Computational analysis of the interaction between transcription factors and the predicted secreted proteome of the yeast Kluyveromyces lactis.

BACKGROUND: Protein secretion is a cell translocation process of major biological and technological significance. The secretion and downstream processing of proteins by recombinant cells is of great commercial interest. The yeast Kluyveromyces lactis is considered a promising host for heterologous protein production. Because yeasts naturally do not secrete as many proteins as filamentous fungi, they can produce secreted recombinant proteins with few contaminants in the medium. An ideal system to address the secretion of a desired protein could be exploited among the native proteins in certain physiological conditions. By applying algorithms to the completed K. lactis genome sequence, such a system could be selected. To this end, we predicted protein subcellular locations and correlated the resulting extracellular secretome with the transcription factors that modulate the cellular response to a particular environmental stimulus. RESULTS: To explore the potential Kluyveromyces lactis extracellular secretome, four computational prediction algorithms were applied to 5076 predicted K. lactis proteins from the genome database. SignalP v3 identified 418 proteins with N-terminal signal peptides. From these 418 proteins, the Phobius algorithm predicted that 176 proteins have no transmembrane domains, and the big-PI Predictor identified 150 proteins as having no glycosylphosphatidylinositol (GPI) modification sites. WoLF PSORT predicted that the K. lactis secretome consists of 109 putative proteins, excluding subcellular targeting. The transcription regulators of the putative extracellular proteins were investigated by searching for DNA binding sites in their putative promoters. The conditions to favor expression were obtained by searching Gene Ontology terms and using graph theory. CONCLUSION: A public database of K. lactis secreted proteins and their transcription factors are presented. It consists of 109 ORFs and 23 transcription factors. A graph created from this database shows 134 nodes and 884 edges, suggesting a vast number of relationships to be validated experimentally. Most of the transcription factors are related to responses to stress such as drug, acid and heat resistance, as well as nitrogen limitation, and may be useful for inducing maximal expression of potential extracellular proteins.

Development of a Brazilian maize core collection.

The aim of this study was to evaluate methods for developing a Brazilian maize core collection. For an initial survey of the active collection, passport information, as well as characterization and evaluation of accessions, were taken into consideration, these then being divided according to geographic region and kernel-type. Multiple sampling methods were evaluated. The strategy of constant sampling generated extensive alterations in extract accession frequency. The multivariate strategy with dispersion graphs and principal components associated with the Tocher method was considered efficient for identifying the most divergent genotypes. The multivariate strategy generated greater alterations in the variance of traits. The average number of traits revealed few modifications with the various sampling strategies used. Therefore, the active collection could be considered as possessing a satisfactory amount of information for most of its accessions. Moreover, the multivariate strategy generated modifications in the variance of the traits, independent of sampling intensity.

Development of a Brazilian maize core collection

The aim of this study was to evaluate methods for developing a Brazilian maize core collection. For an initial survey of the active collection, passport information, as well as characterization and evaluation of accessions, were taken into consideration, these then being divided according to geographic region and kernel-type. Multiple sampling methods were evaluated. The strategy of constant sampling generated extensive alterations in extract accession frequency. The multivariate strategy with dispersion graphs and principal components associated with the Tocher method was considered efficient for identifying the most divergent genotypes. The multivariate strategy generated greater alterations in the variance of traits. The average number of traits revealed few modifications with the various sampling strategies used. Therefore, the active collection could be considered as possessing a satisfactory amount of information for most of its accessions. Moreover, the multivariate strategy generated modifications in the variance of the traits, independent of sampling intensity.

Identification and in silico analysis of the Citrus HSP70 molecular chaperone gene family

The completion of the genome sequencing of the Arabidopsis thaliana model system provided a powerful molecular tool for comparative analysis of gene families present in the genome of economically relevant plant species. In this investigation, we used the sequences of the Arabidopsis Hsp70 gene family to identify and annotate the Citrus Hsp70 genes represented in the CitEST database. Based on sequence comparison analysis, we identified 18 clusters that were further divided into 5 subgroups encoding four mitochondrial mtHsp70s, three plastid csHsp70s, one ER luminal Hsp70 BiP, two HSP110/SSE-related proteins and eight cytosolic Hsp/Hsc70s. We also analyzed the expression profile by digital Northern of each Hsp70 transcript in different organs and in response to stress conditions. The EST database revealed a distinct population distribution of Hsp70 ESTs among isoforms and across the organs surveyed. The Hsp70-5 isoform was highly expressed in seeds, whereas BiP, mitochondrial and plastid HSp70 mRNAs displayed a similar expression profile in the organs analyzed, and were predominantly represented in flowers. Distinct Hsp70 mRNAs were also differentially expressed during Xylella infection and Citrus tristeza viral infection as well as during water deficit. This in silico study sets the groundwork for future investigations to fully characterize functionally the Citrus Hsp70 family and underscores the relevance of Hsp70s in response to abiotic and biotic stresses in Citrus.