In Pieces: The Segmented Genome

by Janie
 

"Segmented genome" is a term I had only heard ap­plied to vi­rus­es un­til re­cent­ly. It re­fers to genomes that con­sist of two or more mo­le­cules, a cha­rac­ter­is­tic that grants an evo­lu­tion­ary ad­van­tage: when mul­tiple vi­rus­es in­fect the same un­for­tu­nate cell, these dif­ferent frag­ments can be mixed and mat­ched to ge­ner­ate new, re­as­sort­ed genomes.
 

Only recently did I hear this term used when describing bacteria – specifically, Borrelia. Members of this genus of spirochetes, which include the causative agents of Lyme disease and relapsing fever, possess genomes on the order of 1.5 Mb that consist of a linear chromosome and a whole host of linear and circular plasmids. The twenty or so plasmids account for a large fraction of the bacteria's coding capacity. In the case of B. burgdorferi B31, that's about 60%. They're often volatile things, at least in Borrelia grown in the lab, where a number are frequently thrown out as the bacteria go all Marie Kondo on their interior design during continuous cultivation.
 

Why Borrelia has such a piecemeal genome is an open question. Does such genome segmentation within Borrelia, like in viruses, facilitate segment reassortment and thereby allow for more genetic variation?
 

Figure 1. The Borrelia burgdorferi genome with its linear chromosome and suite of linear and circular plasmids. The colors indicate similarity to the genome of Borrelia garinii. Regions with matches are red, while regions with no matches are blue. Yellow indicates nearly identical plasmids. Source

Another curious example of segmentation linked to gene-level diversity in Borrelia is the vlsE locus. This stretch of DNA undergoes recombination that leads to antigenic variation when the bacteria infect a mammalian host, the segments shuffled so that the encoded surface protein ends up as a surprise each time. There's a clear advantage to this example of segmentation: it's hard for an immune system to lock sights on a shapeshifting target.
 

Shapeshifting is a theme in Borrelia that extends beyond this single locus, as some of the spirochete's plasmids on occasion switch from linear to circular. But why have a combination of circular and linear plasmids in the first place? Perhaps there is the potential for differential transcription. Unlike linear DNA, circular DNA is not degraded by exonucleases, and since most RNA polymerases have high processivity (these enzymes will often loop around the same plasmid multiple times, producing a long, repeating transcript) circularization in theory could allow for upregulation of transcription. Perhaps the shape of a plasmid could be linked to transcriptional regulation.
 

But then there is the example of the artificially linearized E. coli chromosome, covered on STC years ago and again more recently when Christoph wrote about Borrelia's telomeres and the bidirectional replication of linear chromosomes and plasmids. There was almost no difference in cell viability, morphology, growth rate, and gene expression. And of course, there is the case of Eukarya, where "segmented genomes" – multiple chromosomes – are the norm.
 

Figure 2. The design of the tripartite E. coli genome. In the bottom zoom-in view, the ribosome RNA operons (rrnABCDEHG), oriC and dif, the ter sequences, and the eight genes at the borders are indicated. Source

We could try a different permutation game. Having considered the physical arrangement of a genome into segments, what about switching up the number of segments? For starters, what would happen if we were to chop up the genome of E. coli? The sites at which the genome is chopped and which genes end up on which pieces will be critical. This came into play a couple years ago when Yoneji et al. (2021) split the E. coli genome into three pieces. Their design principle was to keep genome macrodomains intact, so one piece was comprised of the Ori macrodomain, another comprised of the Ter macrodomain, and the final piece carried the rest of the genome (sure enough, all three "pieces" had their own replication origin and par functions). Lo and behold, this tinkering did in fact yield living bacteria, but these survivors grew much more slowly, unsurprisingly as they have no mechanism in place to coordinate the replication of the three pieces. Some also had a filamentous morphology.
 

In the flipside scenario, what would happen if you took a genome as highly segmented as that of Borrelia and joined those pieces together onto one big chromosome?
 

Other bacteria with multipartite genomes have set a precedent. Granted, these species don't have genomes segmented to the level of Borrelia’s, but they are still fascinating examples of how dynamic bacterial genomes can be. Take the case of Vibrio. Up until 2020, all known naturally occurring strains possessed two circular chromosomes, the bigger one around 3 Mb and the smaller one between 0.8 to 2.4 Mb, depending on the species. Like most rules in biology, this one was broken. First, in 2012, came the artificial engineering of a Franken-strain of Vibrio cholerae in which those two chromosomes were fused into one. The only noted difference between the mutant and the wild type was an average doubling time of 29 versus 23 minutes (it's unclear if other aspects of its physiology and virulence were affected). Next came the discovery of Vibrio cholerae strains that naturally have a single chromosome, a fusion of chr1 and chr2. There is also the case of the legume symbiont Sinorhizobium meliloti, which has a 3.65 Mb circular chromosome and two giant circular plasmids that are 1.35 Mb and 1.68 Mb. It turned out that these genetic segments could reversibly and spontaneously merge into one when grown in the lab. The single-chromosome'd strain grew slightly slower, but there was no observed difference in its normal symbiotic association with plants.
 

Figure 3. B. burgdorferi cells in the midgut of a nymphal tick 10 days after feeding. DNA is stained with Hoechst 33342 and oriC is labeled with mCherry (Frontispiece: lower right panel). Source

To make things even more convoluted, Borrelia is already playing with the number of copies of parts of its genome. Recently Takacs et al. (2022) showed live-cell images of B. burgdorferi cells that harbor multiple copies of their linear chromosome during exponential growth both in lab-grown cultures (over thirty copies, in some strains!) and within tick nymphs fed on infected mice. In cultures, that number settled back down to about one as the cells entered stationary phase. The number of plasmids also fluctuated similarly.
 

Thinking of the dynamics of bacterial genomes, whether across the scale of evolutionary history or within the span of a single experiment in the lab, an image that comes to mind is the lava lamp. All the push and pull, the splitting and merging – is there anything that matches the plasticity and diversity of genomes? The only constant in life is change, goes the famous quote…
 

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