Identification of protein-coding sequences using the hybridization of 18S rRNA and mRNA during translation.

We introduce a new approach in this article to distinguish protein-coding sequences from non-coding sequences utilizing a period-3, free energy signal that arises from the interactions of the 3'-terminal nucleotides of the 18S rRNA with mRNA. We extracted the special features of the amplitude and the phase of the period-3 signal in protein-coding regions, which is not found in non-coding regions, and used them to distinguish protein-coding sequences from non-coding sequences. We tested on all the experimental genes from Saccharomyces cerevisiae and Schizosaccharomyces pombe. The identification was consistent with the corresponding information from GenBank, and produced better performance compared to existing methods that use a period-3 signal. The primary tests on some fly, mouse and human genes suggests that our method is applicable to higher eukaryotic genes. The tests on pseudogenes indicated that most pseudogenes have no period-3 signal. Some exploration of the 3'-tail of 18S rRNA and pattern analysis of protein-coding sequences supported further our assumption that the 3'-tail of 18S rRNA has a role of synchronization throughout translation elongation process. This, in turn, can be utilized for the identification of protein-coding sequences.

Analysis of free energy signals arising from nucleotide hybridization between rRNA and mRNA sequences during translation in eubacteria.

A decoding algorithm is tested that mechanistically models the progressive alignments that arise as the mRNA moves past the rRNA tail during translation elongation. Each of these alignments provides an opportunity for hybridization between the single-stranded, 3'-terminal nucleotides of the 16S rRNA and the spatially accessible window of mRNA sequence, from which a free energy value can be calculated. Using this algorithm we show that a periodic, energetic pattern of frequency 1/3 is revealed. This periodic signal exists in the majority of coding regions of eubacterial genes, but not in the non-coding regions encoding the 16S and 23S rRNAs. Signal analysis reveals that the population of coding regions of each bacterial species has a mean phase that is correlated in a statistically significant way with species (G + C) content. These results suggest that the periodic signal could function as a synchronization signal for the maintenance of reading frame and that codon usage provides a mechanism for manipulation of signal phase.

The duckweeds: a valuable plant for biomanufacturing.

Inherent characteristics of duckweed, including fast, clonal growth, small size and simple growth habit, argue for their use as a biomanufacturing platform for proteins, polymers and small molecules. This review addresses five areas relevant to commercialization of the duckweed platform: (1) the characteristics of wild-type duckweed and general cultural requirements; (2) the genetics and biochemistry of the plants and recent scientific developments that provide the technology necessary to genetically modify duckweed; (3) the advantages provided by inherent duckweed characteristics and genetic engineering technology relative to bioproduction; (4) recent progress towards commercialization of duckweed-based products and (5) the major research needs for further R&D.