Wednesday, September 3, 2014

Bacteria Are Intelligent Designers

Biology concepts – nature of science, flagella, intelligent design, irreducible complexity, motility, Gram+, Gram -, ion gradient

You don’t believe it now, but in the weeks ahead we’re going to discuss how bacterial motility, plant reproduction, intelligence, and the location of your heart are all related to whips and eyelashes. Sounds preposterous, but give me a few posts and a little leeway and you’ll be amazed.


Cheetahs can cover about 25 body lengths in a second, but
some Salmonella can move 60-80 of their own lengths in the
same time! See this post for finding out what the fastest
organisms are. Salmonella typhi is the bacterium that causes
typhoid fever and is spread in contaminated water or touch.
Mary Mallon was blamed for 51 cases of typhoid fever as a
carrier (no symptoms but still sheds bacteria). A 2013 study
shows that the bacteria turn on a fat regulator, PPAR-delta, in
macrophages which lets them live inside the cells forever.
Let’s get right to it. Bacteria are small, but they’re quick little devils. They have inboard motors – or are they outboard? – I can never keep those straight. This piece of machinery is so complex and fascinating that some people use it as a sign that someone or something had a hand in designing life on Earth.

The bacterial motor is called the flagellum, but it's so much more than just a way to get around, it’s often the means to saving their own lives. The word flagellum comes from the Latin word flagrum meaning whip, so you can see we are already starting to work on our challenge for these posts. Flagrum could also mean scourge, and this seems to be prophetic, since many flagella (the plural) we study have a hand in causing disease.

In typhoid fever, a potentially deadly disease that affects more than 20 million people each year, flagella are important not just for putting the bacterium, Salmonella enterica typhi, in the correct place to cause disease, but for attaching the bacterium to the gut wall and for invasion of the gut. A study in 1984 showed that even flagella that couldn’t move were still needed for S. typhi to produce disease. More about this in a couple of weeks.

A flagellum is very much like a boat propeller, it spins to produce force along its axis. This is possible because flagella aren’t perfectly straight. One of the main components of the flagellum is called the hook. This hook is located just outside the cell wall and lies in between the basal body and the filament. The basal body is the engine and is what attaches the flagellum to the cell, while the filament is the long whip like end that sticks out into the world.


A cartoon of the bacterial flagellum shows the structures,
filament, hook, and the entire lower part is the basal body
(motor). The filament is hollow and sends new flagellin
subunits up through it to be added on to the end. The electron
microscope image shows the basal body. It looks like art or
engineering.
The hook turns at about 90 degrees, but the degree of turn is different for different bacteria. This means that that filament, when spun by the motor in the basal body whips around in a circle, bigger at the bottom where the hook is located. So instead of rotating like a straight pencil and not generating any forward force, it spins like a propeller.

The basal body attaches the filament and hook to the cell, and is made up of several rings. In Gram+ bacteria there are two basal body rings that anchor the flagella apparatus, the M ring which attaches to the membrane and the P ring which is anchored in the peptidoglycan layer. In Gram- bacteria, the basal body is longer and has more rings since it must anchor the flagella into the LPS (the L ring) and the M ring has a buddy in the inner membrane called the S ring. All these rings support the rod, which is turned by the rotor and then spins the hook and the filament.

The filament is pretty cool. It’s either a left- or right-handed helix of subunits of a protein called flagellin. The filament is a prescribed length in each bacterium, but we aren’t exactly sure how the length is regulated. Scientists know that it grows faster at first and then slows down, but if broken it will start to grow again at the faster pace.


The filament of the bacterial flagella is capped by a small
protein called FLiD. This is an amazing protein that
regulates and mediates the assembly of the filament
subunits of flagellin at the tip of the growing filament.
The flagellin units are straight as they travel through the
middle of the filament, but their final shape is bent. The
FliD mediates this folding at the tip.
The amazing thing is that the filament grows from the tip, not the base where it attaches to the hook. The flagellin filament is hollow, and subunits of the protein travel from the cytoplasm up through the basal body and hook and then through the existing filament out to the end. Then they are attached to make the filament longer. That’s a pretty neat system because it alleviates the need for a way of exporting the parts, regulating their movement to the end of the filament and then attaching them. Sometimes, but only sometimes, evolution finds the simpler way to do something.

The energy for the motion of the flagellum comes from the movement of ions across the membrane of the cell. We have seen before how protons (or other ions) being pumped out and then allowed to enter through a pore can create the force needed to do work. That’s how ATP is made, how the neural action potential works, and how photosynthesis proceeds. But here, the proton motive force is used to spin the hook and the filament, driving the bacterium forward.

The flagella spin one way to move forward, but when they spin the other way, the bacterium just sort of tumbles around. We’ll talk more about this next time. We’re just now starting to learn how the motor can go from spinning counter clockwise (forward motion for a left handed filament) to spinning clockwise in no time whatsoever and without slowing down. Nothing looks very different in the basal body, the hook or the filament, but the direction of spin is reversed.


This is a complicated picture so stick with me. A) is the shape
of the FLiG protein from a certain bacterium. The end we are
interested in is red, it holds the charge for interacting with the
ion gradient across the membrane. B) shows the positive and
negative bubbles of charge in the helix. Below, see the ring of
FLiG proteins of the rotor. When spinning different directions,
the positive and negative bubbles are reversed, one shape
makes it go clockwise, the other, counterclockwise. It all has to
do with the pushing and pulling by same and opposite charges
as the ions pass through the membrane.
I can hear you thinking out there, “Well, just reverse the direction that the protons move, instead of outside to inside, go inside to outside.” Nope, when a flagellum switches direction, the protons keep moving the same direction. We do have information that one of the proteins that connect the motor (electrochemical gradient) to the physical turning (rotor), a protein called FLiG, can change shape.

