Wednesday, September 17, 2014

Should I Stay Or Should I Go

Biology concepts – bacteria, motility, flagella, quorum sensing, bacterial swarming, biofilms, pathogenesis

Nomads are wanderers. They come in different flavors.
Hunter-gatherers follow the animals as they graze in
different places. Pastoral nomads have animal herds and
move them around to where the grazing is best. But the
interesting ones are the peripatetic nomads. These are
people that move around within cities and other
populated areas, often to sell services or trades. Romanis,
or gypsies as they are sometimes called, are a
group of peripatetic nomads.
We humans have complex interactive behaviors with one another - these can make things better or, oh so much worse. We form herds as nomadic tribes, or we settle to form cities. Each has its own set of niches and behaviors that must be fulfilled by members of the group. But, it's important that we realize that we aren’t doing anything new, apparently bacteria have been roaming and settling for billions of years.

Our current series has been talking about flagella and how they help bacteria become motile (amongst other things). A relatively new discovery has opened our eyes to an exceptional movement by flagellated bacteria, swarming.

Swimming is when a bacterium on a liquid/surface interface or in liquid moves around by itself using its flagella as a propeller. But groups of bacteria can use their flagella to create a swarm; a mass of bacteria moving as one unit, often faster than the individuals can move on their own.

Bacteria moving as a unit is like tribes of humans moving from one place to another. But there are also those bacteria that choose to hunker down in one location and build a “city.” This prokaryotic Gotham is called a biofilm. We should do a whole series on biofilms, but for now let’s just talk about them in general.

When a number of bacteria of the same type, or sometimes even of different types, are in the same place at the same time, they may begin to form a biofilm. Certain bacteria will secrete proteins as filaments, polysaccharides in the form of slime, and some other structures. All of these together form a network of tunnels, tubules, cavities, and surfaces onto which the bacteria adhere. The biofilm also adheres to whatever surface is nearby. It’s a bacterial city.

The plaque on your teeth is a biofilm. The saliva and
crevicular fluid (between root and gum) provides some
proteins and sugars to build the film. Above is a
photomicrograph of plaque showing that yeast and
bacteria are both involved in mature plaque.
The biofilm matures over time, and different bacteria will have different jobs. The bacteria are stronger together than they are on their own, since the biofilm can prevent antibacterial agents from working. Biofilms are turning out to be important virulence factors (structures that enhance an organism’s ability to cause disease) and are crucial for pathogenesis (patho = disease, and genesis = beginning or course).

Some bacterial colonies settle to form cities and some move on en masse to another location – it really does sound like humans tribes. But biofilms and swarming are not mutually exclusive, in some cases you will see the bacteria at the edge of a biofilm start to swarm and expand, just like urban sprawl creates bigger cities.

There's organization to the swarm as well. Swarming isn’t an, “Everybody run!” kind of movement. Swarming requires controls, regulation, and numerous gene products spread out over the colony. Even though they work as a group, the bacteria might not all go the same direction.

Since bacteria divide by binary fission (one form of asexual reproduction), they tend to form masses in one location, often circular. When they give the signal(s) to swarm, some may take off in this direction, and some in another, based on where they are in the circle. Look at the picture below and right. Pretty, but it shows that colony swarm has multiple leading edges that will travel out into the unknown, and part of the colony will follow behind each.

Every once in a while, a new leading edge might branch off and swarm in a different direction, taking some followers with it. Other types of bacteria seem to swarm equally in all directions, forming concentric circles of new colonies.

This is a false color image showing the branching of a
bacteria colony in a swarm. Dr. Eshel Ben-Jacob from
Tel Aviv University produces these images as science
and art. See many of his images at this site.
The disease-causing bacteria Pseudomonas aeruginosa branches when it swarms, but even this is coordinated. A 2014 paper used a computer to model the branches seen in P. aeruginosa. They occur over a very narrow range of parameters. This means that the bacteria are limiting their activities and conducting themselves within a finely adapted range of behaviors and signals. Bottom line - their movement isn’t random.

Many behaviors occur in swarming bacteria that don’t occur in swimming bacteria. The leading edge cells may secrete surfactant, a combination of chemicals that reduce the surface tension on the plane so that the bacteria can move with less resistance.

The leading edge bacteria grow extra flagella, become elongated, and secrete slime for easy movement - but only the leading edge cells. They band together, becoming like rafts; in fact that’s what they’re called, rafts. The movement of the leading edge plows a furrow in the material they're moving across. This is partly due to the leading edge cells, but it has more to do with the cells behind them. The following cells form roiling masses, and together they push the leading edge along, like pushing a plow to form a ditch for planting seeds.

