Hepatitis A Virus
Dongyou Liu in Handbook of Foodborne Diseases, 2018
The viral capsid is composed of 60 units each of three proteins, namely, VP1, VP2, and VP3 (known also as 1D, 1B, and 1C, respectively), and encloses a linear, single-stranded, positive-sense RNA genome of approximately 7500 nucleotides in length. The viral RNA includes a 5′-untranslated region (UTR), a single open reading frame, and a 3′-UTR with a short polyadenosine tail. The 5′-UTR contains an internal ribosomal entry site, which is important for initiation of cap-independent translation of the viral RNA. The open reading frame codes for a large polypeptide, which undergoes cotranslational and posttranslational cleavage into several structural (VP1, VP2, and VP3) and nonstructural (2B, 2C, 3A, 3B, 3Cpro, and 3Dpol) proteins, and proteins with unclear functions (VP4 and 2A).5 This cleavage is mediated by a viral cysteine protease (3Cpro) and another unidentified protease of host origin.
Regulation of Gastrointestinal Neuropeptide Gene Expression and Processing
Edwin E. Daniel in Neuropeptide Function in the Gastrointestinal Tract, 2019
The 5′-untranslated regions in the mRNA vary considerably in length, from 3 to 572 nucleotides, with 70% of them being in the range of 20 to 80 nucleotides. The translational start site is usually the most 5′-proximal AUG triplet in the mRNA (encoding the amino acid methionine [Met]), but in a minority of cases a more distal triplet is the functional one, suggesting that the nucleotides surrounding the AUG triplet also seem to play a role when choosing the correct start site.73,74 Based on this assumption, a consensus sequence has been derived which covers almost all cases of different start sites, e.g., 5′-CC[A/G]CCAUGG-3′.74,75 However, there are still a few cases where the first AUG has the correct surrounding, but still a second AUG triplet distal from the first has been shown to be the functional site. This has tentatively been explained by a “reinitiation” process occurring after an early stop, at a stop proximal to the functional second start site assuming that the ribosomal subunit “scans” the mRNA and remains on the mRNA after the first early stop.73–75
The N-Myc Oncogene in Pediatric Tumors: Diagnostic, Prognostic and Biological Aspects
John T. Kemshead in Pediatric Tumors: Immunological and Molecular Markers, 2020
As mentioned above, N-myc was originally discovered during low stringency hybridization studies by virtue of its partial sequence homology with the nuclear proto-oncogene c-myc.23 Subsequent sequencing of the entire N-myc gene34 has defined the extent of this homology and revealed striking similarities with c-myc in its overall topography. Both genes contain three exons of similar length with coding elements being located in the second and third exons only and both genes have unusually long 5’ untranslated regions in their mRNAs. These long noncoding mRNA regions contain imperfect, inverted repeat (dyad symmetries) which by forming stable stem and loop structures,5 are thought to be involved in translational control of gene expression.35 Although the exact mechanism is uncertain, the proposed stem and loop structures are assumed to interfere with the interaction between the myc mRNA and its ribosomes.
Site specific hypermethylation of CpGs in Connexin genes 30, 26 and 43 in different grades of glioma and attenuated levels of their mRNAs
Published in International Journal of Neuroscience, 2019
Jayalakshmi J., Arambakkam Janardhanam Vanisree, Shantha Ravisankar, Rama K.
MethPrimer and Primer Blast were used to design primers for BSP and MeDIP-qPCR (Table 1). Promoter region (Figure 1) and transcription factor binding sites were predicted with PROMO and TESS software (Figure 2). As there is no CpG island in Cx43 promoter region, CpGs in intron were chosen for this study. The first exon that contains the 5′-untranslated region (5′-UTR) with the transcription start site and a second exon that contains a small amount of the 5′-UTR, complete coding region and the 3′-UTR were analysed. These two exons are separated by intron [14–17]. There are four CpG islands in the intron region. The sequence (GenBank Accession No. NG_008308 with respect to the major transcription start site +1) from +3461 to +3623 in the intron was used to design the primer by Methprimer software.
Phase variation of Clostridium difficile virulence factors
Published in Gut Microbes, 2018
Brandon R. Anjuwon-Foster, Rita Tamayo
C. difficile surface proteins mediate adherence to other microbial species, mucus, and intestinal cells within the colon for colonization.5 The peritrichous flagella produced by C. difficile aid in motility and modulate colonization in an animal model of infection.6 In addition, TcdA and TcdB production is linked to flagellum biosynthesis.7-10 SigD (σD), an alternative sigma factor encoded within the early stage flagellar gene operon (flgB operon), is essential for transcription of late stage flagellar genes, and also positively regulates transcription of the toxin genes (Fig. 1).11,12 Therefore, factors that regulate expression of the flgB operon not only control bacterial motility, they are also likely to impact toxin production and therefore virulence of C. difficile. The 5′ untranslated region (UTR) of the flgB operon mRNA contains a riboswitch (Cd1) specific to the nucleotide second messenger cyclic diguanylate (c-di-GMP).13,14 C-di-GMP binding to Cd1 causes premature transcription termination within the first 160 nucleotides of the 5′ UTR of the flgB operon mRNA, inhibiting flagellar gene expression, motility, and toxin production. Because the flgB 5′ UTR is 498 nucleotides, we postulated that an additional cis-acting regulatory element downstream of Cd1 could control flagellar and toxin gene expression.
The roles and mechanisms of G3BP1 in tumour promotion
Published in Journal of Drug Targeting, 2019
Cong-Hui Zhang, Jun-Xia Wang, Mei-Lian Cai, Rongguang Shao, Hong Liu, Wu-Li Zhao
mRNA stability associated with proliferation plays an essential role in tumour development. Many factors affect mRNA stability, such as the 5′ cap, 3′ poly (A) tail, 5′ untranslated region, and 3′ untranslated region [26–28]. G3BP1 binds specific RNA via its C-terminal RRM and cleaves between cytosine and adenine residues to regulate mRNA stability, thereby controlling multiple signalling pathways [29]. Studies have shown that G3BP1 has two different effects on mRNA stability: stabilisation, as for TAU mRNA [30], and degradation as for BART [31], CTNNB1 [32], ATP5B [33], peripheral myelin protein 22 (PMP22) [29], IGF-II and GAS5 [34]. For example, PMP22 is a growth arrest-specific gene and repressing PMP22 expression promotes breast cancer cell proliferation [35]. Winslow et al. found that G3BP1 suppresses PMP22 mRNA expression, thereby boosting breast cancer cell proliferation [29]. In addition, overexpressed G3BP1 can recruit microRNAs into stress granules and suppress the translation of microRNA targeting proteins via microRNA interference [36]. On the other hand, G3BP1 expression is regulated by microRNAs. Deng et al. reported that miR-193a-3p inhibits G3BP1 expression and the progression of non-small cell lung cancer in vitro and in vivo [37]. Thus, the regulation of proliferation-associated mRNA stability may be one of the mechanisms by which G3BP1 promotes proliferation.
Related Knowledge Centers
- Coding Region
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- Start Codon
- Virus
- Messenger Rna
- Upstream & Downstream
- Translation
- Nucleic Acid Secondary Structure