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

In mammalian cells, transcribed enhancers (TrEns) play important roles in the initiation of gene expression and maintenance of gene expression levels in a spatiotemporal manner. One of the most challenging questions is how the genomic characteristics of enhancers relate to enhancer activities. To date, only a limited number of enhancer sequence characteristics have been investigated, leaving space for exploring the enhancers' DNA code in a more systematic way. To address this problem, we developed a novel computational framework, Transcribed Enhancer Landscape Search (TELS), aimed at identifying predictive cell type/tissue-specific motif signatures of TrEns. As a case study, we used TELS to compile a comprehensive catalog of motif signatures for all known TrEns identified by the FANTOM5 consortium across 112 human primary cells and tissues. Our results confirm that combinations of different short motifs characterize in an optimized manner cell type/tissue-specific TrEns. Our study is the first to report combinations of motifs that maximize classification performance of TrEns exclusively transcribed in one cell type/tissue from TrEns exclusively transcribed in different cell types/tissues. Moreover, we also report 31 motif signatures predictive of enhancers' broad activity. TELS codes and material are publicly available at http://www.cbrc.kaust.edu.sa/TELS.
Enhancer Elements, Genetic ; Genomics ; methods ; Humans ; Nucleotide Motifs ; Sequence Analysis, DNA ; methods ; Transcription, Genetic

Animals ; Base Pairing ; Binding Sites ; CCCTC-Binding Factor ; metabolism ; Consensus Sequence ; Humans ; Mutation ; Nucleotide Motifs

Virophages have crucial roles in ecosystems and are the transport vectors of genetic materials. To shed light on regulation and control mechanisms in virophage--host systems as well as evolution between virophages and their hosts, the promoter motifs of virophages were predicted on the upstream regions of start codons using an analytical tool for prediction of promoter motifs: Multiple EM for Motif Elicitation. Seventeen potential promoter motifs were identified based on the E-value, location, number and length of promoters in genomes. Sputnik and zamilon motif 2 with AT-rich regions were distributed widely on genomes, suggesting that these motifs may be associated with regulation of the expression of various genes. Motifs containing the TCTA box were predicted to be late promoter motif in mavirus; motifs containing the ATCT box were the potential late promoter motif in the Ace Lake mavirus . AT-rich regions were identified on motif 2 in the Organic Lake virophage, motif 3 in Yellowstone Lake virophage (YSLV)1 and 2, motif 1 in YSLV3, and motif 1 and 2 in YSLV4, respectively. AT-rich regions were distributed widely on the genomes of virophages. All of these motifs may be promoter motifs of virophages. Our results provide insights into further exploration of temporal expression of genes in virophages as well as associations between virophages and giant viruses.
Base Sequence ; Evolution, Molecular ; Genome, Viral ; genetics ; Genomics ; Nucleotide Motifs ; genetics ; Promoter Regions, Genetic ; genetics ; Satellite Viruses ; genetics

OBJECTIVETo clone SABATH methyltransferase (rLjSABATHMT) gene in Lonicera japonica var. chinensis, and compare the gene expression and intron sequence of SABATH methyltransferase orthologous in L. japonica with L. japonica var. chinensis. It provide a basis for gene regulate the formation of L. japonica floral scents.

METHODThe cDNA and genome sequences of LjSABATHMT from L. japonica var. chinensis were cloned according to the gene fragments in cDNA library. The LjSABATHMT protein was characterized by bioinformatics analysis. SABATH family phylogenetic tree were built by MEGA 5.0. The transcripted level of SABATHMT orthologous were analyzed in different organs and different flower periods of L. japonica and L. japonica var. chinensis using RT-PCR analysis. Intron sequences of SABATHMT orthologous were also analyzied.