Several studies have shown this change, and it is hypothesized that the change moves charged amino acids of FLiG around in relation to the cation gradient. By changing them, it changes the direction of the turning of the rotor (see the picture to the right). This might be akin to reversing the poles of a mag-lev train by flipping the electrical charge can make the train go the opposite direction.

Different bacteria have flagella that look similar but they have small differences. Nevertheless, it can be seen that this is a very complex machine for such a supposedly “primitive” domain of organisms. We have to remember that bacteria have been here the longest; they must be doing something right. There are over 40 genes that are required to build a flagellum, and they all fit together just so.

This complexity and order leads some people to declare that flagella couldn’t have evolved on their own. The concept is called irreducible complexity. People who support the idea of intelligent design (ID) say that some biologic components are so complex and have so many working parts that they could not arise through a series of mutations.

All the parts of a flagellum must be present for it to work (therefore they say it is irreducible) and must be assembled all at once which suggests it could not be random (complex in ID means improbably occurs by chance). Therefore, a flagellum could not have evolved over time and, ipso facto, it must have been designed as one unit by someone or something.

ID proponents haven’t always focused on the flagellum. They first talked of the blood coagulation cascade as irreducibly complex, but then it was shown that portions of the cascade were not necessary for function – whales don’t have factor XII and jawless fishes only use about half the proteins that vertebrates use. It was also shown how the cascade evolved over time.


A vibrio bacterium can make two different flagella types,
signified by the two sides of the dotted line above. The ions are
different that run the gradient, and the genes are different for
the motor/rotor. Are there two different irreducibly complex
flagella or did one modify into the other – then they aren’t
“complex.” Vibrio vulnificus is shown on the bottom. It has been
unusually numerous this summer (2014) and causes a disease
that looks like flesh eating disease, but isn’t.
Over the years, ID has proposed that the eye, the immune system, the flagellum and the eukaryotic cilia and its production system were irreducibly complex.  But each time, the ideas of specified, irreducible and complex (must have all come together at once) have been refuted for each example.

For the bacterial flagellum, arguments against ID include the facts that different bacteria use different systems, although they are all variations on a theme. One exception is the Vibrio. They use two different kinds of flagella on the same cells, each needing its own genes. Likewise some bacteria don’t use protons for the gradients, they use Na+ ions. The bacterium Vibrio parahemolyticus is an exception in both cases.

It uses a single flagellum at its end (polar) to swim in liquid water, but many flagella all around its cell when in something thicker. The polar flagellum uses Na+ ions to drive the rotor, while the lateral ones use protons. The genes are different for each flagellar type and mutations in one don’t hurt the other.


The top cartoon shows that when a gene duplicates (and they
do, often) one copy can drift and acquire mutations without
hurting the cell. This can lead to better function or new
function. Over generations, one set of genes for a function
can be replaced with another set – this would hardly be
called irreducibly complex. On the bottom, you see the type III
secretory system for injecting bacterial toxins on the left and
the flagellum on the right. They are very similar, so why is the
flagellum irreducibly complex and the not the type III system?
Lastly, only some Vibrio and other bacteria have a protein sheath over their flagellar filaments. These protein sheaths cover the filament and aid in sensing changes in chemicals outside the cell. So which flagellar type is irreducibly complex and which is not?

Spirochetes don’t even have flagella that protrude from the cell, they’re located between the inner and out membranes (endoflagella). This is a different system and again argues against irreducible complexity in flagella, unless different systems were designed differently. More about spirochete motion next week.

Please read more about ID and decide for yourself if it holds up to the tenets of science - that something that is true must be observable, repeatable, and able to be refuted if incorrect. Irreducible complexity is refutable, and has been for every example proffered by ID. But the conclusion that ID draws – that a designer must be involved, is a belief not a hypothesis – you can’t refute a belief, it doesn’t rely on observable evidence, therefore ID is not science. It doesn't make it wrong - it just makes it faith, not science.

Next week, let’s look at the different ways flagella help bacteria move, and some exceptions in bacterial motility.




Eisele NA, Ruby T, Jacobson A, Manzanillo PS, Cox JS, Lam L, Mukundan L, Chawla A, & Monack DM (2013). Salmonella require the fatty acid regulator PPARδ for the establishment of a metabolic environment essential for long-term persistence. Cell host & microbe, 14 (2), 171-82 PMID: 23954156

Lee LK, Ginsburg MA, Crovace C, Donohoe M, & Stock D (2010). Structure of the torque ring of the flagellar motor and the molecular basis for rotational switching. Nature, 466 (7309), 996-1000 PMID: 20676082

Minamino T, Imada K, Kinoshita M, Nakamura S, Morimoto YV, & Namba K (2011). Structural insight into the rotational switching mechanism of the bacterial flagellar motor. PLoS biology, 9 (5) PMID: 21572987

Carsiotis M, Weinstein DL, Karch H, Holder IA, & O'Brien AD (1984). Flagella of Salmonella typhimurium are a virulence factor in infected C57BL/6J mice. Infection and immunity, 46 (3), 814-8 PMID: 6389363




For more information or classroom activities, see:
Bacterial flagella –
   You must be careful to vet the source of material on flagella, much “science” is actually put out by Intelligent Design proponents, masking it as science.

Intelligent design –

Typhoid fever and Typhoid Mary –

Vibrio bacteria -