Tuesday, June 30, 2015

Molecular bits of living things with fun names

Most of the fancy words used by life science folks are dry but effective. However, every once in a while a researcher will discover a new gene or small molecule and decide to gift it with a fun and creative name.

The bacterium Photorhabdus luminescens has a gene called makes caterpillars floppy (mcf), which encodes a toxin that causes caterpillars to go all floppy like before it kills them. P. luminescens is a super interesting little bug. It hangs out in the gut of a worm that infects insects, helping the worm to kill and digest its host. It's bioluminescent and may produce antibiotics, and apparently managed to get inside the wounds of soldiers fighting in the American Civil War and make them glow.

Floppy caterpillar is floppy

The bacterium Proteus mirabilis, which can cause urinary tract infections, has a gene named zapA (one of the researchers who found this gene was a Zappa fan). The gene encodes a protein that helps the bacterium change how it moves around, contributing to its ability to cause disease.

Tigger, roopogo, mariner, gypsyhobo, and Jordan (discovered in 1993) are specialized pieces of DNA called transposons capable of bouncing/travelling/jumping around the genome of an organism.

The cabbage looper, a moth that in its caterpillar form eats several important crops, has a gene named bagheera controlling its eye colour. While adults normally have gray-brown eyes, a mutation in the gene causes them to change to yellow.

In 1983, a sheep was born with particularly well defined muscles in its hindquarters. This was subsequently determined to be the result of it possessing a particular variant of a gene named callipyge (from Greek calli-, beautiful; -pyge buttocks).

Vertebrates have a gene called Sonic hedgehog (Shh), which is named after the video game character and encodes a protein secreted by cells so they can communicate with one another. The protein is involved in ensuring that we develop properly in the womb (e.g. that our brain is put together the right way). It also regulates angiogenesis and the division and migration of cells in adult bodies, and thus can have a role in cancer development. Sonic hedgehog is related to the hedgehog gene (hh), which was discovered earlier in fruit flies. Altering the hh gene in fly embryos causes them to become covered with small spikes as they develop, such that they look a bit like a really gross tiny hedgehog.

Robotnikinin is a small molecule that can bind to Shh protein and disrupt its function. It's named after Dr. Ivo "Eggman" Robotnik, noted foe of Sonic.

Pikachurin is a protein found in the retina of the eye. It's named after Pikachu and is necessary for normal vision, having a role in ensuring the proper transfer of rapid electrical signals between the eye and the brain.

The stargazer gene in mice encodes a brain protein named stargazin. A mutant version of the gene apparently causes mice to develop a specific form of epilepsy where they stagger around with their heads twitching toward the sky.

Beefy meaty peptide (BMP) (aka delicious peptide) is a specific chain of eight amino acids that was at one point thought to be responsible for the taste of red meat. However, BMP was subsequently shown to not be appreciably present in cooked beef and to have a strong acidic and astringent taste. Bummer.

Fortunately, there's at least one other food reference to be had. Sushi domains are repeating sequences of amino acids found in some proteins that fold in such a way that they resemble the food (look at figure 8).

Diablo, sickle, grim, and reaper are proteins that promote apoptosis, aka programmed cell death.

Not sure what Jane Austen would have made of it, but darcin is a protein pheromone found in the urine of male mice that causes females to be sexually attracted to male urinary scent.

Finally, there are oodles of silly yet appropriate names for genes found in Arabidopsis plants, fruit flies, and zebrafish. This is largely due to the widespread use of these organisms as models for all sorts of genetic investigations. Some of my favourites:

Arabidopsis genes
  • bubble-bath (bub) controls the number of vesicles present within plant cells; plants with certain mutations in this gene have so many vesicles that their cells appear to be full of bubbles (look at J and K of this figure)
  • crabs claw (crc) and knuckles (knu) are involved in flower and silique development; mutations can result in a claw- (compare figure 1 A and C) or knuckle-like (look at C) appearance to their seed capsules
  • poltergeist helps to maintain stem cell populations in plant roots and shoots; mutations in the gene don't visibly alter plants unless they also have mutations in a second gene (like a ghost, the effects of this gene can't be detected under normal conditions)
  • superman also regulates flower development; mutations can result in flowers with extra stamens
  • kryptonite initiates a pathway by which expression of superman is inhibited by its transformation into clark kent (by DNA methylation)
  • time for coffee contributes to the ability of plants to synchronize their actions with the changing availability of light throughout each 24 hour rotation of the earth, specifically regulating gene expression late at night when coffee would help a person stay awake

Fruit fly genes
  • bruchpilot apparently means crash pilot in German; mutants are bad at flying
  • couch potato is involved in nervous system development and function; some mutants won't fly unless prodded
  • fuzzy onions mediates the fusion of mitochondria in sperm cells; mutants are sterile and their unfused mitochondria have an onion-like and fuzzy appearance (look at E)
  • ken and barbie mutants don't develop external genitalia
  • maggie mutants stop developing as larvae, kenny mutants have crappy immune systems and so tend to die young
  • cheap date mutants are sensitive to alcohol, lush mutants are strongly attracted to alcohol, hangover is required for the development of alcohol tolerance, ether-a-gogo mutants shake their legs when under the effects of ether
  • bagpipe is required for the development of the fly midgut (incidentally, koza and zampogna are related genes found in frogs), concertina and saxophone regulate embryo development such that their mutation causes embryos to develop weirdly and vaguely resemble these instruments (this is totally a guess on my part)
  • arleekin, valient, tungus, and many others are involved with long-term memory (named after Pavlov's dogs)
  • tinman mutants don't grow a heart, the lungs of breathless mutants fail to develop properly
  • hamlet regulates the development of IIB cells, capulet is involved in the creation of egg cells, malvolio is required for normal sense of taste (mutants, like the Twelfth Night character, "taste with a distempered appetite"), prospero influences the fate of certain developing cells

Zebrafish genes
  • dracula encodes an enzyme (ferrochelatase) involved in the synthesis of heme; the red blood cells of fish with a certain mutation in this gene are readily broken apart by exposure to light, resulting in anemia
  • one-eyed pinhead mutants look just as described
  • cabernetchardonnaygrenachemerlotzinfandel, and others are involved in the formation of red and white blood cells
  • spock, van gogh, dog-eared, what's up, half stoned, and teeny rocks are all involved in the development of the ear of a zebrafish including its stones


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