Protein spotlight

Protein Spotlight (ISSN 1424-4721) is a monthly review written by the Swiss-Prot team of the Swiss Institute of Bioinformatics. Spotlight articles describe a specific protein or family of proteins on an informal tone.

Recent articles

  • sting by vgerrits (2019/11/19 10:16)
    Venom has a language of its own. The recurring message is not a nice one, and usually expresses one thing: back off. Certain animals use venom - a cocktail of molecules - to ward off predators or, at the very least, to divert oncoming danger. We all know what a wasp's sting is like and many of us may have felt the sting of a jellyfish, or perhaps even the bite of a snake. It is a painful experience. To what end? The reason is twofold: one, we at once recoil from the animal that has just caused pain and two, our body is instantly told where it hurts. Concomitantly, the animal takes flight while our body attends to our wound. The feeling of pain itself is caused by the opening and closing of minute channels that riddle the membranes of our nerve cells just under our skin. This gives rise to pain signals that originate at the location of the sting, or bite, and are relayed to our brain. Understanding how pain occurs on the molecular plane helps scientists find ways of designing pain relievers. However, more often than not, pain is usually accompanied by swelling which has a protective role. So we face a conundrum: how do you relieve pain while preserving inflammation? One particular scorpion toxin, the Black Rock scorpion toxin known as the wasabi receptor toxin or WaTx, may well provide an answer.
  • lure by vgerrits (2019/10/17 16:55)
    Walking down a busy main street a few days ago, from the corner of my eye I saw a teenager rooting rapidly through a wallet he had just pulled out of a girl's backpack. Before I had registered what was going on, a young man approached me to ask where he could catch a bus. Flustered, I told him. In between times, the teenager and the stolen wallet had disappeared. Minutes later, I realised what had just occurred. The young man who had asked me about a bus had - successfully - diverted my attention from what his accomplice was doing. This is very similar to the kind of lure a plant pathogen known as Phytophthora sojae uses to confound soybean's immune response to infection. P.sojae secretes a protein known as XEG1 into the soybean plant where it can do significant harm. Soybean, however, reacts to the infection and muffles the effects of XEG1 thanks to a protein known as GIP1. To bypass this inconvenience, P.sojae promptly secretes a second protein - XLP1 - that soybean GIP1 mistakes for XEG1. XEG1 is then free to continue infection while the plant's immune system is tricked to attend to XLP1. This is a perfect example, in Nature, of two entities working together to confound a third.
  • a sense of direction by vgerrits (2019/09/19 11:21)
    Survival depends on cues, mobility and a medium to evolve in. Cues - such as scents, sounds or colours for example - will attract organisms towards food, mating grounds and an environment in which they feel protected and are happy to stay. Thanks to them, organisms usually head off in a direction they expect will be to their advantage, using the means of locomotion they have, to cross all sorts of media. A few organisms use yet additional systems to reach a given destination. An example? Magnetotactic bacteria have learned to use the Earth's magnetic field as a speedy highway to travel to nutrients of interest. They do this by way of minute iron-rich pouches - or magnetosomes - that are aligned along their middle and act much like a compass would. Many macromolecules are required to model this fascinating system. One of particular interest is a protein known as MamB which is at the heart of magnetosome initiation. Magnetosomes have also long intrigued those behind the microbiology blog Small Things Considered, and this article echoes a lovely piece on magnetotactic bacteria and their navigation skills written by Christoph Weigel earlier this week, and whose artwork illustrates this text.
  • the scent of guile by vgerrits (2019/08/01 11:12)
    All kinds of strategies are used by living beings for their survival. Humans lay down traps to catch prey, chameleons melt into their environment to hide from predators and foxes cross water to bewilder those hunting them. Because of their inability to move, plants have devised the most elaborate ways of deceiving their environment in order to grow. They can exude scents or even produce fake fruit to attract pollinators for instance. They can also synthesize hosts of different molecules that, once released, fight off microbes. But there is yet another master plan used by many plant species as a means of defence. European maize, for example, is able to synthesize a molecule known as (E)-β-caryophyllene which is released by the plant's leaves and roots in the presence of larvae feeding on them. (E)-β-caryophyllene does not actually kill off the larvae but attracts yet other organisms that will feed on the herbivorous parasites, thus stalling harm that could be made to the plant. The enzyme at the heart of (E)-β-caryophyllene synthesis is a terpene synthase, known as TPS23.
  • on versatility by vgerrits (2019/06/11 18:00)
    Diversity is one of Nature's fortes. See how she has spread life and let it flow into Earth's every nook and cranny: oceans and seas, rivers and lakes, woodland, forests and jungles, mountains, valleys, deserts, marshland and glaciers, and even stifled cities where weeds push their way through bricks - and flies, rats and pigeons feed on our waste. Though humans seem set on diminishing diversity, there is still a great variety of living organisms on most of the planet's surfaces. It continues on a smaller scale too. Consider a cell and the myriads of different molecules inside it all working together in relative harmony, to keep the cell alive and healthy. It may seem a paradox but the principle of economy is one of diversity's driving forces, and the world of proteins illustrates this beautifully. Imagine a basic sequence, a template if you like, then add a methyl group here or remove a phosphate group there, and you have a protein that behaves in two different ways. This is the realm of post-translational modifications, or PTMs. In cells, special enzymes - of which there are many - have the task of adding or removing molecules onto or from proteins to this end. One of these is SET domain protein 3, or SETD3 which shifts the behaviour of a certain kind of actin.
