Functional Genomics of Microbial Pathogens for Crop Improvement

Abstract

Sequencing bacterial genomes over the past two decades has opened a new era in the analysis of pathogenic bacteria. Analyses of genomic sequences provided important insights into evolution of pathogenicity and antibiotic resistance. Genomic comparison between pathogenic bacteria and their less harmful relatives showed that virulence factors may be acquired by horizontal transfer of pathogenicity islands. Therefore, in addition to the presence of virulence and antivirulence genes, several features of the bacterial genome such as the GþC content, the genome size, and the proportion of genes encoding specific functions could help identify pathogens and assess their intrinsic virulence. Genomic information provides a background for additional high-throughput functional studies such as in silico metabolic modelling and wet-lab experimentation at the RNA and protein levels. Transcriptome studies of microbial pathogens using microarrays and RNA sequencing are particularly focused on changes in gene expression. Genome-wide targeted gene inactivation has been used to construct mutants and identify those with an altered phenotype. Targeted inactivation has been difficult to do in bacteria showing barriers to transformation. Although the role of bacteriophages in the evolution, virulence, and antibiotic resistance of bacteria has been recognized, only a few functional genomics studies of these viruses have been performed so far. Such studies are important for use of bacteriophages and their proteins in bacterial identification and infection control. It has been shown that several human diseases and disorders correlate with changes in microbiota profiles, suggesting that bacterial communities may play a causative role of disease. In conclusion, the expanding field of functional genomics provides powerful tools and insights for assessing the contribution of pathogens and microbial communities to disease as well as the characteristics of the host response and will contribute to development of new prevention and therapeutic strategies.