Connecting genomic islands across prokaryotic and phage genomes via protein families

Abstract

Prokaryotic genomes evolve via horizontal gene transfer (HGT), mutations, and rearrangements. A noteworthy part of the HGT process is facilitated by genomic islands (GIs). While previous computational biology research has focused on developing tools to detect GIs in prokaryotic genomes, there has been little research investigating GI patterns and biological connections across species. We have pursued the novel idea of connecting GIs across prokaryotic and phage genomes via patterns of protein families. Such patterns are sequences of protein families frequently present in the genomes of multiple species. We combined the large data set from the IslandViewer4 database with protein families from Pfam while implementing a comprehensive strategy to identify patterns making use of HMMER, BLAST, and MUSCLE. we also implemented Python programs that link the analysis into a single pipeline. Research results demonstrated that related GIs often exist in species that are evolutionarily unrelated and in multiple bacterial phyla. Analysis of the discovered patterns led to the identification of biological connections among prokaryotes and phages. These connections suggest broad HGT connections across the bacterial kingdom and its associated phages. The discovered patterns and connections could provide the basis for additional analysis on HGT breadth and the patterns in pathogenic GIs.

Investigating the nature of prokaryotic genomic island locations within a genome

“…As mentioned in our previous work [ 17 ], the top species in the data set which make up the largest proportion of the data set are Escherichia coli , Salmonella enterica , Klebsiella pneumoniae , Bordetella pertussis , and Pseudomonas aeruginosa . A histogram was built for each of the top species in the data set that reflect the true location of the GIs in relation to the oriC.…”

“…The prokaryotic data set used in this research is the same as the data set used in our prokaryotic patterns detection paper [ 17 ], which is from the IslandViewer4 website and is composed of genomes along with the GIs and their proteins. See that paper for details of obtaining the data.…”

Non-Canonical Aspects of Antibiotics and Antibiotic Resistance

“…With the millions of copies per milliliter of extracellular DNA encoding carbapenemases being dumped into wastewater [ 213 ]; the fact that fragmented (≥20 bp) and damaged DNA can be acquired by transformation [ 214 ]; that transformation can occur in unexpected places, such as the phylloplane of edible vegetables [ 215 ]; and AR genes being routinely found in phages (even towards the “last resort” antibiotic colistin [ 216 ])—from the fecal “phageome” of healthy humans [ 217 ], food samples [ 218 ] (up to the point that the liver of farm chickens can be considered as a reservoir of AR genes [ 219 ]). Furthermore, genomic islands shared by distantly related bacteria were likely mobilized between them by phages [ 220 ]. While transformation is often conceived as the almost passive uptake of free DNA, transformation competence is induced by different forms of stress, most likely to achieve genetic diversification and survive such stress [ 221 ].…”