Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior

Contains fulltext : 95738.pdf (publisher's version ) (Open Access)BACKGROUND: Sigma-54 is a central regulator in many pathogenic bacteria and has been linked to a multitude of cellular processes like nitrogen assimilation and important functional traits such as motility, virulence, and biofilm formation. Until now it has remained obscure whether these phenomena and the control by Sigma-54 share an underlying theme. RESULTS: We have uncovered the commonality by performing a range of comparative genome analyses. A) The presence of Sigma-54 and its associated activators was determined for all sequenced prokaryotes. We observed a phylum-dependent distribution that is suggestive of an evolutionary relationship between Sigma-54 and lipopolysaccharide and flagellar biosynthesis. B) All Sigma-54 activators were identified and annotated. The relation with phosphotransfer-mediated signaling (TCS and PTS) and the transport and assimilation of carboxylates and nitrogen containing metabolites was substantiated. C) The function annotations, that were represented within the genomic context of all genes encoding Sigma-54, its activators and its promoters, were analyzed for intra-phylum representation and inter-phylum conservation. Promoters were localized using a straightforward scoring strategy that was formulated to identify similar motifs. We found clear highly-represented and conserved genetic associations with genes that concern the transport and biosynthesis of the metabolic intermediates of exopolysaccharides, flagella, lipids, lipopolysaccharides, lipoproteins and peptidoglycan. CONCLUSION: Our analyses directly implicate Sigma-54 as a central player in the control over the processes that involve the physical interaction of an organism with its environment like in the colonization of a host (virulence) or the formation of biofilm

Selected Works in Bioinformatics

This book consists of nine chapters covering a variety of bioinformatics subjects, ranging from database resources for protein allergens, unravelling genetic determinants of complex disorders, characterization and prediction of regulatory motifs, computational methods for identifying the best classifiers and key disease genes in large-scale transcriptomic and proteomic experiments, functional characterization of inherently unfolded proteins/regions, protein interaction networks and flexible protein-protein docking. The computational algorithms are in general presented in a way that is accessible to advanced undergraduate students, graduate students and researchers in molecular biology and genetics. The book should also serve as stepping stones for mathematicians, biostatisticians, and computational scientists to cross their academic boundaries into the dynamic and ever-expanding field of bioinformatics

Heterologous expression, characterization and applications of metagenome- and genome-sourced enzymes.

Microorganisms encompass the largest resource of metabolic and genetic diversity encountered on Earth. This unparalleled biodiversity risks remaining inaccessible since the major part of the microbiota is unculturable by traditional methods. Metagenomics (i.e. the culture-independent analysis of the genetic complement of an entire habitat) represents a promising and innovative tool for the exploitation of the biotechnological potential encrypted in microbial communities. The present PhD dissertation has been developed in the frame of the FP7 European project MetaExplore, whose aim was the identification through metagenomics of novel biocatalysts involved in the biodegradation of recalcitrant natural molecules, such as chitinases, enzymes with many industrial and environmental applications. The first part of the dissertation focuses on the heterologous production in Escherichia coli and biochemical, functional and structural characterisation of two metagenome-sourced chitinases, Chi18H8 and 53D1. The enzymes are endowed with innovative and valuable features, making them interesting candidates for the biocontrol of plant pathogenic fungi and for the sustainable and environment-friendly treatment and valorisation of seafood wastes, respectively. The second section describes the employment of the Gram-positive bacteria Streptomyces spp. as alternative expression platforms for the production of two proteins, VanYn and Chi18H8. Finally, in the third section the possibility to employ chitinolytic enzymes as alternatives to traditional chemical-based insect pesticides is investigated

Heterologous expression, characterization and applications of metagenome- and genome-sourced enzymes.

Microorganisms encompass the largest resource of metabolic and genetic diversity encountered on Earth. This unparalleled biodiversity risks remaining inaccessible since the major part of the microbiota is unculturable by traditional methods. Metagenomics (i.e. the culture-independent analysis of the genetic complement of an entire habitat) represents a promising and innovative tool for the exploitation of the biotechnological potential encrypted in microbial communities. The present PhD dissertation has been developed in the frame of the FP7 European project MetaExplore, whose aim was the identification through metagenomics of novel biocatalysts involved in the biodegradation of recalcitrant natural molecules, such as chitinases, enzymes with many industrial and environmental applications. The first part of the dissertation focuses on the heterologous production in Escherichia coli and biochemical, functional and structural characterisation of two metagenome-sourced chitinases, Chi18H8 and 53D1. The enzymes are endowed with innovative and valuable features, making them interesting candidates for the biocontrol of plant pathogenic fungi and for the sustainable and environment-friendly treatment and valorisation of seafood wastes, respectively. The second section describes the employment of the Gram-positive bacteria Streptomyces spp. as alternative expression platforms for the production of two proteins, VanYn and Chi18H8. Finally, in the third section the possibility to employ chitinolytic enzymes as alternatives to traditional chemical-based insect pesticides is investigated

Heterologous expression, characterization and applications of metagenome- and genome-sourced enzymes.

Microorganisms encompass the largest resource of metabolic and genetic diversity encountered on Earth. This unparalleled biodiversity risks remaining inaccessible since the major part of the microbiota is unculturable by traditional methods. Metagenomics (i.e. the culture-independent analysis of the genetic complement of an entire habitat) represents a promising and innovative tool for the exploitation of the biotechnological potential encrypted in microbial communities. The present PhD dissertation has been developed in the frame of the FP7 European project MetaExplore, whose aim was the identification through metagenomics of novel biocatalysts involved in the biodegradation of recalcitrant natural molecules, such as chitinases, enzymes with many industrial and environmental applications. The first part of the dissertation focuses on the heterologous production in Escherichia coli and biochemical, functional and structural characterisation of two metagenome-sourced chitinases, Chi18H8 and 53D1. The enzymes are endowed with innovative and valuable features, making them interesting candidates for the biocontrol of plant pathogenic fungi and for the sustainable and environment-friendly treatment and valorisation of seafood wastes, respectively. The second section describes the employment of the Gram-positive bacteria Streptomyces spp. as alternative expression platforms for the production of two proteins, VanYn and Chi18H8. Finally, in the third section the possibility to employ chitinolytic enzymes as alternatives to traditional chemical-based insect pesticides is investigated

Heterologous expression, characterization and applications of metagenome- and genome-sourced enzymes.

Microorganisms encompass the largest resource of metabolic and genetic diversity encountered on Earth. This unparalleled biodiversity risks remaining inaccessible since the major part of the microbiota is unculturable by traditional methods. Metagenomics (i.e. the culture-independent analysis of the genetic complement of an entire habitat) represents a promising and innovative tool for the exploitation of the biotechnological potential encrypted in microbial communities. The present PhD dissertation has been developed in the frame of the FP7 European project MetaExplore, whose aim was the identification through metagenomics of novel biocatalysts involved in the biodegradation of recalcitrant natural molecules, such as chitinases, enzymes with many industrial and environmental applications. The first part of the dissertation focuses on the heterologous production in Escherichia coli and biochemical, functional and structural characterisation of two metagenome-sourced chitinases, Chi18H8 and 53D1. The enzymes are endowed with innovative and valuable features, making them interesting candidates for the biocontrol of plant pathogenic fungi and for the sustainable and environment-friendly treatment and valorisation of seafood wastes, respectively. The second section describes the employment of the Gram-positive bacteria Streptomyces spp. as alternative expression platforms for the production of two proteins, VanYn and Chi18H8. Finally, in the third section the possibility to employ chitinolytic enzymes as alternatives to traditional chemical-based insect pesticides is investigated