RESULTThe cDNA of LjSABATHMT was 1 251 bp, had a complete coding frame with 365 amino acids. The protein had the conservative SABATHMT domain, and phylogenetic tree showed that it may be a salicylic acid/benzoic acid methyltransferase. Higher expression of SABATH methyltransferase orthologous was found in flower. The intron sequence of L. japonica and L. japonica var. chinensis had rich polymorphism, and two SNP are unique genotype of L. japonica var. chinensis. The motif elements in two orthologous genes were significant differences.

CONCLUSIONThe intron difference of SABATH methyltransferase orthologous could be inducing to difference of gene expression between L. japonica and L. japonica var. chinensis. These results will provide important base on regulating active compounds of L. japonica.

Base Sequence ; Cloning, Molecular ; Computational Biology ; Evolution, Molecular ; Gene Expression Regulation, Plant ; Lonicera ; enzymology ; genetics ; Methyltransferases ; genetics ; Nucleotide Motifs ; Phylogeny ; Sequence Alignment ; Sequence Analysis

Microbial recognition by multicellular organisms is initially accomplished by a group of pattern recognition receptors which are specialized to recognize microbe-associated molecular patterns (MAMPs) such as lipopolysaccharide, bacterial lipoprotein, CpG DNA motif, double strand RNA and flagellin. Toll-like receptors (TLRs) are the representative pattern recognition receptors, and microbial recognition by TLRs elicits innate and inflammatory responses. Ten TLR family members have been presently identified in human genome, and numerous studies discovered that intracellular responses from MAMPs-TLR engagements are mediated by a participation of at least 4 immediate adaptor molecules such as myeloid differentiation primary response gene-88 (MyD88), MyD88 adaptor-like (Mal) (also known as Toll/IL-1 receptor domain-containing adaptor protein [TIRAP]), Toll/IL-1 receptor domain-containing adaptor-inducing interferon-beta (TRIF) and TRIF-related adaptor molecule (TRAM) leading to activate transcription factors including nuclear factor kappaB, activator protein-1 and interferon-regulatory factors. Given that large amounts of commensal microbiota constantly reside in the intestinal lumen, enteric microbial recognition by TLRs at the intestinal epithelium provides a critical impact on regulating intestinal homeostasis. Indeed, aberrant TLR4 and TLR5 activations are etiologically associated with the development and progress of intestinal inflammatory diseases including inflammatory bowel disease and necrotizing enterocolitis. In this review article, we present the molecular mechanism by which TLRs elicit intracellular signal transduction, and summarize the physiological relevance of TLRs related to the gastrointestinal tract.
Enterocolitis, Necrotizing ; Flagellin ; Gastrointestinal Tract ; Genome, Human ; Homeostasis ; Humans ; Immunity, Innate ; Inflammatory Bowel Diseases ; Interferon-beta ; Intestinal Mucosa ; Intestines ; Lipoproteins ; Metagenome ; Nucleotide Motifs ; Receptors, Pattern Recognition ; RNA ; Signal Transduction ; Toll-Like Receptors ; Transcription Factor AP-1 ; Transcription Factors

Twenty-seven ERF transcription factor family genes were isolated from Arnebia euchroma, with an average size of 1,010 bp, each gene encoded a 212 amino acids on average. The gene structure and expression of physicochemical properties, subcellular localization, signal peptides, senior structural domains and conservative forecasting, and analysis of A. euchroma were studied comparing with ERF gene gi261363612 of Lithospermum erythrorhizon, and phylogenetic analysis of A. euchroma ERF family was carried out. The results showed the existence of three conserved domains in this family, the senior structure based on random coil and it clustered into CBF/DREB and ERF subfamilies.
Amino Acid Motifs ; Amino Acid Sequence ; Boraginaceae ; genetics ; Cloning, Molecular ; Computational Biology ; Genome, Plant ; genetics ; High-Throughput Nucleotide Sequencing ; Medicine, Chinese Traditional ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Plant Proteins ; chemistry ; genetics ; Plants, Medicinal ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Analysis, DNA ; Transcription Factors ; chemistry ; genetics ; Transcriptome