Vibrio fischeri, a symbiotic bacterium with pathogenic congeners

There are a number of species found within the Vibrionacea family of marine proteobacteria; some of which live symbiotically and others which have pathogenic interactions with animal tissue.

Using strain ES114 (the model-light organ symbiont of the squid Euprymna scolopes) of the proteobacteria V. fischeri the aim was to begin identifying features that were common to both the beneficial and the pathogenic bacteria in order to understand the symbiotic activities by which the bacteria adjust to the environment of host tissues.

Within this family, pathogenic species such as Vibrio cholera, Vibrio parahaemolyticus and Vibrio vulnificus have had their genome sequenced, but a symbiotic species of the Vibrio genus had never been sequenced.

The genomic DNA of V. fischeri was mechanically sheared and 2-3kb (kilo-base pair) fragments were isolated. Ends of the fragments were filled using Klenow fragment and ligated into SmaI-digested pGEM3 to produce a high-copy-number, small-insert library. Greater molecular mass genomic DNA was partially digested with Sau3A to construct a cosmid library. Undigested, unsheared DNA was used in PCR as a template for amplification of chromosomal regions which were not represented in the plasmid or cosmid libraries.

Whole genome shotgun sequencing was performed on around 35,000 plasmids and 400 cosmids, as well as gap-spanning PCR products.

They found that automated contig-assembly algorithms were ineffective in determining the number and orientations of the highly homologous rRNA operons; therefore those regions where assembled manually from sequenced PCR products. Potential open reading frames (ORF’s) were identified.

The finished genome underwent initial automated annotation followed by a manual gene-by-gene curation. (Results of their analysis are found at www.ergo-light.com)

The genome sequencing revealed many points that both show differences between and also links the pathogenic species to the beneficial symbiotic species of Vibrionacea.

Firstly, a plasmid known as pES100 was found within ES114; homologous plasmids are common among other strains of V. fischeri, but it is not required for host association and similar plasmids are found in pathogenic species.

Secondly, in V. fischeri G+C content is lowest of all 27 species. Despite this low content V. fischeri is more closely related to the higher G+C containing pathogenic Vibrio than to any other sequenced bacterium.

Thirdly, chromosomal density of apparent ORFs is almost 10% greater in V. cholera compared to V. fischeri.

Fourthly, a 4 fold greater percentage of unique genes are present on Chr II of this species when compared to others on a completed database. Thus, the smaller chromosomes characteristic of this genus may turn out to be a rich source of genes that define the unique potential of individual Vibrio species, and perhaps their specific lifestyles.

Fifthly, V. fischeri contains mobile genetic elements which share sequence similarity with V. cholera.

Sixthly, there is a presence of multiple pilus gene clusters in V. fischeri which suggest that different pili may be expressed to aid this bacterium either in the diverse environments it inhabits or during the multiple stages of its development as a symbiont.

Finally, Vibrio genes encode a putative toxin called RTX (which seems to affect regulators of host cell actin polymerisation). RTX has not yet been investigated, but it is known to have both beneficial and pathogenic effects on host cells.

This study begins to shed light on the unifying themes underlying contrasting bacteria-host interactions, using comparative genomic approaches of two closely related beneficial and pathogenic species from the Vibrionacea family; studies similar to this must continue to use genomic techniques to help us reveal the mechanisms by which pathogens associate with marine invertebrates as benign or even beneficial symbionts.

A review of:

Ruby, E. G., Urbanowski, M., Campbell, J., Dunn, A., Faini, M. et al. (2004). Complete genome sequence of Vibrio fischeri: A symbiotic bacterium with pathogenic congeners. Proceedings of the National Academy of Sciences. Vol. 102 (8). pp. 3004-3009