Subcellular localization of sugarcane (Sccharum spp.) proteins : in silico characterization and functional evaluation / Localização subcelular de proteinas de cana-de-açucar (Sccharum spp.) : caracterização in silico e avaliação funcional

AUTOR(ES)
DATA DE PUBLICAÇÃO

2008

RESUMO

Plant cells are highly organized and many biological processes are associated with specialized subcellular structures. Subcellular localization is a key feature of proteins, since it is related to biological function. The determination of subcellular localization using computational prediction is a highly desirable strategy because experimental approaches are time-consuming. In order to develop a method for the enhanced prediction of subcellular localization, the outputs of some prediction tools were integrated so as to optimally exploit the potential of each one. The prediction performance (with 90%of accuracy) of this new method was clearly superior to all the methods used to create the predictor. Using this method, the first in silico genome-wide subcellular localization analysis was performed for sugarcane (with 11,882 predicted proteins). It was found that most of the proteins are localized to four compartments: nucleus (44%), cytosol (19%), mitochondria (12%), and secretory destination (11%). It is also shown that about 19%of the proteins are localized to multiple compartments, and that a potential set of sugarcane proteins can show dual targeting by use of N-truncated form of proteins. The subcellular localization of 96 sugarcane proteins fused with GFP were evaluated using transient expression in onion epidermal cells. Constructs containing the Nand C-terminal fusion of genes encoding both endogen and GFP proteins were transiently expressed, and the localization of the fusion proteins were detected by fluorescent microscopy. It was reported the characterization of ScBAK1, a sugarcane leucine-rich repeat receptor-like kinase, with sequence similarity to brassinosteroid insensitive1-associated receptor kinase1. We have found that ScBAK1 transcripts accumulated at higher levels in bundle-sheath than in mesophyll cells. ScBAK1-GFP fusions were localized to the plasma membrane. This spatial distribution and expression pattern indicates that ScBAK1 might be potentially involved in cellular signaling cascades mediated by high levels of sugar in this organ. The nucleotide sequence flanking the translation initiation codon affects the translational efficiency of eukaryotic mRNAs, and may indicate the presence of an alternative translation initiation site (TIS) to produce proteins with different properties. Multi-targeting may reflect the translational variability of these other protein forms. In this study it was also developed a computational method to investigate the usage of alternative TISs for the synthesis of new protein variants that might have different subcellular localization. To contribute to our understanding of the genome complexity of sugarcane, we undertook a genome wide TIS analysis in sugarcane data. It is demonstrated that up-regulated transcripts show a stronger TIS when compared with the down-regulated, and that ubiquitous transcripts have a high frequency of alternative TIS in the next downstream AUG codon. The same occurs for fast-evolving genes, and leaf and internodes specific transcripts, that may encode different polypeptides by N-terminal polymorphism

ASSUNTO(S)

sugarcane cana-de-açucar proteinas - tradução proteins subcellular localization localização subcelular

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