Reynoutria japonica Houtt., belonging to Polygoneae of Polygonaceae, is a Chinese medicinal herb with the functions of draining dampness and relieving jaundice, clearing heat and detoxifying, dispersing blood stasis and relieving pain, and relieving cough and resolving phlegm. In this study, we carried out high-throughput sequencing for the chloroplast genome sequences of five cultivars of R. japonica and analyzed the genome structure and variations. The chloroplast genomes of the five R. japonica cultivars had two sizes (163 376 bp and 163 371 bp) and a typical circular tetrad structure composed of a large single-copy (LSC) region of 85 784 bp, a small single-copy (SSC) region of 18 616 bp, and a pair of inverted repeat (IR) regions (IRa/IRb) which are spaced apart. A total of 161 genes were obtained by annotation, which consisted of 106 protein-coding genes, 10 rRNA-coding genes, and 45 tRNA-coding genes. The total GC content was 36.7%. Specifically, the GC content in the LSC, SSC, and IR regions were 34.8%, 30.7%, and 42.7%, respectively. Comparison of the whole chloroplast genome among the five cultivars showed that trnk-UUU, rpoC1, petD, rpl16, ndhA, and rpl12 in coding regions had sequence variations. In the phylogenetic tree constructed for the 11 samples of Polygoneae, the five cultivars of R. japonica clustered into one clade near the root and was a sister group of Fallopia multiflora (Thunb.).
Base Composition ; Genome, Chloroplast/genetics* ; Open Reading Frames ; Phylogeny ; Reynoutria

Norovirus ; chemistry ; genetics ; physiology ; ultrastructure ; Open Reading Frames ; Virus Replication

With the development of modern sequencing techniques and bioinformatics, genomes that were once thought to be noncoding have been found to encode abundant functional micropeptides (miPs), a kind of small polypeptides. Although miPs are difficult to analyze and identify, a number of studies have begun to focus on them. More and more miPs have been revealed as essential for energy metabolism homeostasis, immune regulation, and tumor growth and development. Many reports have shown that miPs are especially essential for regulating glucose and lipid metabolism and regulating mitochondrial function. MiPs are also involved in the progression of related diseases. This paper reviews the sources and identification of miPs, as well as the functional significance of miPs for metabolism-related diseases, with the aim of revealing their potential clinical applications.
Humans ; Open Reading Frames ; Peptides ; Glucose ; Genome ; Metabolic Diseases

Turnip yellow mosaic virus (TYMV) is a spherical plant virus that has a single 6.3 kb positive strand RNA genome. Information for TYMV replication is limited, except that the 3'-terminal sequence and 5'-untranslated region are required for genome replication. When a foreign sequence was inserted at the position upstream of the coat protein (CP) open reading frame (ORF), replication of the recombinant TYMV was comparable to wild type, as long as an RNAi suppressor was provided. In contrast, when the foreign sequence was inserted between the CP ORF and the 3'-terminal tRNA-like structure, replication of the recombinant virus was not detected. This result suggests that the CP ORF contains an essential replication element which should be appropriately spaced with respect to the 3'-end. Analysis of TYMV constructs containing a part or a full additional CP ORF indicates that the 3' quarter of the CP ORF is required for TYMV replication.
Animals ; Brassica napus ; Ecthyma, Contagious ; Genome ; Open Reading Frames ; Plant Viruses ; RNA ; Tymovirus ; Viruses

HExDB is a database for analyzing exon and splicing pattern information in Homo sapiens. HExDB is useful for specific purposes: 1) to design primers for exon amplification from cDNA and 2) to understand the change of ORFs by alternative splicing. HExDB was constructed by integrating data from AltExtron which is the computationally predicted exon database, Ensemble cDNA annotation, and Affymetrix genome tile published recently. Although it may contain false positive data, HExDB is good starting point due to its sensitivity. At present, there are as many as 2,046,519 exons stored in the HExDB. We found that 16.8% of the exons in the database was constitutive exons and 83.1% were novel gene exons.
Alternative Splicing* ; Animals ; DNA, Complementary ; Ecthyma, Contagious ; Exons* ; Genome ; Humans* ; Open Reading Frames

Human papillomavirus (HPV) 16, E7 proteins derived from the prototype (Bac73) and natural variant (Bac101) E7 open reading frame were produced in Sf9 insect cells. The variant E7 gene occurred naturally by substitution mutation at the position of 88 nucleotide, resulting serine instead of asparagine. Using E7 specific monoclonal antibody (VD6), both E7 proteins were identified in recombinant baculovirus infected SF9 cells. Radiolabelling and immunoprecipitation analysis revealed that both E7 proteins were phosphoproteins. Immunostaining result showed that E7 proteins were mainly localized in the cytoplasm. Nuclear form of E7 proteins was also detected after a sequential fractionation procedure for removing chromatin structure. Considering that the VD6 recognition site in E7 protein is located within 10 amino acid at the N-terminus, this region appears to be blocked by the nuclear component. Western blot analysis revealed that nuclear form was more abundant than cytoplasmic E7 proteins. Time course immunostaining showed that the primary location of E7 protein was the nucleus and exported to the cytoplasm as proteins were accumulated. These events occurred similarly in both Bac73 and Bac101 infected Sf9 cells, suggesting that these two proteins may have similar biological functions.
Asparagine ; Baculoviridae* ; Blotting, Western ; Chromatin ; Cytoplasm ; Humans* ; Immunoprecipitation ; Insects ; Open Reading Frames ; Phosphoproteins ; Serine ; Sf9 Cells