The furrows are then followed and expanded by the cells behind the leading edge, growing larger and easier to follow. That way, they can push the leading edge better. All these changes and functions lead to faster movement, which is why the swarm can move faster than individuals.

One amazing thing discovered in a 2013 series of experiments was that the leading edge cells secrete DNA. This nucleic acid doesn’t function as genetic material, but is apparently important for keeping the leading edge cells together and moving in the same direction, as well as stimulating movement at all. In experiments where this DNA was chewed by enzymes, the swarming movement stopped completely. Amazing - if they were a marching band in a parade, the DNA would be the banner carried by the drum majors that's emblazoned with their school and nickname. Everybody follows the banner and the drum major.

Integral to the concepts of swarming and biofilm development is the idea of multicellularity in bacteria. They're all clones of one another (except for mutation and any lateral gene transfer), but they work together and may take on different jobs, structures, and morphologies. They are working together to accomplish more than they could on their own. That sounds a lot like a multicellular organism where the different cell specialize into different types in order to perform different functions.

On the left is a cartoon that illustrates how the electron
donor hydrogen sulfide can’t donate electrons unless
something is available to accept them. The oxygen is the
acceptor, and the bacteria provide the cable to connect
them. The filaments of bacteria are shown on the right.
Photocredit to Nils Risgaard-Petersen.
One example comes from a 2012 study. Sea floor bacteria that bridge an area of high oxygen and low hydrogen sulfide to one of low oxygen and high hydrogen sulfide actually form filaments that act as power cables. Electron pass long a length of millions of cells to complete a circuit between the two sets of cells and this provides the energy to make ATP. Bacteria seem to work together in tough environments better than humans do on our best day.

We don’t know all the bacteria that are capable of swarming, but it's probably many more than we have found so far. And we aren't sure just why do they do it. Perhaps it's to leave an area of poor food value behind and strike out for better hunting grounds. Moving faster than they would as individuals might be important when trying to find, and then take advantage of a new food source. Eat up before someone else finds it.

Perhaps swarming is for protection. Like for biofilms, there is evidence that bacteria are less susceptible to antibiotics when swarming. Or it may have something to do with the best way to achieve full biochemical development. There are many studies that suggest that infectious organisms must swarm in order to create disease. Please remember, they aren’t trying to cause disease, but it shows that swarming must be important in their colonial development and a byproduct of this may be disease.

Three colonies of the same bacteria that were not clonal (not
from same exact ancestor - A, B, and C) were grown on the same
plate and they expanded in a swarm-like behavior. Where the
different colonies meet is the Dienes line. On the right is a false
color close up of a Dienes line, showing the battlefield. The
black line is 50 µm long.
They may also swarm to protect a new environment. Bacteria from one colony that grow and begin to swarm can tell their brethren apart. They can even discriminate between bacteria of the same type that have come from separate colony. When the two colonies swarm, they set a boundary between them, called a Dienes Line. A 2013 study showed that in Proteus mirabilis, a bacterium that causes urinary tract infections (UTIs), this boundary is really a battleground.

P. mirabilis has the ability to produce a type VI secretion system that acts as a needle. It punctures an adjacent bacterium and injects toxins. When a swarming colony invades another colony, they all start to produce their type VI secretion needles.

They attack any cell that makes contact with them, in a preemptive sort of fashion. There are many friendly fire incidents, but kin will survive the attack while cells from the other colony will be killed (they aren't immune to the specific toxin). The deeper invader is usually the dominant colony and will kill off the other colony, even though they may be of the same strain. Man - bacteria can be ruthless.

The key to both biofilm development and swarming is quorum sensing (quorum is from Latin qui meaning who, it means the number of members that must be present to transact business). The bacteria sense when their numbers reach a certain tipping point because the levels of certain chemicals reach critical concentrations.

We aren’t sure just why one behavior happens instead of the other, the situations that will induce either biofilm formation or swarming, but the number of bacteria and the state of their environment is key. Therefore, if you can stop the quorum sensing, you can stop swarming or biofilm formation, or both. This would be key to battling some pretty nasty infectious organisms since we said they are often important for pathogenesis.

Proteus mirabilis is a bacteria that swarms in concentric
circles. It causes urinary tract infections in both men and
women. In the lower image you can see the many flagella
of the organism – and this is before it starts to swarm and
leading edge organisms differentiate.
Several recent studies (here and here for example) have shown that certain natural or man made chemicals have the ability to interrupt quorum sensing or swarming/biofilms. Even cranberries seem to do the job.

We have discussed in prior posts about the amazing ability of cranberry to prevent UTIs. A 2013 paper shows that at least part of the cranberry's action on UTI-causing P. mirabilis is through the prevention of swarmer cell differentiation. Work with other bacteria shows that it is quorum sensing that is disrupted by the cranberry compounds, so the swarm in P. mirabilis might be stopped via the bacteria not knowing how many of their brothers are around. Bacteria won't pick a fight unless they know their gang is big enough - it's West Side Story in your bladder.