  • twisting fate by vgerrits (2019/05/10 14:21)
    Life thrives on reproduction. Over time, it has found very imaginative ways to proliferate in multitudinous forms - from protozoa wriggling in the bottom of pools to big cats racing across the African plains and birds flying swiftly through the air. All forms of life - or certainly the great majority - require help of some sort to reproduce: mammals need a partner, plants rely on insects for pollination and many amphibians are dependent on favourable conditions for spawning. There are life forms, too, that not only count on others to multiply but also damage them in the process, frequently to the extent of killing them. This is the realm of infection. Though their ultimate aim is not to kill their hosts, pathogens such as viruses, bacteria or fungi invade other organisms to take advantage of their resources - so doing, if left unchecked, they can destroy their hosts. In this way, the AIDS virus diminishes our immune cells, the poliovirus attacks our motor neurons and a variety of fungi infect plant cells, ultimately wiping out complete crops. Phytophthora infestans is a fungus-like organism that invades potato plants in particular. Scientists are slowly unveiling how P.infestans uses potato cells to develop, and which molecules are involved. Notably: a protein known as PexRD54.
  • another kind of harmony by vgerrits (2019/04/12 09:48)
    Would Nature not tend instinctively towards symmetry? In our eyes, symmetry often spells equilibrium, a source of beauty. Consider the work of architects, or engineers. Houses, skyscrapers, bridges and dams are usually symmetric which is not only, and in a mysterious way, emotionally reassuring but also in keeping with the laws of physics. In the same vein, a face that strikes us as being attractive is a face whose sides echo one another. Anything that drifts from these unsaid boundaries strikes us as being odd, if not ugly: think of the Elephant Man. Despite this, life is defined by an underlying lack of symmetry. In fact, Nature frequently seeks a way to break symmetry. Take humans: our heart is not symmetric, neither is the arrangement of our organs inside us, and our brain hemispheres are involved in very different aspects of intelligence. Why has Nature chosen asymmetry? And how does it occur in the first place? The field of research is relatively recent and the answers to these questions are still far from satisfactory. However, we do know that a certain form of myosin, known as myosin 1D, is directly involved in paving the paths of asymmetry in zebrafish.
  • paths of discomfort by vgerrits (2019/03/15 09:34)
    We are all bound to become prey, predator or competitor one day. Whichever way you look at it. That is why, over time, all living beings have acquired their very own palette of defence mechanisms. Roses grow thorns. Bacteria fire toxins. Panthers run fast, chameleons blend into the environment and humans hurl a few well-chosen words. The whole point of developing such mechanisms is to shun the threat of some sort of insult, or worse: death. Bees sting, dogs bite, ivy poisons, humans humiliate... Everything that has to do with defence frequently involves hurt or physical pain. Why? Because it is the best way to say: "go away, and don't come back". Cone snails have developed one of the most varied and plentiful venomous cocktails that are known, which have been extensively studied. Recently, researchers discovered that one component of such a cocktail makes humans itch. This is an intriguing discovery since itching is - so scientists believe - not far removed from pain. The component is a particular conotoxin, a venom peptide coined conorfamide.
  • dark horse by vgerrits (2019/02/13 16:08)
    There are many proteins crouching in the recesses of databanks whose role in vivo eludes researchers. Despite similarities of all kinds they may share with other proteins, they seem to have been designed for another purpose. A few of them may even have an unexpected function in an organism that does not synthesize them at all - much in the way a pair of scissors can be used to hammer a nail into the wall. This is precisely the case of a protein known as gamma-conglutin, found in the seeds of lupins. Unlike the majority of proteins in lupin seeds, gamma-conglutin does not seem to be used as a source of nourishment for seedlings. However, it does have an effect on sugar levels in our blood! Lupin seeds have been part of our diet in various parts of the world for centuries and their beneficial effects on our health long acknowledged. Today, thanks to technological advances, scientists are able to discern what is going on at the molecular level.
  • silent walls by vgerrits (2019/01/17 12:05)
    Though it may seem a paradox, life is riddled with barriers. This is because it is sometimes necessary to create dead ends to keep things at a healthy distance. Obstructions of this kind exist at all levels of living matter. Specialized pores are found in membranes surrounding cells but also within cells, to ensure that only specific molecules are able to cross while the transit of others is barred. Aquaporin and sodium channels are two examples through which only water molecules or sodium ions fit, respectively. Another vital barrier is the one that keeps spermatozoa that belongs to one species from fertilizing eggs that belong to another - which would only bring about chaos. Though the mingling of germinal fluids and how life ensues have been discussed since the days of Aristotle, on the molecular level very little is known, still, on how species keep to themselves. A recent find in zebrafish has lifted a veil: scientists discovered a protein on the membranes of zebrafish eggs, which only allows access to zebrafish sperm. They called it Bouncer.