Diversity and Evolutionary Dynamics of Antiphage Defense Systems in Ralstonia solanacearum Species Complex

Abstract

Over the years, many researchers have reported a great diversity of bacteriophages infecting members of the Ralstonia solanacearum species complex (RSSC). This diversity has driven bacterial evolution by leading the emergence and maintenance of bacterial defense systems to combat phage infection. In this work, we present an in silico study of the arsenal of defense systems that RSSC harbors and their evolutionary history. For this purpose, we used a combination of genomic, phylogenetic and associative methods. We found that in addition to the CRISPR-Cas system already reported, there are eight other antiphage defense systems including the well-known Restriction-Modification and Toxin-Antitoxin systems. Furthermore, we found a tenth defense system, which is dedicated to reducing the incidence of plasmid transformation in bacteria. We undertook an analysis of the gene gain and loss patterns of the defense systems in 15 genomes of RSSC. Results indicate that the dynamics are inclined toward the gain of defense genes as opposed to the rest of the genes that were preferably lost throughout evolution. This was confirmed by evidence on independent gene acquisition that has occurred by profuse horizontal transfer. The mutation and recombination rates were calculated as a proxy of evolutionary rates. Again, genes encoding the defense systems follow different rates of evolution respect to the rest of the genes. These results lead us to conclude that the evolution of RSSC defense systems is highly dynamic and responds to a different evolutionary regime than the rest of the genes in the genomes of RSSC.

Phenotypic and Genomic Comparison of Klebsiella pneumoniae Lytic Phages: vB_KpnM-VAC66 and vB_KpnM-VAC13

“…We also observed the presence of methyltransferases in both genomes (ORF145 in vB_KpnM-VAC13 and ORF123 in vB_KpnM-VAC66), that are able to methylate the phage DNA to evade attacks of the bacterial restriction enzymes, involved in the restriction/methylation defense system [29]. These proteins play a role in the phage defense against their hosts, together with other mechanisms [30].…”

Global diversity and distribution of prophages are lineage-specific within the Ralstonia solanacearum plant pathogenic bacterium species complex

“…These may have been geographical barriers as the phylotypes are thought to have arisen from geographical isolation (98) although prophages were found to have widespread, often overlapping, geographical distributions. Alternatively, inter-phylotype prophage transmission may be limited by biological transmission barriers, such as phage defence systems, which are abundant in R. solanacearum (7). Furthermore, it is possible that prophages could encode specific auxiliary genes that lead to phylotype-specific ecological differences, which reduce the likelihood of strains coexistence and horizontal movement of prophages.…”

“…Lytic phages can impose strong bottom-up density regulation of bacteria across different ecosystems, driving nutrient turnover by infecting their host bacteria (5,6). They can also drive bacterial diversification through frequency-dependent selection (5), whilst selecting for phage resistance evolution via the acquisition of phage defence systems (7) and cell membrane alterations that disrupt phage infection (8). As phage resistance mechanisms are often associated with fitness trade-offs (9,10), these evolutionary changes can further alter phage-bacteria population dynamics leading to eco-evolutionary feedbacks in microbial communities (for review see (11)).…”

Global diversity and distribution of prophages are lineage-specific within the Ralstonia solanacearum species complex

“…Lytic phages can impose strong bottom-up density regulation of bacteria across different ecosystems, driving nutrient turnover by infecting their host bacteria [ 5 , 6 ]. They can also drive bacterial diversification through frequency-dependent selection [ 5 ], whilst selecting for phage resistance evolution via the acquisition of phage defence systems [ 7 ] and cell membrane alterations that disrupt phage infection [ 8 ]. In contrast, temperate prophages tend to have a more modest effect on bacterial population dynamics as they often replicate during bacterial cell division and become lytic only when induced by environmental stresses such as UV irradiation or antibiotic treatment [ 9 , 10 ].…”