An event-driven approach for studying gene block evolution in bacteria

Abstract

Motivation: Gene blocks are genes co-located on the chromosome. In many cases, gene blocks are conserved between bacterial species, sometimes as operons, when genes are co-transcribed. The conservation is rarely absolute: gene loss, gain, duplication, block splitting and block fusion are frequently observed. An open question in bacterial molecular evolution is that of the formation and breakup of gene blocks, for which several models have been proposed. These models, however, are not generally applicable to all types of gene blocks, and consequently cannot be used to broadly compare and study gene block evolution. To address this problem, we introduce an event-based method for tracking gene block evolution in bacteria.Results: We show here that the evolution of gene blocks in proteobacteria can be described by a small set of events. Those include the insertion of genes into, or the splitting of genes out of a gene block, gene loss, and gene duplication. We show how the event-based method of gene block evolution allows us to determine the evolutionary rateand may be used to trace the ancestral states of their formation. We conclude that the event-based method can be used to help us understand the formation of these important bacterial genomic structures.Availability and implementation: The software is available under GPLv3 license on http://github.com/reamdc1/gene_block_evolution.git. Supplementary online material: http://iddo-friedberg.net/operon-evolutionContact: i.friedberg@miamioh.eduSupplementary information: Supplementary data are available at Bioinformatics online.

Unraveling a tangled skein: Evolutionary analysis of the bacterial gibberellin biosynthetic operon

“…This suggests that selective pressures specific to the rhizobia, presumably their symbiotic relationship with legumes, may have driven this heterogeneity in the operon. To better understand the evolutionary history of the GA operon in the α-rhizobia, a more thorough analysis was carried out with Reconstruction of Ancestral Genomes Using Events (ROAGUE) software [25, 33]. ROAGUE generates a phylogenetic tree with selected taxa that contain gene blocks (i.e.…”

“…The terms reference taxa, neighboring genes, gene blocks, events, and orthologous gene blocks or orthoblocks have been described previously [25]. Briefly, the reference taxon is a strain in which the operon in question has been experimentally validated.…”

“…Using an algorithm developed to analyze the assembly and evolution of gene blocks (i.e. genes within operons/clusters) [25], the distribution and phylogeny of the GA operon was further analyzed within the α- rhizobia, which display a large amount of diversity in operon structure and genetic content. Altogether, this thorough assessment of the underlying genetics and biochemistry of the GA operon allows for the formulation of informed hypotheses regarding the biological function of GA production within diverse bacterial lineages.…”

A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries

“…Due to the lack of a systematic framework, very few studies have attempted to examine the role of evolutionary events on operon structure(6,7). Phylogenetic-tree based classification of 197 ATP binding motif sequences associated with operon-encoded bacterial ATP-binding cassette (ABC) transporters was successful in resolving two evolutionarily distinct transporter clades associated with import and export functions(8).…”

“…Gene duplications have been shown to play an important role in driving protein superfamily expansion among bacterial genomes and its frequency is significantly correlated with genome size(9). The study of co-localized “gene blocks” across bacteria has also shown that gene duplication, loss, and rearrangement play important roles in shaping the large-scale organization of bacterial genomes(7). Key to these analyses is the use of a rigorous and systematic approach for assigning genes into evolutionarily related ‘families’ that are likely to share similar functions.…”