"You need all sorts" - Lessons from the deer tick genome

A wise person in Fargo, ND, once told me, “You need all sorts”. The adage seems to be true in parasitology. You need all sorts of studies to understand parasitosis. Epidemiological studies that assess risk factors, microepidemiological studies that describe new haplotypes, drug studies of anti-parasitological agents, studies on parasite behavior and biology, novel techniques to diagnose and control parasites, new applications of old techniques – all of these are needed, and more. Among the latter are extensive studies that map out entire genomes of parasites. As always, the early scientist gets the worm, or in this case, the acarine.
  

The genome of Ixodes scapularis, the deer tick, one of the most feared ticks in North America, has been sequenced and insights were revealed to the general public in a recent paper published in Nature Communications, entitled ‘Genomic insights into the Ixodes scapularis tick vector of Lyme disease’ by an impressive knot of ~93 authors, the who’s who of tick biologists on the planet. 

 
(Source of image: Sandy Rae, Wikimedia Commons. This file is licensed under the Creative Commons Attribution-Share Alike 3.0 Unported License)

The key features of interest from the publication have been summarized below.
  

Large haploid genomes seem to be the norm, and by “large”, the authors mean >1Gbp. That is 1, followed by 9 zeros. Previous studies by Ullmann et al in 2005, estimated the genome size to be around 2.1 x 10^3 Mbp, with 34% of the DNA being unique. The other part had been found to be made up of highly repetitive (27%) and moderately repetitive elements (39%). A summary of the assembly statictics in the Nature Communications paper estimates that the I.scapularis genome has 20,486 genes, with a mean length of 10,589 bp, and an average coding sequence length of 855 bp. 60% of the genome has orthologous genes in other species, with 22% of the genes being paralogs.

The authors used FISH based karyotyping to identify 26 acrocentric autosomes and 2 sex chromosomes. Their experiments also revealed a high percentage of tandem repeats in the centromeres and pericentromeric areas, which is in line with the previously described repetitive areas. To look at some beautiful karyograms, head over to the original paper.

Class I and II transposable elements were also found. Annotators found 41 long terminal repeat reterotransposon family elements, 37 Ty3/gypsy group, 234 miniature inverted-repeat transposable elements, Mag, CsRn1, Squirrel, Toxo, mariner and piggybac.

So, why should you and I care? What great insights does the genome reveal? What lessons can a fellow parasitologist learn?
  

Lesson 1: Once bitten, twice shy

When ticks feed, they inject saliva into the feeding area. And tick saliva is more complex than that of mosquitoes. The authors believe that 0.4% of the predicted proteome of I.scapularis, that is, about 74 proteins, contain a Kunitz domain. Kunitz domain-containing proteins essentially are protease inhibitors, and so play roles in inhibiting coagulation. Since even mosquitoes have less than 10 of these protease inhibitor proteins, it is easy to believe how effective the tick saliva is in inhibiting coagulation, angiogenesis and vasodilation.  The authors also found about 40 lipocalin genes in the saliva, that have anti-inflammatory properties, and 34 metalloprotease genes, all ensuring that the blood, like wine, keeps flowing at the tick banquet.

Lesson 2: Blood is thicker than water, till it is lysed

It is well known that ticks ingest blood. What is not so well known is that RBCs hemolysed in the tick midgut are pinocytosed into gut epithelial cells, where enzymes like cathepsin D, cathepsin L and serine carboxypeptidase aid in the digestion of haemoglobin, releasing heme, which is curiously spelt as “haem” in the article, which is transported to “haemosomes” to be detoxified and stored as hematin aggregates. The authors were able to identify the genes that code for the enzymes that orchestrate the above.

Lesson 3 : “I can’t make it on my own, I need you”, says Ixodes scapularis

The authors identified genes that coded for two families of haem storage proteins, since ticks are unable to synthesize haem de novo. These two families – haemlipoglyco-carrier proteins and vitellogenins protect the tick from the dangers of a haem rich diet, and help store haem for the embryo. Essentially, the iron that the tick embryo  needs for haem synthesis is supplied by the host indirectly.

Lesson 4 : I’m not crazy, my reality is just different than yours

Neuropeptides act via their corresponding GPCRs. From the genome of I.scapularis, the authors identified 39 neuropeptide genes, which play important roles in molting, synthesis and hardening of the cuticle, diuresis, development and reproduction, and to a large extent behavior and life styles. So, why in the world is this important, you ask ? Well, the 100 fold size increase in size of the tick body after feeding, must be accommodated, and these molecules – buriscon alpha and beta, corazonin and eclosion , are vital. The G protein coupled receptors that these neuropeptides associate with are also numerous. The authors were able to identify GPCRs like kinins, inotocin, tachykinin, allostatin-A etc. Given the different essential conditions needed to thrive in a tick world, it makes sense that the crazy numbers and amounts of neuropeptides synthesized by the ticks, contributes to a complexity that is not seen in many higher taxa.

