Genetic code expansion (GCE) allows the incorporation of unnatural amino acids into proteins via using stop codons. GCE may achieve site-specific labeling of proteins in combination with the click reaction. Compared with other labeling tools such as fluorescent proteins and tagged antibodies, the compound molecules used in protein labeling by GCE technology are smaller, and therefore, may less interfere the conformational structure of proteins. In addition, through click reaction, GCE allows a 1:1 stoichiometric ratio of the target protein molecule and the fluorescent dye, and the protein can be quantified based on the fluorescence intensity. Thus, GCE technology has great advantages in the researches that require the exposition of living cells under high laser power for longer time, for example, in the context of single molecule tracing and super-resolution microscopic imaging. Meanwhile, this technology lays the foundation for improving the accuracy of positioning and molecule counting in the imaging process of living cells. This review summarized the GCE technology and its recent applications in functionally characterizing, labeling and imaging of proteins.
Amino Acids/chemistry* ; Fluorescent Dyes/chemistry* ; Genetic Code ; Proteins/chemistry*

Periodontitis is a common oral disease that is characterized by infection and inflammation of the tooth supporting tissues. While its incidence is highly associated with outgrowth of the pathogenic microbiome, some patients show signs of predisposition and quickly fall into recurrence after treatment. Recent research using genetic associations of candidates as well as genome-wide analysis highlights that variations in genes related to the inflammatory response are associated with an increased risk of periodontitis. Intriguingly, some of the genes are regulated by epigenetic modifications, supposedly established and reprogrammed in response to environmental stimuli. In addition, the treatment with epigenetic drugs improves treatment of periodontitis in a mouse model. In this review, we highlight some of the recent progress identifying genetic factors associated with periodontitis and point to promising approaches in epigenetic research that may contribute to the understanding of molecular mechanisms involving different responses in individuals and the early detection of predispositions that may guide in future oral treatment and disease prevention.
Animals ; DNA Methylation ; Epigenomics ; Genetic Variation ; Histone Code ; Humans ; Inflammation ; Metagenome ; Mice ; Periodontitis ; Recurrence ; Tooth

The primary clue for locating protein-coding regions is the open reading frame and the determination of ORFs (Open Reading Frames) is the first step toward the gene prediction, especially for prokaryotes. In this respect, we have developed a web-based ORF search tool called ORF Miner. The ORF Miner is a graphical analysis utility which determines all possible open reading frames of a selectable minimum size in an input sequence. This tool identifies all open reading frames using alternative genetic codes as well as the standard one and reports a list of ORFs with corresponding deduced amino acid sequences. The ORF Miner can be employed for sequence annotation and give a crucial clue to determination of actual protein-coding regions.
Amino Acid Sequence ; Animals ; Ecthyma, Contagious ; Genetic Code ; Open Reading Frames ; Resin Cements

It has been increasingly recognized that the pathogenesis of B-cell lymphoma closely relates to the epigenetic disregulations. Epigenetics is a subdiscipline, which means heritable changes in gene expressions without alterations in the DNA sequence, and the DNA methylation, histone modification and miRNA maily were involved. Histone modification is the most important epigenetic modification, the researches showed that the aberrant histone modification is the important pathogenesis in B-cell lymphoma, especially the aberrant histone methylation and acetylation. In the meantime, the tumor can be treated by changing the epigenetic modification, which become a research hotpoint. This review summarizes the pathogenesis of B cell lymphoma and discusses the epigenetic treatment of B cell lymphoma mainly in terms of histone modification regulation for B cell development in the germinal center and mutation of histone madification enzymes.
DNA Methylation ; Epigenesis, Genetic ; Histone Code ; Histones ; Humans ; Lymphoma, B-Cell

Epigenetic modification, especially histone modification, plays an important role in maintaining plant genome stability, regulating gene expression and promoting regeneration in vitro. MtSERK1 is an important marker gene involved in establishing of embryogenic callus during in vitro regeneration of Medicago truncatula. In order to understand the regulation Epigenetic modification, especially histone modification, plays an important role in maintaining plant genome stability, regulating gene expression and promoting regeneration in vitro. MtSERK1 is an important marker gene involved in establishing of embryogenic callus during in vitro regeneration of Medicago truncatula. In order to understand the regulation relationship between dynamic histone modification and MtSERK1s expression during the processes of in vitro organogenesis, the expression of MtSERK1 was analyzed by qRT-PCR, and the modification status of H3K9me2, H3K4me3 and H3K9ac in the promoter region and different regions included in the gene body was analyzed by chromatin immunoprecipitation (ChIP). We found expression activation of MtSERK1 was related to the dynamic changes of histone H3K4me3 and H3K9ac in the 5' and 3' regions. This study will provide important theoretical guidance for understanding of the regulatory mechanism of MtSERK1 and also for establishing efficient genetic transformation system of Medicago truncatula.
Epigenesis, Genetic ; Gene Expression Regulation, Plant ; Genome, Plant ; Histone Code ; Medicago truncatula ; genetics ; growth & development ; Protein Kinases ; genetics ; Regeneration

