The three genomic RNAs of alfalfa mosaic virus each contain a unique 5' untranslated region (5' UTR). Replacement of the 5' UTR of RNA 1 by that of RNA 2 or 3 yielded infectious replicons. The sequence of a putative 5' stem-loop structure in RNA 1 was found to be required for negative-strand RNA synthesis. A similar putative 5' stem-loop structure is present in RNA 2 but not in RNA 3.

Infection by human rhinovirus (HRV) is a major cause of upper and lower respiratory tract disease worldwide and displays considerable phenotypic variation. We examined diversity by completing the genome sequences for all known serotypes (n = 99). Superimposition of capsid crystal structure and optimal-energy RNA configurations established alignments and phylogeny. These revealed conserved motif...

Shine-Dalgarno (SD) sequence has been considered as one of the common features of 5' end untranslated region (5'UTR) of prokaryotic transcripts. However, more leaderless bacteria and archaea mRNAs are being increasingly reported in recent years. To understand the distribution of SD-led genes and non-SD-led genes, we have analyzed 162 completed prokaryotic genomes leading to various new conclusi...

The incidence of melanoma continues to rise globally and is increasing at a rate greater than any other cancer. To systematically search for new genes involved in melanomagenesis, we collated exome sequencing data from independent melanoma cohort datasets, including those in the public domain. We identified recurrent mutations that may drive melanoma growth, survival or metastasis, and which ma...

Natural regulatory RNAs like riboswitches and RNA thermometers (RNAT) have considerable potential in synthetic biology. They are located in the 5' untranslated region (UTR) of bacterial mRNAs and sense small molecules or changes in temperature, respectively. While riboswitches act on the level of transcription, translation or mRNA stability, all currently known RNATs regulate translation initia...

Methane-producing Archaea are of interest due to their contribution to atmospheric change and for their roles in technological applications including waste treatment and biofuel production. Although restricted to anaerobic environments, methanogens are found in a wide variety of habitats, where they commonly live in syntrophic relationships with bacterial partners. Owing to tight thermodynamic ...

Trypanosomatid type I nitroreductases (NTRs), i.e., mitochondrial enzymes that metabolise nitroaromatic pro-drugs, are essential for parasite growth, infection, and survival. Here, a type I NTR of non-virulent protozoan Trypanosoma rangeli is described and compared to those of other trypanosomatids. The NTR gene was isolated from KP1(+) and KP1(-) strains, and its corresponding transcript and 5...

Chronic alcohol intake is associated with a wide variety of adverse health outcomes including depression, diabetes, and heart disease. Unfortunately, the molecular mechanisms through which these effects are conveyed are not clearly understood. To examine the potential role of epigenetic factors in this process, we examined the relationship of recent alcohol intake to genome wide methylation pat...

We previously reported that the AUG-burdened 5' untranslated region (UTR) of IL-15 mRNA impedes its translation. Here we demonstrate that the nucleotide or protein sequences of the IL-15 signal peptide and carboxyl terminus also contribute to the poor translation of IL-15 transcripts. In particular, the exchange of the IL-15 signal peptide coding sequence with that of IL-2 increased cellular an...

MOTIVATION It is well known that eukaryotic mRNAs are translated at different levels depending on their sequence characteristics. Evaluation of mRNA translatability is of importance in prediction of the gene expression pattern by computer methods and to improve the recognition of mRNAs within cloned nucleotide sequences. It may also be used in biotechnological experiments to optimize the expres...