Exploring the evolutionary dynamics of plasmids: the Acinetobacter pan-plasmidome
Marco Fondi, Giovanni Bacci, Matteo Brilli, Cristiana M Papaleo, Alessio Mengoni, Mario Vaneechoutte, Lenie Dijkshoorn, Renato Fani
Bacteria belonging to the genus Acinetobacter are found in diverse ecosystems such as, soil, water and even animals. Some like A. baumannii are well-known opportunistic human pathogens while others can be useful in bioremediation because of their ability to degrade toxic hydrocarbons. Many of these bacteria have been found to have plasmids of different sizes that probably encode genes that help Acinetobacter sp. survive in the different ecosystems. The goal of this study was two-fold: i) reconstruct the evolutionary dynamics of plasmids of Acinetobacter sp. and ii) investigate the evolutionary cross-talk between plasmid and chromosome. A total of 29 plasmids and seven Acinetobacter genomes from NCBI were included in this study. A computation tool called Blast2Network was used for visualzing plasmid and chromosome relationships. For goal one, the authors retrieved 493 protein sequences form all 29 plasmids and used them as input for the Blast2Network program. This resulted in a network where each plasmid is represented by a ring of balls, each ball being a single protein. In addition there are lines connecting homologous proteins. Changing the degree of identity between proteins generates different networks, such that at 50% sequence identity more proteins are linked together than at 100% sequence identity. Overall the pattern remains the same with three distinct clusters. The first represents a group of plasmids called the pKLH-group that were isolated from different species/strains of Acinetobacter. The second cluster includes plasmids form A. baumannii strains and cluster three has plasmids form other Acinetobacter species. This shows that the pKLH plasmids are the most closely related since they have interlinks among all members even at 100% protein sequence identity, while interlinks decrease for the other two clusters. Thus, although the pKLH plasmids were isolated from different hosts, they have a high relatedness. This is an interesting result, since many of these plasmids are tra- and mob- making conjugation an impossible mechanism of gene transfer between bacteria. Another interesting observation is that plasmids from the same strain often have no connections at 100% identity meaning that no recent genetic exchange probably took place between them. This is surprising because transposition and recombination are common means of gene exchange between plasmids residing in the same host. On the other hand, some proteins, were found to have 100% identity between homologs on plasmids from clusters two and three, meaning that some gene exchange did take place between plasmids from different hosts. Thus, overall these networks are an easy way to visualize complex data. Next they analyzed the functional classes of proteins with the most interlinks. Not surprisingly they found transposition related proteins and mercury resistance related proteins to have high connectivity. It is also interesting that out of 493 proteins, 280 did not have any connections, suggesting that plasmids from Acinetobacter encode a high number of unknown functions. For the second goal, the authors included the genomes of seven completely sequenced Acinetobacter sp. and generated a network of plasmid and chromosome encoded proteins, similar to the network generated previously. The networks show the existence of interconnections between all chromosomes and most of the plasmids. The only exception to this is, four plasmids belonging to cluster three which have no connections to any of the chromosomes. The pKLH group on the other hand was found to be strongly interconnected to two A. baumannii strains. These connections were mostly with mercury resistance related proteins and transposases. Interestingly enough, some plasmids belonging to the same strain such as p1ABAYE, p2ABAYE and p4ABAYE were not found to have any connections to proteins of their host chromosome. This means that gene exchange did not take place between plasmid and chromosome in this case. There are many plasmid-encoded proteins that do not have sufficient identity to chromosome-encoded proteins, suggesting that these may have been acquired from other species/strains of Acinetobacter or other genera. Thus, this study provides an interesting visualization of plasmids of Acinetobacter and their relationships to each other and to some Acinetobacter genomes. I think the most surprising and interesting fact I learned is that tra- and mob- plasmids are promiscuous too and their evolutionary history is often independent of their hosts. There were a couple of areas that were unclear to me, such as, their identity thresholds, which seem to be absolute values instead of a range of values. Also, they do not say why they did not use all twenty-nine Acinetobacter genome sequences and restricted their study to only seven genomes. An interesting feature from figure 4, that they seemed to have overlooked is the fact that single plasmid-bearing proteins have numerous, multiple hits on the same chromosome (A. baumannii SDF) at the 90% threshold. To summarise, their illustrations are really pretty and show the different types of plasmid-chromosome relationships. With the availability of more sequences, such figures may get more difficult to create.
University of Idaho