Enhancers activate transcription in a distance-, orientation-, and position-independent manner, which makes them difficult to be identified. Self-transcribing active regulatory region sequencing (STARR-seq) measures the enhancer activity of millions of DNA fragments in parallel. Here we used STARR-seq to generate a quantitative global map of rice enhancers. Most enhancers were mapped within genes, especially at the 5' untranslated regions (5'UTR) and in coding sequences. Enhancers were also frequently mapped proximal to silent and lowly-expressed genes in transposable element (TE)-rich regions. Analysis of the epigenetic features of enhancers at their endogenous loci revealed that most enhancers do not co-localize with DNase I hypersensitive sites (DHSs) and lack the enhancer mark of histone modification H3K4me1. Clustering analysis of enhancers according to their epigenetic marks revealed that about 40% of identified enhancers carried one or more epigenetic marks. Repressive H3K27me3 was frequently enriched with positive marks, H3K4me3 and/or H3K27ac, which together label enhancers. Intergenic enhancers were also predicted based on the location of DHS regions relative to genes, which overlap poorly with STARR-seq enhancers. In summary, we quantitatively identified enhancers by functional analysis in the genome of rice, an important model plant. This work provides a valuable resource for further mechanistic studies in different biological contexts.
Acetylation ; Base Sequence ; Deoxyribonuclease I ; metabolism ; Enhancer Elements, Genetic ; Epigenesis, Genetic ; Genes, Plant ; Genomics ; methods ; Histone Code ; genetics ; Histones ; metabolism ; Models, Genetic ; Oryza ; genetics ; Promoter Regions, Genetic ; genetics ; Repetitive Sequences, Nucleic Acid ; genetics ; Sequence Analysis, DNA ; Transcription, Genetic

OBJECTIVETo screen and characterize the variable region gene about prostate specific membrane antigen (PSMA) of the Chinese Fab fragment, and to establish a new approach to researches on PSMA and prostate gene therapy.

METHODSWe used purified PSMA protein as antigen, stuck it on the ELISA plate and scanned the phage Fab fragment antibody library by phage display technology. After five cycles of "absorbing-elution-amplification", we got the Fab fragment phage antibody of PSMA with high antigen binding ability and specificity, and tested it with immunodetection and sequencing.

RESULTSThe sequence of Fd fragment was 696 base pairs encoding 232 amino-acid residues, with 98% homological similarity to the human immunoglobulin gamma chain, while the light chain was constructed by 630 base pairs encoding 210 amino-acid residues, with 93% homological similarity to kappa chain.

CONCLUSIONUsing phage display technology, we obtained the gene sequence of Fab antibody fragment specific to PSMA, and the antibody gene has the classic structural features of immunoglobulin light chain and heavy chain. The coding output of the antibody gene has the specificity and immunological competence to PSMA.

Cloning, Molecular ; Enzyme-Linked Immunosorbent Assay ; Genetic Code ; Humans ; Immunoglobulin Fab Fragments ; genetics ; Immunoglobulin Variable Region ; genetics ; Male ; Peptide Library ; Prostate-Specific Antigen ; immunology

Catalytic Domain ; genetics ; Dual Specificity Phosphatase 3 ; chemistry ; genetics ; metabolism ; Genetic Code ; Humans ; Mutation ; Phosphorylation ; Protein Conformation ; Signal Transduction ; genetics ; Structure-Activity Relationship ; Tyrosine ; analogs & derivatives ; chemistry ; genetics

The gene encoding urease subunit A (ureA) of Helicobacter pylori (H. pylori) was cloned from H. pylori isolate by polymerase chain reaction (PCR). Sterile distilled water instead of DNA served as negative control. The nucleotide sequence of the amplified product was determined. Homologous analysis of the ureA against that reported by Clayton CL and the GenBank and SwissProt databases were performed with the BLAST program at the Genome Net through the Internet. 0.8 kb PCR product was amplified from all H. pylori clinical isolators. The nucleotide sequence of the ureA was determined. The nucleotide sequence of the ureA began with ATG as the initiation codon and terminated in TAA as stop codon. The coding regions had a 44% G + C content. The DNA sequence was 98% homologous to that reported by Clayton CL (688 out of 702 residues were identical). The derived amino-acid sequences of the ureA were 99% homologous to that reported by Clayton CL (232 out of 234 residues were identical). The nucleotide sequence and the predicted protein showed significant homology to ureA of H. pylori in the NCBI Entrez database.
Base Sequence ; Cloning, Molecular ; DNA, Bacterial ; chemistry ; genetics ; Genes, Bacterial ; Genetic Code ; Helicobacter Infections ; microbiology ; Helicobacter pylori ; enzymology ; genetics ; isolation & purification ; Humans ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Transcription, Genetic ; Urease ; genetics ; metabolism

It is believed that in the RNA world the operational (ribozymes) and the informational (riboscripts) RNA molecules were created with only three (adenosine, uridine, and guanosine) and two (adenosine and uridine) nucleosides, respectively, so that the genetic code started uncomplicated. Ribozymes subsequently evolved to be able to cut and paste themselves and riboscripts were acceptive to rigorous editing (adenosine to inosine); the intensive diversification of RNA molecules shaped novel cellular machineries that are capable of polymerizing amino acids-a new type of cellular building materials for life. Initially, the genetic code, encoding seven amino acids, was created only to distinguish purine and pyrimidine; it was later expanded in a stepwise way to encode 12, 15, and 20 amino acids through the relief of guanine from its roles as operational signals and through the recruitment of cytosine. Therefore, the maturation of the genetic code also coincided with (1) the departure of aminoacyl-tRNA synthetases (AARSs) from the primordial translation machinery, (2) the replacement of informational RNA by DNA, and (3) the co-evolution of AARSs and their cognate tRNAs. This model predicts gradual replacements of RNA-made molecular mechanisms, cellular processes by proteins, and informational exploitation by DNA.
Amino Acid Sequence ; Amino Acyl-tRNA Synthetases ; genetics ; metabolism ; Base Composition ; DNA ; chemistry ; genetics ; metabolism ; Eosinophil Cationic Protein ; chemistry ; genetics ; Evolution, Molecular ; Genetic Code ; Models, Genetic ; Molecular Sequence Data ; RNA ; chemistry ; genetics ; metabolism ; Sequence Homology, Amino Acid