based upon the oriC of S. caespitosus and several Streptomyces spp. revealed that S. caespitosus differed extensively from the Streptomyces spp. This result supports the separation of Streptoverticillum from Streptomyces.
Actinomycetales ; genetics ; Base Sequence ; Blotting, Southern ; Cloning, Molecular ; Conserved Sequence ; Molecular Sequence Data ; Plasmids ; Replication Origin ; genetics ; Streptomyces ; genetics ; Transformation, Bacterial

We wished to assess the role of chlamydia micro virus capsid protein Vp3 in recombinant molecules, chart its molecular evolution, screen the wild-type strain, and reveal its value in clinical research. Using a protein BLAST multiple-alignment program, we compared various strains of Chlamydia micro virus capsid protein Vp3 sequences. Using a "distance tree" of those results, we created a phylogenetic tree. We applied the Karplus-Schulz method of flexible-region analyses for highly conserved alignments of amino-acid sequences. Gamier-Robson and Chou-Fasman methods were employed to analyze two-level structures of sequences. The Emini method was used for analyses of the accessibility of surface epitopes. Studies of hydrophilic proteins were undertaken using Kyte-Doolittle and Hopp-Woods methods. Analyses of antigen epitopes helped to reveal the antigen index using the Jameson-Wolf method. All sequences in the six strains of chlamydia micro virus capsid protein Vp3 were highly conserved, with the main differences being between Vp3 protein in Chp1 and the other five strains of the micro virus. The viral strain of Vp3 protein was based mainly on micro-alpha helix structures, and multiple epitopes were noted in highly conserved regions. Vp3 protein was highly conserved structurally, and was an important protein of the chlamydiaphage capsid. Vp3 protein has a complicated molecular structure, highly conserved regions with strong immunogenicity, and has considerable research value.
Amino Acid Sequence ; Capsid Proteins ; chemistry ; genetics ; immunology ; Chlamydia ; genetics ; immunology ; Conserved Sequence ; Epitope Mapping ; Evolution, Molecular ; Molecular Sequence Data ; Recombination, Genetic

Using universal primer Ty1-copia retrotransposon RT,43 Ty1-copia like retrotransposon RT with high heterogeneity, stop codon mutation and frameshift mutation were amplified by PCR from genomic DNA of Zhejiang Lin'an (C15) and Yunnan Guangnan (A39) of Dendrobium officinale. The length of these sequences varied from 260 to 266 bp, and was rich in AT and consistency ranged from 47.1% to 97.7%. Different c/s-acting regulatory elements induced by low temperature, heat, light, all kinds of plant growth regulating substances and the starting transcription signals, corresponding to CAAT box, TATA box conserved sequences and some other regulatory elements. When being translated into amino acids, ten sequences presented stop codon mutation, five sequences presented frameshift mutation, and thirty-seven sequences presented conserved sequence "SLYGKQ" mutation. Six categories were identified through phylogenic analysis after alignment analyses of their amino acid sequences, and with other plants (eg. Triticum aestivum, Eleocharis quinqueflora) having high homology, which indicated that horizontal transmission of retrotransposon occurred among the plants in the past.
Amino Acid Sequence ; Cloning, Molecular ; Conserved Sequence ; DNA, Plant ; genetics ; Dendrobium ; enzymology ; genetics ; Molecular Sequence Data ; Phylogeny ; RNA-Directed DNA Polymerase ; chemistry ; genetics ; Retroelements ; genetics ; TATA Box ; genetics

Trichoderma/Hypocrea is a genus of soil-borne or wood-decaying fungi containing members important to mankind as producers of industrial enzymes and biocontrol agents against plant pathogens, but also as opportunistic pathogens of immunocompromised humans. Species identification, while essential in view of the controversial properties of taxa of this genus, has been problematic by traditional methods. Here we will present a critical survey of the various identification methods in use. In addition, we will present an update on the taxonomy and phylogeny of the 88 taxa (which occur as 14 holomorphs, 49 teleomorphs and 25 anamorphs in nature) of Trichoderma/Hypocrea that have been confirmed by a combination of morphological, physiological and genetic approaches.
Chromosome Mapping ; methods ; Conserved Sequence ; Evolution, Molecular ; Genome, Fungal ; Hypocrea ; classification ; genetics ; Phylogeny ; Sequence Analysis, DNA ; methods ; Sequence Homology, Nucleic Acid ; Species Specificity ; Trichoderma ; classification ; genetics