Protein spotlight

「Protein Spotlight」 (ISSN 1424-4721) は、スイスバイオインフォマティクス研究所Swiss-Protチームの月間レビューである。特定のタンパク質やタンパク質ファミリーについて、やさしく解説している。


  • 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.
  • ice whisperer by vgerrits (2018/12/19 15:30)
    No one likes the cold. Humans wear scarves, fur boots, quilted coats and woollen hats to keep the harshness of winter out while other creatures grow their own fur or line their bodies with a thick layer of blubber. There are those, too, who have a more subtle approach to dealing with extreme temperatures and, instead of sporting a protective coating of fur or fat, tame the cold by acting upon its actual source. As an example, various species of fish or bacteria who live in Arctic environments have evolved systems to keep ice crystals from developing further inside them or sometimes even in the surrounding extracellular medium. For what reason? Because ice crystals can damage cell membranes by puncturing them or causing them to rip, which is life threatening. One particular Arctic yeast known as Leucosporidium has developed a system that - in freezing conditions - hinders the growth of ice crystals by secreting a protein that binds to them and ultimately lowers their freezing point. This particular protein has been coined Leucosporidium ice-binding protein, or more simply LeIBP.
  • on mar and motion by vgerrits (2018/11/16 09:15)
    Movement is what sustains life. Organisms need to move to find food, seek shelter and to reproduce. Mobility is also essential inside organisms where cells are continuously dividing and migrating. There is also unceasing movement inside every cell where myriads of molecules are being trafficked, and cellular compartments of all shapes and sizes shifted. What keeps things moving? Years ago, scientists discovered a protein they coined actin. Actin is a small globular protein that has many different roles in eukaryotic cells. One characteristic feature is its capacity to polymerize into microfilaments that stretch from one end of a cell to another to form the cell's cytoskeleton - which speaks for itself. Though the formation of a cell's cytoskeleton is perhaps considered as actin's fundamental role in the cytoplasm, the protein is also involved in many other activities, one of which is mobility. Actin is also present in the nucleus but, until recently, scientists believed that microfilaments did not form there. It turns out that they do: damaged DNA seems to be oriented towards repair centres thanks to actin microfilaments whose growth is prompted by a protein complex known as Arp2/3.
  • best left unsaid by vgerrits (2018/09/28 09:42)
    There are times in life when things are best left unsaid. So you bite your tongue or someone bites it for you. Either way, you are silenced and no - or less - harm is done. Nature also has its techniques for muffling genes whose products are not necessary at a given time, or that are perhaps harmful once expressed. One technique, which seems to have been with us for a very long time, is DNA methylation. DNA methylation is like locking a door with a key that you promptly throw away: you're making things difficult for someone to open it and see what's on the other side. In the same vein, DNA methylation has the capacity to keep a gene in a locked - or silent - state, thus hindering the production of an undesirable protein and a probable adverse downstream metabolic pathway. DNA methyltransferase 3C is one of the many enzymes able to gag a gene. Although not any old gene: DNA methyltransferase 3C seems to silence specifically retrotransposons.
  • on the right track by vgerrits (2018/08/24 08:45)
    Left only to the passage of time, everything gravitates towards chaos. Gardens become overgrown. Roads gather potholes and cracks. Relationships wither, and teeth rot. We have ways of dealing with this however. Gardeners look after the lawns, engineers inspect the roads, therapists have a go at unravelling relationships, and dentists tend to our mouths. Life, too, has its keepers. Left unattended, the very essence of life - our DNA - will collect unfortunate mutations that have the power to wreak havoc inside us. Over time, our cells have found ways of coping with this by promoting, for example, self-destruction so as not to propagate what has become unhealthy, or by repairing damaged DNA. As a result, cells are kept on the right track. Who, though, is the keeper? Different keepers are summoned at different stages and depending on the cell's fate. One protein, however, seems to be the orchestrator. Its name is p53, and it has been studied extensively since the 1970s because when it goes wrong, life is at stake.
