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

  • integrity by vgerrits (2020/07/01 02:03)
    Mistakes and misinterpretation are common incidents. We are usually aware of those we can see, or hear, such as a bird flying into an undetected window or a person who has misunderstood a question. Yet, mistakes are also a recurring phenomenon at a level no living being can readily observe: the molecular level. Take, for instance, mutations that occur in an organism's DNA. Though the evolution of species may sometimes thrive on such flaws, they are also frequently the source of serious drawbacks. This is why, over time, Nature has devised different systems whose role is to detect mistakes in DNA and offer a means to fix them. Until recently, repair systems had only been considered on double-stranded DNA where the untouched strand acts as a template to re-establish an error found on the second. But when damage is found on single-stranded DNA, what happens? Is it even possible to make amends? Against all odds: yes. Such a repair system involves a protein that has been coined HMCES, which is found throughout the three domains of life, and even in certain viruses it seems.
  • beneath us by vgerrits (2020/05/26 21:02)
    While our life is spent above ground level, myriads of other creatures spend theirs below it. There are those, too, who share their time between both worlds - like moles, ants and trees for example. Soil offers protection but it is also a great source for food. Plants and fungi are perhaps among the organisms which make the best out of this state of affairs as they forage underground for essential nutrients while, above, leaves suck in sunlight for energy and mushrooms ripen to spread spores. Seeking sustenance underground requires a system that can rummage through earth, like roots in plants or rhizomorphs in fungi. In the recent years, there has been much talk about tree roots which are able to form intricate networks underground. The same goes for the mycelia of fungi. One particular fungus, Armillaria gallica, created a buzz in the 1990s when scientists announced that they had found a colony whose rhizomorphs seemingly stretched over tens of acres. However, as rhizomorphs grow, they also spend a lot of time fending off microbes that also want to prosper. Consequently, fungi yield numerous antimicrobial products, among them: melleolides, whose synthesis depends on an enzyme known as protoilludane synthase, or PRO1.
  • on light, buds and bursts by vgerrits (2020/04/23 20:59)
    Nature is bursting into life these days. Every year at this time in the Northern hemisphere, and despite what may be troubling the world - wars, forced migrations, terrorism, earthquakes, locusts or, lately, a virus - spring simply unfolds as it always has. Much in the way your grandfather would perhaps stroll down a path, whistling a tune to himself with his hands deep in his pockets and his thoughts miles away, spring, too, seems quite content and happily unconcerned by what is going on around it. Nature can only spring into action, however, if it gets the right cues. And there are several: sunlight and starch to name but two. Thanks to daylight, for instance, plants are able to make carbohydrates - i.e. energy - and then use them for their growth and development. Consequently, sugars are continuously trafficked from one part of a plant to another, and stored or indeed broken down for energy. For shoots to appear along the length of a rose's stem, for example, besides light, sugars are required in huge quantities and, for this, many enzymes are triggered into action. In the common modern rose, Rosa hybrida, one such enzyme is a vacuolar invertase - acid beta-fructofuranosidase 1 - which specifically breaks down sucrose to provide rosebuds with what they need to bloom.
  • a way in by vgerrits (2020/03/26 20:55)
    As children in Scotland, back home from school and when the weather was dry, we would fling our schoolbags into the hall and grab a few golf clubs, a ball and a tee. There was no need for a change of clothes or shoes, whatever we were wearing was good enough. The course was along the coast on the edge of the North Sea, and the balls we used were found in the dunes where they had been lost by more experienced players. We had four clubs - a driver, two irons and a putter. Putting was the best part of the game. You would aim carefully for the long slim rod with the little red flag, taking into account the odd clump of grass or small mounds on the green and then, holding your breath, watch the little white ball as it made its meandering way to the base of the rod to drop, almost as an afterthought, into the hole. Well... it so happens that viruses infect cells in a similar manner... Viruses need to get inside cells in order to multiply, and this is what brings on infection. Like the flagged pole that marked the way in for our golf ball, viruses recognise molecules on the surface of cells to which they bind, thus enabling them - or parts of them - to enter the host cells where they rapidly spread. The coronavirus which is wreaking havoc across the planet as I write these words, is able to recognise a protein on the surface of a variety of human cells known as angiotensin-converting enzyme 2, or ACE2.
  • "the unwalkable disease" by vgerrits (2020/02/21 20:52)
    Health is really all a question of balance. Not too much of this, not too little of that. Gout is no exception. Throughout history, this particular form of arthrosis has been associated with the exaggerated consumption of rich foods and excessive alcohol, and consequently described as "arthritis of the rich" since, in the early days, only the higher classes of society seemed to suffer from it. However, as the excessive indulgence in over-rich foods has spread across a great part of the world, gout too has spread - and not only on a geographical scale but also throughout the various strata of human society. Gout is an inflammation caused by the accumulation of needle-like crystals of uric acid deposited in joints, tendons or their surrounding tissues. Uric acid comes from the breakdown of purine we ingest from the food we eat, and is usually processed by our kidneys and then eliminated with our urine. When too much uric acid is produced however, it precipitates as urate crystals that slowly build up finally causing excruciating pain - surprisingly at the base of the big toe in about half of gout cases. Why is uric acid elimination sometimes insufficient? Besides certain diets, there are a number of other reasons and one of them is the inherited dysfunction of a protein pump known as ABCG2.
  • backlash by vgerrits (2020/01/17 20:45)
    Every cell is a world of its own. Within its boundaries, there are entities of all shapes and sizes each busy accomplishing specific activities - transcribing genes, synthesizing proteins, modifying proteins, ferrying molecules from one part of the cell to another, building molecular motorways, erecting scaffoldings, repairing scaffoldings, collecting waste, shifting waste, digesting waste... To keep this state of affairs going, there needs to be a continuous exchange between the cell and the outside world as various goods are shuttled across its membrane in both directions. There are checkpoints nevertheless, which is why cell membranes are riddled with canals or pumps that are more or less selective: not everything can come in or go out, while some things must come in and others are better out. It is a case of survival. Toxic compounds that find their way into microorganisms, for instance, are usually funnelled out by what are known as efflux pumps. These pumps pose one problem for humans however, and that is drug resistance. One such pump is the Trichophyton rubrum ABC multidrug transporter MDR3.
  • dropping barriers by vgerrits (2019/12/18 20:33)
    Blood. It is deep red, liquid and essential to life, and courses through us from the very early stages of our development to our final gasp. It cannot have taken long for our ancestors to make the link between blood and life. They will have seen the rich red fluid seep from wounds alongside the lifeless bodies of animals they had just hunted down, and understood that the same fluid flows through their own bodies. Blood is indeed a tissue (albeit liquid) of vital importance, composed of myriads of crucial cells and nutrients, which is why - when lost - it is transfused. There is a snag however: no two bloods are identical. But all human bloods can be sorted into well-defined groups of which the most representative are the A, B, AB and O blood groups. The O blood group can be transfused to everyone, while the other blood groups cannot. This is why scientists have been searching for ways, literally, to shift A, B and AB blood types to the 'universal' O blood type - which could resolve the problem of insufficient stocks in blood banks. There have been several attempts, none of which conclusive. One more promising attempt involves bacteria from our gut microbiome, and two enzymes: a D-galactosamine deacetylase and a D-galactosamine galactosaminidase.
  • sting by vgerrits (2019/11/19 19:16)
    Venomé hasà 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 (2019/10/18 01:55)
    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 20:21)
    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.