TISs-ST: a web server to evaluate polymorphic translation initiation sites and their reflections on the secretory targets

The predicted subcellular localisation of the sugarcane proteome

Plant cells are highly organised, and many biological processes are associated with specialised subcellular structures. Subcellular localisation is a key feature of proteins, since it is related to biological function. The subcellular localisation of such proteins can be predicted, providing information that is particularly relevant to those proteins with unknown or putative function. We performed the first in silico genome-wide subcellular localisation analysis for the sugarcane transcriptome (with 11 882 predicted proteins) and found that most of the proteins were localised in four compartments: nucleus (44%), cytosol (19%), mitochondria (12%) and secretory destinations (11%). We also showed that ~19% of the proteins were localised in multiple compartments. Other results allowed identification of a potential set of sugarcane proteins that could show dual targeting by the use of N-truncated forms that started from the nearest downstream in-frame AUG codons. This study was a first step in increasing knowledge about the subcellular localisation of the sugarcane proteome.

The rus operon genes are differentially regulated when Acidithiobacillus ferrooxidans LR is kept in contact with metal sulfides

Acidithiobacillus ferrooxidans is a gram-negative bacterium that obtains energy from the oxidation of ferrous iron or reduced sulfur compounds. In this bacterium, the proteins encoded by the rus operon are involved in electron transfer from Fe(II) to O(2), and the first two proteins in this pathway also participate in the electron transfer pathway from Fe(II) to NAD(P). In this work we analyzed the expression, by real-time PCR, of the eight genes from the rus operon when A. ferrooxidans LR was grown in the presence of iron (control) and then kept in contact with chalcopyrite (CuFeS(2)) and covellite (CuS). A small decrease in rus operon gene expression was observed in the presence of chalcopyrite, while in the presence of covellite the expression of these genes showed a remarkable decrease. These results can be explained by the absence of ferrous iron in covellite. To explain the expression difference observed between the gene cyc1 and the gene rus, we investigated the information content presented at the Translation Initiation Site (TIS) of both genes. cyc1 showed a highly information content (8.4 bits) that can maximize translation, and rus showed a less favorable context (5.5 bits). Our hypothesis is that the energetic metabolism in A. ferrooxidans may be controlled at the transcriptional and posttranscriptional level by different mechanisms.