Lesson 5 : Growing pains

To start vitellogenesis, ticks use molecules called ecdysteroids. These have names like “disembodied”, “Halloween” and “spook”/”spookier”. Genes for enzymes of the mevalonate-farnesal and other pathways involved in the production and reactions of juvenile hormone III were also found to be present.

Lesson 6: You purpose to kill me. How dare you sport thus with life?

The authors found a record number of detoxification genes of the CYP450 fame (206 genes) and a whole lot of carboxylesterase/cholinesterase-like genes (~75 genes). They postulate that ticks may need to detoxify toxic factors in the blood of hosts that they feed on and also substances that they encounter off the host. But those numbers seem incredible when compared to the body louse, which has 36 genes with detoxification functions, but also feeds on blood.

Lesson 7: Grandma, what a large hypostome you have! All the better to taste you with, my dear!

The rule is, ticks have to first find their hosts before they can feed on their (host) blood. They set out on their quest equipped with an impressive array of sensory organs. In the genome, 62 gustatory receptor genes, and 29 ionotrophic Glutamate receptors were found. Cuticular lipids, and non-volatile mounting pheromones in the females and males are suspected to be produced, that aid not just in questing for hosts, but also another member of the species.

Lesson 8: The eye is the lamp of the body

As far as eyes go, ticks don’t have large complex eyes like humans, but only have “photon- sensitive receptors”. Opsin G protein coupled receptors were identified in the genome, and are thought to be involved in long-wavelength light perception. The authors could not identify UV and short wavelength receptors, postulating that since ticks do not rely on vison to locate hosts, mates and oviposition sites, the sensations accorded by the highly developed thermal, mechanical, and olfactory receptors were enough.

Lesson 9: Of parasites, vectors and defense against the dark ones

As vectors extraordinaire, ticks are capable of carrying pathogens. But, it would be highly beneficial for them to not be afflicted by these same pathogens that they so willingly ferry from one host to the next susceptible one. The genome encodes for the appropriate orthologs of Toll, Jak-STAT, AMPs, caspases, akirins, ixoderins, lysozyme and RNAi genes (especially Ago genes, but upto 121 unique genes that may be involved in anti-viral defense), among others, all of which protect the tick from the pathogens of vertebrates.

The ticks also apparently take good care of the pathogens that they transmit, by synthesizing proteins and receptors that aid in their survival and transmission, such as Salp15, Salp20, receptor for Borrelia lipoprotein BBE31, P11, among others. Pathogens take full advantage of the hospitality offered by helping the tick, or by being a disruptive visitor. Anaplasma helps the tick survive better in cold climates, by upregulating putative “anti-freeze” genes. But being dual faced, it also inhibits apoptosis in the tick gut, establishing infections in them, and using other mechanisms, such as protein misfolding to evade cellular responses.

When a pathogen is a bad guest, tick responses include, but are not limited to, extrinsic apoptosis pathway induction in the salivary glands, decreasing glucose metabolism, changing the way protein is processed, producing HSPs, and increasing subolesin.

Lesson 10: Never compare, unless you absolutely have to

The authors used quantitative proteomics to identify differences between tick-Anaplasma interactions in actual infections, and in an artificial infection in a tick cell line. They found that at least 83 proteins were different, with differential gene expression being evident over the course of the infection. (Please look at the supplementary materials in the original paper for details)

Wrapping up with some epidemiology

The authors also studied the population structure of I. scapularis in North America, by studying SNPs from 8 populations, from the USA. Northern and Southern populations were found to be considerably different, compared to the mid- west (WI and IN) populations. There was also differences between the lab adapted Wikel strain and wild types from the field.

So, what now? What next?

The authors were able to identify novel genes that are potential targets for acaricidal drugs, developing drugs against which would ensure the selective toxicity we desperately seek with chemotherapeutics. The paper is a illuminating in the sense that it is not a list of genes. Genomic finds have been beautifully tied to function. With ~93 authors, 38 supplementary tables, 25 supplementary figures, and no doubt hours of mental and CPU labor, we don’t expect any less.
 
References:

M. Gulia-Nuss et al., Genomic insights into the Ixodes scapularis tick vector of Lyme disease. Nat Commun 7, 10507 (2016).

A. J. Ullmann, C. M. Lima, F. D. Guerrero, J. Piesman, W. C. Black, Genome size and organization in the blacklegged tick, Ixodes scapularis and the Southern cattle tick, Boophilus microplus. Insect Mol Biol 14, 217-222 (2005).