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:
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).