Enterotoxigenic B. pagilis (ETBF) strains which produce a 20 kDa zinc metalloprotease toxin (BFI) have been associated with diarrheal disease of animals and young children. Using B. pngilis toxin gene (bfi) from strain 86-5443-2-2 (piglet isolate) as a probe, the gene was identified in 74/77 human and animal ETBF strains but only 2/97 non-toxigenic B. fragilis (NTBF) strains. The region flanking bp was mapped with several restriction enzymes and 8 resriction fragments aacent to bft were used to probe colony blots of 77 KTBF and 97 NTBF strains. All 74 bft-positive ETBF strains hybridized to the 8 probes spanning a ca. 18 kb chromosomal region; however, this 18 kb region was absent in the 3 ETBF strains lacking p, and 47 of the 97 (48%) NTBF strains lacked the entire 18 kb region. Of note, the 2 NTBF strains containing btf did not have a ca. 12 kb region upstream of btfp. A ca. 9 kb fragment flanking the btf gene has been sequenced. Analysis of this data revealed several open reading frames (ORF) of which 3 are of particular interest (ORFs 1, 2 and 3). ORF1 and ORF3 encode proteins with significant homology to mobilization proteins, and ORF2 encodes a protein with significant homology to metalloprotease proteins, but only 50% similarity and 30% identity to BFf. These results suggest: 1) the btf genes are flanked by at least 18 kb of DNA largely unique to ETBF strains indicating a putative pathogenic island, 2) another metalloprotease protein present in ETBF strains may contribute to the pathogenicity and variable virulence of these diarrheagenic strains and 3) the pathogenic island may be mobiTized among different Bacteroides strains, and possibly among different species of intestinal bacteria.
Animals ; Bacteria ; Bacteroides fragilis* ; Bacteroides* ; Child ; DNA ; Genomic Islands* ; Humans ; Open Reading Frames ; Virulence* ; Zinc

African swine fever virus (ASFV) infection leads to a mortality rate of up to 100%, causing devastating disasters to the pig industry. Understanding the ASFV infection and replication is therefore of great importance. ASFV has more than 150 open reading frames, among which the inner coat protein p17 encoded by the D117L gene is involved in the formation of the icosahedral structure of the virus. However, little is known about the mechanism how p17 regulates host cell function. In this study, the potential host proteins interacting with ASFV p17 were screened by immunoprecipitation technique combined with protein profiling analysis. The interactions of p17 with mitochondrial membrane protein TOMM70 and heat shock protein HSPA8 were confirmed by co-immunoprecipitation technique and laser confocal experiments. This study provides important information for further exploring the function of p17 during ASFV infection.
African Swine Fever ; African Swine Fever Virus/metabolism* ; Animals ; Open Reading Frames ; Swine ; Viral Proteins/metabolism*

Long non-coding RNA (lncRNA) refers to non-coding RNA longer than 200 nt, with one or more short open reading frames (sORF), which encode functional micro-peptides. These functional micro-peptides often play key roles in various biological processes, such as Ca²⁺ transport, mitochondrial metabolism, myocyte fusion, cellular senescence and others. At the same time, these biological processes play a key role in the regulation of body homeostasis, diseases and cancers development and progression, embryonic development and other important physiological processes. Therefore, studying the potential regulatory mechanisms of micro-peptides encoded by lncRNA in organisms will help to further elucidate the potential regulatory processes in organisms. Furthermore, it will provide a new theoretical basis for the subsequent targeted treatment of diseases and improvement of animal growth performance. This review summarizes the latest research progress in the field of lncRNA-encoded micro-peptides, as well as the progress in the fields of muscle physiological regulation, inflammation and immunity, common human cancers, and embryonic development. Finally, the challenges of lncRNA-encoded micro-peptides are briefly described, with the aim to facilitate subsequent in-depth research on micro-peptides.
Animals ; Humans ; Neoplasms/therapy* ; Open Reading Frames ; Peptides/chemistry* ; RNA, Long Noncoding/genetics*

Small proteins (SPs) are defined as peptides of 100 amino acids or less encoded by short open reading frames (sORFs). SPs participate in a wide range of functions in cells, including gene regulating, cell signaling and metabolism. However, most annotated SPs in all living organisms are currently lacking expression evidence at the protein level and regarded as missing proteins (MPs). High efficient SPs identification is the prerequisite for their functional study and contribution to MPs searching. In this study, we identified 72 SPs and successfully validated 9 MPs from Saccharomyces cerevisiae based on SPs enrichment strategy. In-depth analysis showed that the missing factors of MPs were low molecular weight, low abundant, hydrophobicity, lower codon usage bias and unstable. The small protein-based enrichment can be used as MPs searching strategy, which might provide the foundation for their further function research.
Codon ; Open Reading Frames ; Peptides ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae Proteins ; analysis