  • life, a subtle balance by vgerrits (2018/07/26 10:56)
    Life is a continuous balance between what needs to remain, and what must disappear. We are not aware of it but our bodies unceasingly shed cells that have received orders to die, which is a necessary process if tissues are to be renewed or to stay healthy. It does seem an odd paradox, but this surprising phenomenon is an integral part of every living being and known as regulated cell death. There are different ways of dying, and cells are imaginative. One of the more select ways has been coined ferroptosis. Ferroptosis occurs when the level of iron-dependent lipid hydroperoxides has become toxic for a cell, which is then left to perish. But before this occurs, cells have to be equipped with the necessary means to prevent precocious poisoning, or they will never be able to get on with what they are expected to. This regulation of the level of toxins is ensured by a special version of an enzyme known as glutathione peroxidase 4, or GPX4, that carries a very rare amino acid in its active site: selenocysteine.
  • tainted by vgerrits (2018/06/21 18:16)
    It has happened to all of us. You are seated in a good restaurant and the waiter has just brought you the wine you ordered. He solemnly shows you the label. You nod, and he proceeds to slit open the lead seal with the tip of his corkscrew. Pealing the seal off the bottle neck, he then screws the screw into the cork which he extracts with a muffled pop. He may bring the cork to his nostrils and sniff it, then with one hand behind his back, he will carefully fill the glass of the person who is to inform him whether the wine tastes fine, or not. And on rare occasions, it does not. But you're never quite sure. So you ask the person sitting opposite whether they would care to try. And they're not sure either, so you both say to the waiter that the wine is lovely, thank you. Yet, over dinner, there's a slight musty taste each time you take a sip of wine. This characteristic faint off-taste - coined cork taint - is caused by the presence of chemical molecules known as chloroanisoles in the wine. Scientists recently characterized an enzyme, that they named chlorophenol O-methyltransferase, from the filamentous fungus Trichoderma longibrachiatum that is responsible for their production.
  • giving in to time by vgerrits (2018/05/19 11:19)
    Time runs its treacherous fingers along everything. The smoothed edges of a pebble. The polished wood of a staircase. The worn joints in our bones. Sometimes, even, the erosion of our memory. Every day, every hour, every minute, we get a little older. Until we reach that invisible threshold when we actually begin to feel the years, and what getting older means. Our pace becomes slower and our muscles, stiff. Our bodies gradually bend forward and parts cave in. One hand begins to shake. Our thoughts are not so nimble. And perhaps for the first time we overhear someone say that we are old. Yet it is less a question of us getting old, than our bodies giving in to time. Cells inside us are losing touch. Information is being lost. Metabolic pathways become hesitant. Cells become weary, stifle and die. Many factors are involved in the very complex process of ageing. One of them is Plasminogen activator inhibitor 1 - or PAI-1. Scientists, however, discovered that a particular mutation in PAI-1 may actually be partly responsible for lengthening a person's life as opposed to shortening it.
  • more to it by vgerrits (2018/04/19 11:01)
    Multitasking is not limited to computers. On a day-to-day basis, humans frequently deal with more than one thing at a time - for the sake of speed, convenience and no doubt productivity. We brush our teeth while taking a shower, eat a sandwich while answering mails, wash the dishes while calling a relative. Though we are pretty good at it, humans are far from the only multitaskers on this planet. We also harbour a few inside us. Just consider cells... One cell can synthesize proteins, while secreting others, repairing its cytoskeleton and maintaining its membrane. And we now know that the odd protein is also able to juggle with more than one task - thus applying yet another layer of obsolescence to the not-so-old "one gene, one protein, one function" hypothesis. Such is the case for a protein known as dual function macrocyclase-peptidase, or POPB. POPB is involved in making amatoxins, which are very small cyclic peptides found in some mushrooms and particularly poisonous when ingested.
  • it's a thin line by vgerrits (2018/03/23 07:20)
    One cell. One organism. One fate: male, or female. The way Nature designs things, you would expect traits as fundamental as those that make a boy a boy or a girl a girl, for instance, to be inscribed in their respective DNA from the very start. In a way they are, of course, but there is a subtlety: if what defines gender is for some reason missing, then the other sex may emerge almost by default. So the process is far more than a simple case of gender that is genetically predetermined. The same goes for Musca domestica, or the common housefly, as it does for many other animals. There seems to be a sort of switch which, when on or off, will produce one sex or the other. This particular part of the sex decision system is preserved in many organisms, and scientists are beginning to realise that the upstream mechanisms leading to the definitive sex switch are surprisingly diverse and, in the case of Musca domestica, can even change from fly to fly. But one thing is preserved: to become male or female, you need a factor that will ultimately push the on/off sex switch. In the housefly, that factor is Mdmd, or Musca domestica male determiner.