Ever feel like you’re just tumbling your way through life until you find something that feels “right?” Bacteria have a similar plight.
Say we smell something we like. The smell comes from molecules of the scent-y part of that thing binding to receptors in our nostrils that use nerves to send the message to our brain, which then uses other nerve cells to send a message to our muscles to get a move on. But it doesn’t send that message to all of our muscles or we’d just start randomly “tumbling”
Instead, the message only gets sent to muscles whose action would take us where we want to go. And this is possible because our bodies are stuffed full of lots and lots of cells of different types that we can control somewhat “independently.” But what if you just have a single cell? How do you get anywhere “on purpose”? This is the situation faced by bacteria.
Similarly to our nose cells, they can detect signals with receptors that bind attractant molecules. They have a class of receptors called methyl-accepting chemotaxis proteins (MCPs) that can recognize and bind different ones and shape-change. And since these MCPs span the membrane, they can relay this message into the cell.
BUT they can’t control different muscles because they don’t have muscles – they don’t even have multiple cells! So the best they can do is “steer” the cell kinda like rowing a boat. Instead of oars they have long flexible proteins called flagella that stick out (typically they have 4-6 of these) – and instead of rowing on the left side or the right side, they control flagellar motors that rotate their flagella clockwise (CW) or counter-clockwise (CCW).
CCW rotation is the “default” – if all the “rowers” rotate CCW, the flagella to twist into a nice “tail” that’s good for swimming straight. But rotating CW (even if it’s just one of the flagella gone rogue) unbundles the tail and causes the filaments to each “do their own thing” leading to random tumbling. This is good for when you don’t know which way to go. But once you set sights on paradise, you want to stop tumbling and move straight towards it. And this requires sending the message to all the rowers to switch back to CCW.
Key to controlling this is a kinase (one of those phosphate-adders we talked about last week) called CheA that’s bound to the base of the receptor (if you imagine the receptor as a flower where the attractant binds the rosebud part and the stem goes through a membrane into the cell, CheA is bound to the base of the stem. And you actually have a “bouquet” of stems held together by a hexagonal (six-sided) array of CheA & and a scaffold called CheW.
The situation’s kinda like a bee landing on a bud and resulting in a gnat getting kicked off the stem. The shape of the stem is impacted by changes that occur in the “bud” part and that impacts whether CheA is “awake” or “asleep”. When an attractant binds, the receptor gradually switches to a “kinase off state” but when there isn’t attractant the kinase stays bound in an “on” state.
CheA is “on” when it does NOT get any message about paradise-spotting (NO ligand bound). The first thing it does it grabs an ATP and uses it to phosphorylate itself (autophosphorylation) and then it passes that phosphoryl group onto a regulatory protein called CheY
This is like “waking up the coxswain” – the phosphorylated version of CheY (phospho-CheY) gets the rowers “out of sync” by binding the flagellar motors and getting them to “bypass their default setting.” With CheY’s encouragement, the motors turn CW and the bacterium tumbles.
When CheA DOES get a message that paradise has been spotted (LIGAND BOUND) it can “relax” – it “turns off” so CheY “falls back asleep” and the rowers “get lazy” and default to their CCW rotation for a smooth swim.
no attractant -> CheA “on” -> CheY “on” -> motors bypass the default & go CW -> tumble
But when CheY isn’t phosphorylated the motors go back to default giving a smooth swim. And you want this when attractant is bound, so
attractant bound -> CheA “off” -> CheY “off” -> motors on default setting (CCW) -> smooth swim
Bacteria go through phases of runs & tumbles, leading to a “biased random walk” with more tumbling happening when there isn’t a lot of attractant.
There are only 6 or so flagella but there are a LOT of CheY’s floating around – and potentially running into CheA. So, when there isn’t much attractant around and the kinase is really active, you now you have a bunch of phospho-CheY floating around and potentially running into one of those motors. It’ll only bind the motor if it’s been phosphorylated. So the more phospho-CheY, the higher the chance of a phospho-CheY running into one and getting the rotor to switch to CW, and causing the cell to tumble.
You don’t want to tumble forever so you tumble in short bursts because another protein, CheZ, comes by and dephosphorylates the phospho-CheY. But if there are a lot of phospho-CheY still hanging out nearby you’ll quickly be back to tumbling. The less attractant around, the more phospho-CheY so the higher the chances of tumbling.
But if there is a lot of attractant around, the kinase is “sleeping” so CheY isn’t phosphorylated so it can’t bind the rotor and it stays in its default for smooth sailing.
But you don’t want to get “Stuck off” – no getting complacent – there could still be better things out there! Or what if your course is a bit off? Or the attractant moves? You need to be able to adapt.
ADAPTATION is carried out through another type of modification – methylation – this time of the receptor itself in its methylation region (a part of the “stem” above the part where CheA binds but still inside the cell). Methyl is -CH3 and methylation is a modification that, like phosphate, can be added to proteins after they’re made (post-translationally) and can be taken off if they’re no longer wanted, thus allowing for regulation. But unlike phosphate, it’s neutral.
The places it gets added on CheA are 4-5 glutamates. Glutamate (Glu) is an amino acid (protein letter) that has the option of existing in a – state or a neutral state depending on the pH. At higher pH (more basic/alkaline conditions) there are fewer H+ around, so it’s more likely to be negative). Charge often makes things more “flexible” because like charges repel, so if you stick charges nearby they’ll want to move away – and if they’re attached to other stuff that stuff’ll get disrupted too.
So, similarly to how 1 rogue rower can mess up the whole boat, when these Glu’s are negative the receptor’s shape favors the “kinase off” stem shape that CheA doesn’t like. But if there’s a methyl group stuck to it, the Glu has to be neutral, so the stem stays in the “kinase on” shape. So the shape of the stem impacts whether CheA is awake or asleep, and the stem shape is impacted both by whether attractant is bound and whether (and to what extent) it’s methylated, which offers a path to fine-tuning receptor sensitivity.
Since there are 4-5 of the Glu’s that can get methylated, the receptor can “fine-tune” sensitivity (kinda like requiring the attractant to pass a “background threshold”) so that you don’t want to go one way unless you’re sure it’s the right way. And since the methylation/demethylation is a lot slower than the phosphorylation/dephosphorylation, the methylation state can serve as a sort of shortish-term molecular memory.
The methyl groups are added by a protein called CheR – it adds methyl groups which stabilize the receptor in the “kinase on” state – good for when there are high levels of attractant and you don’t want to “overreact” But you don’t want to get “stuck on” and not be able to sense anything because you can’t stop tumbling – so a protein called CheB removes methyl groups, and the receptor returns to the “kinase off state”
CheR is better at adding the methyls to the attractant-bound form, so it raises the threshold for turning off the kinase when there’s lots of attractant around. But, the methyl-remover, CheB, is activated by CheA. So the more active CheA is, the more active CheB is so the methyl groups are more likely to be removed. When there’s still attractant around, CheR will keep adding them back, but when the attractant isn’t around, CheR stops adding them so the threshold gets lowered back down.
This post is part of my weekly “broadcasts from the bench” for The International Union of Biochemistry and Molecular Biology (@theIUBMB). Be sure to follow the IUBMB if you’re interested in biochemistry! They’re a really great international organization for biochemistry.
link to that cool new article: http://www.jbc.org/content/early/2019/09/10/jbc.RA119.009865