“The very strangeness of Echinodermata is partly responsible for the dedication that specialists in the group feel. We revel in their weirdness.”
-Rich Mooi
Given that every biology student in the world has been introduced to the standard genetic code, and likely uses it frequently, it is kind of baffling that so few of us ever bother to think much about it. As a longtime lover of systematics/molecular evolution, the knowledge that the “universal genetic code” is not actually universal has always caused me some level of concern when imagining how scientists cope with such an issue or if they even cope with the issue at all.
Usually when you look this up you find a lot of “the code is essentially universal, only a few exceptions have been found” which would imply that maybe one or two extremely obscure microorganisms violated this rule slightly. But mammals mitochondria actually contains four out of 64 codons that do not match the universal code. Echinoderms, yeast, platyhelminth worms, all follow slightly different mitochondrial DNA codes and protozoan and some bacteria even follow different nuclear DNA codes (nuclear being the only DNA bacteria have).
While there are 64 codons, there are fewer than 64 tRNAs, which use an anticodon sequence to recognize a codon on mRNA and carry the appropriate amino acid at the other end. Different tRNAs with the various amino acids will sort of float in and out until the right one’s bound. The third position of the anticodon (the ‘wobble position’) however, binds very loosely to the DNA which is why the tRNA usually relies on recognizing the first two nucleotides. Some amino acids can have multiple tRNAs recognizing them but RNA modifications in the anticodon region of tRNAs can result in the evolution of a deviation to the universal genetic code. The echinoderm’s genetic code evolution is particularly intriguing which is hardly surprising given everything else about them.
A recent Nature paper shows an example of how this works in echinoderms. In echinoderm mitochondrial DNA, the codon AAA, which according to the “universal code” should code for a lysine, actually codes for an asparagine. Analyzing the tRNALys isolated from a sea urchin, they discovered a modified hydroxylated nucleoside; hydroxyl-N6-threonylcarbamoyladenosine. This modified nucleoside adjacent to the anticodon prevents the mt-tRNALys from misreading AAA as lysine, allowing AAA to code for an asparagine.
Mitochondria generally use a codon-anticodon pairing rule that allows unmodified uridine at the anticodon first position to pair with all four nucleotides at the third codon position. When an amino acid only has two codons corresponding to it, the G forms a base-pair with pyrimidine, and modified uridines (5-carboxymethylaminomethyl-uridine being a commonly heard modification to the wobble position base) can discriminate purines from pyrimidines. The presence of a pseudouridine in starfish mt-tRNAAsn in the middle of the anticodon allows the tRNA to decode the AAA codon more efficiently than the unmodified tRNA. Also interesting, the mt-tRNAs possessing anticodons similar to tRNAAsn, but which only decode two codons each (tRNAHis, tRNAAsp and tRNATyr) all possess unmodified U (position 35), further indicating pseudouridine (Ψ35) is important for decoding the three codons.
While certainly not all examples of a modified genetic code work quite this way, it’s intriguing to realize how something generally portrayed as being set in stone, is relatively labile and dynamic.
Given that systematics has favored mitochondrial DNA for many phylogenetic analyses, this could have an effect on the results if using an amino acid alignment or a distance matrix where each amino acid change is weighted a certain amount. You could imagine an alignment between mammals, echinoderms, and reptiles for example, where an AAA to an AAG would be a synonymous mutation (as in, not changing the protein) in mammals and reptiles, but a nonsynonymous mutation (changing the amino acid) in echinoderms, thus deserving a different score. AGA and AGG which both code Arginine in the ‘universal’ code, code for a stop codon in our mtDNA, while our nuclear DNA’s stop codon (UGA), codes a tryptophan. An AUA isoleucine in our nuclear DNA is read as a methionine in our mtDNA. There are likely many more “exceptions to the rule” that we have no idea exist.
Sources:
- Hydroxylation of a conserved tRNA modification establishes non-universal genetic code in echinoderm mitochondria. Asuteka Nagao, Mitsuhiro Ohara, Kenjyo Miyauchi, Shin-ichi Yokobori, Akihiko Yamagishi, Kimitsuna Watanabe & Tsutomu Suzuki. Nature Structural & Molecular Biology (2017).
, & The presence of pseudouridine in the anticodon alters the genetic code: a possible mechanism for assignment of the AAA lysine codon as asparagine in echinoderm mitochondria. Nucleic Acids Res.27, 1683–1689 (1999).
Active compounds of soy include isoflavones- daidzein, genistein, and glycitein. They act as phytoestrogens, a word which seems to frighten some people. A popular belief amongst anti-soy people is that men who ingest too much soy are going to re-enter puberty and turn into estrogen-filled feminized men (heaven forbid).
Their venom, though nonlethal, causes excruciating pain for hours or days and is essentially nonresponsive to morphine. Only nerve-blocking agents (or antivenom) can provide relief.
So while venom in mammals is very rare now, it may actually be an ancestral characteristic. Venom relatively expensive to have as it requires some method of injection into another animal, a gland, and then the making of proteins. It’s also suspected to be expensive because the loss of venom in animals that are no longer under pressure to produce any, is very common. Venom has a weak phylogenetic signal—similar types of venom are not necessarily found near each other on a phylogenetic tree, so genetically it seems not very “difficult” for various venoms to arise.
While O1 causes the majority of outbreaks, O139 is confined to Southeast Asia. Recently however, it’s been discovered that soft-shelled turtles in China are big carriers of O139. While a lot of aquatic animals spread cholera, the soft-shelled turtles have been definitively linked to human disease and make excellent hosts as they are unaffected by the bacteria which clings to many of their surfaces and intestines. These turtles are then consumed by people, to spread more cholera to new unsuspecting hosts. If turtles being cute wasn’t a good enough reason to stop eating them, maybe this is?
). This incongruence between chromosomal and phenotypic sex can be explained by feminization of genetic males induced by Wolbachia. Two strains of Wolbachia, wCI and wFem, have been found in E. mandarina and the females having male chromosomes (ZZ) are consistently infected with both wCI and wFem. However females with only wCI are true females (ZW). Despite having male chromosomes, ZZ females are physically female and fully fertile.
Since it’s pride month, I thought the evolution of homosexuality warranted some attention. It turns out homosexuality is common throughout the animal kingdom, while homophobia is only seen in one species.
A classic female-female coupling that actually makes a lot of evolutionary sense from a reproductive point of view, is the Laysan Albatross. The Laysan Albatross is monogamous and mates for life, and almost a third of the parent pairs are both female. This is useful as sometimes males will mate with more than the just their one female mate (basically he cheats on her in the hopes of making more offspring) and as the Albatross has evolved to require high parental care from both parents, female-female parents are actually a necessity in many cases where the father is absent.
A study of gay sheep, was actually pretty historical as it really confirmed that there is a biological basis for sexual preference in animals. Sheep do seem to have a much higher rate of homosexuality than other animals where as many as 1 in 10 rams can be gay. Rams have undergone a lot of selective breeding which may provide some evidence that genes are involved in sexual preference. A region in the hypothalamus which is generally much bigger in rams than in ewes was found in gay rams to be the same size as the female’s. The hypothalamic region size variations effected levels of aromatase, an enzyme which converts androgens into estrogens. This supported the theory that hormones present during fetal development plays a role in determining sexual preference.
