Researchers have developed a database to make it easier to identify target proteins that can help fight infectious diseases.
Scientists from the Department of Biochemistry and Molecular Biology of the Universitat Autònoma de Barcelona and Centre of Genomic Regulation said it will also accelerate development of new antimicrobial agents.
The BacFITBase database contains 90,000 entries with information on pathogenic bacterial genes and their contribution to in vivo infectious conditions in five different host species. Studies that are in vivo look at effects on whole, living organisms or cells. Many mechanisms underlying bacterial pathogenesis are still poorly understood, according to the study published in the Nucleic Acids Research journal.
It includes information on 15 bacteria including two variants of Salmonella enterica, three types of E. coli, Vibrio cholerae, Campylobacter jejuni, Klebsiella pneumoniae, Acinetobacter baumannii, and Vibrio parahaemolyticus with information across 10 different tissues.
Researchers hope to continue growing the database in the next few years as a repository of bacterial proteins which could be important targets in the fight against infectious diseases.
Genes needed during host infection
Infectious diseases are caused by pathogenic microorganisms that enter, colonize and grow within a host organism and produce an infection. Proteins coded by the bacterial genes are responsible for biochemical processes that help the pathogen.
Other studies have shown that to identify these genes, in vivo information is needed on what happens with the bacteria in an infected host. The in vitro studies, which are those recreated in laboratories with cell and bacterial cultures, do not always match data from in vivo studies. This is because pathogenic bacterial genes essential for producing infections depend on the environment of the colonized organism. Infectious diseases can only be properly understood in the context of host–pathogen interactions as pathogenic bacteria do not grow alone but in a complex host environment.
Based on results of in vivo experiments, researchers characterized the bacterial genes relevant for host cell invasion and infection. All experiments were based on a technique known as transposon mutagenesis, where the DNA fragments called transposons are transferred to the organism’s pathogenic genes, so inactivate them. This means their role in infection can be observed directly and researchers can determine which are needed for a specific host organism to become infected.
It includes Salmonella Typhimurium ST4/74 from a cow, pig and chicken in three different tissue types and Salmonella Typhimurium SL1344 from a mouse. E. coli O157:H7 from the feces of a cow, E. coli M12 and E. coli CFT073 from mice and Campylobacter jejuni 81–176 from a mouse.
BacFITBase has a text search to find specific pathogenic bacterial genes, a BLAST search function to find bacterial genes similar to a protein or nucleic acid sequence of interest, a browse ability to identify genes of high fitness impact during infection, and a tutorial section. Both pathogen and/or host species can be specified in the drop-down menus on the search page.
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