Next week - some prokaryotes don't move. Just like couch potatoes, they wait for someone to bring them their dinner.

Gloag ES, Turnbull L, Huang A, Vallotton P, Wang H, Nolan LM, Mililli L, Hunt C, Lu J, Osvath SR, Monahan LG, Cavaliere R, Charles IG, Wand MP, Gee ML, Prabhakar R, & Whitchurch CB (2013). Self-organization of bacterial biofilms is facilitated by extracellular DNA. Proceedings of the National Academy of Sciences of the United States of America, 110 (28), 11541-6 PMID: 23798445

Deng P, de Vargas Roditi L, van Ditmarsch D, & Xavier JB (2014). The ecological basis of morphogenesis: branching patterns in swarming colonies of bacteria. New journal of physics, 16, 15006-15006 PMID: 24587694

McCall J, Hidalgo G, Asadishad B, & Tufenkji N (2013). Cranberry impairs selected behaviors essential for virulence in Proteus mirabilis HI4320. Canadian journal of microbiology, 59 (6), 430-6 PMID: 23750959

Alteri CJ, Himpsl SD, Pickens SR, Lindner JR, Zora JS, Miller JE, Arno PD, Straight SW, & Mobley HL (2013). Multicellular bacteria deploy the type VI secretion system to preemptively strike neighboring cells. PLoS pathogens, 9 (9) PMID: 24039579

For more information or classroom activities, see:

Quorum sensing –

Biofilms –

Bacterial swarming -

Wednesday, September 10, 2014

Bacteria Can Really Get Around

Biology concepts – motility, microbiology, bacteria, evolution, gliding, twitching, flagella, pilus

The Giant Devil Ray, or mobula ray (Mobula mobular) can reach
18 ft. (5.4 m) wide. It’s not so much that they fly or glide, they
just breach the waves and look like they are trying to flap wings.
They were almost fished to extinction in the 1970’s. Their meat
was sold as scallops after they cut it out with a round cookie cutter!
How many different ways can humans move about? Walk, crawl, run, hop, swim, dance - you could say walk on hands or do the worm but I don’t think they count as normal modes of locomotion. Birds can fly, walk, or swim. Fish can swim and at least two think they can fly – flying fish and mobula rays. But the winners are……bacteria, again. They basically move forward, backward or turn, but they have several unique ways of accomplishing this.

The most common type of movement for bacteria is called run and tumble. Sounds a little like a toddler learning to walk; however, the bacteria aren’t falling down, it’s more like run and wander for them. The run is easy enough to explain; the flagella we talked about last week spin and the bacteria swims forward in its fluid environment like a little torpedo.

It’s not quite that simple, but close. We explained last time that a flagellum is made of subunits of the flagellin protein and that these are joined together into a hollow helix. The helix is most often left-handed (as you rise, the curve moves to the left). So when these bacteria spin their flagella counterclockwise (looking from behind the flagellum), the helix is pressed tight together and spins efficiently – lots of forward movement. For those bacteria with right-handed helices in their flagella, a clockwise spin is for forward movement, but this is less common.

When the flagellum/flagella rotate the opposite direction, you might think they would go backwards, but not so much. Many bacteria have more than one flagellum and they work together when all spinning one for forward motion (more next week). They bundle together like the trailing hair of a girl who is swimming forward in a pool. But what happens when she stops or turns around quickly? Her hair ends up in a tangled mess and she has to brush it out of her eyes – that is unless she starts swimming again, then it trails behind in a bundle again.

The run of a bacterium uses flagella that are all rotating the same
direction and work together. The tumble occurs when the turn
differently and work against each other. On the bottom, the left
side shows a random path with runs and tumbles, but the right
shows how a bacterium can get closer to a food source when run
goes up gradient but every tumble is completely random.
This is similar to the flagellar movement, except that with bacteria the flagella are the source of the movement, not just passive followers. When they switch from forward direction spinning, the bundles fall apart and they each start pushing in a different direction. This is why the bacterium tumbles, it just jerks around turning in random directions.

For a bacterium with a single flagellum, the reversal of spin pushes the bacterium backwards, but then it runs into the flagellum and all efficiency is gone. In a motor boat, the propeller is fixed a certain distance from the back of the hull, so when it reverses direction, the movement may be less efficient, but the boat doesn’t run into its own propeller. But with a flagellum, the bacterium gets pulled right into the flagellum and movement is hampered severely. The tumble begins.

Tumbling is just a random turning based on the various places the flagella are inserted into the bacterial cell, the nature of the flow of the fluid the bacterium is in, and the efficiency of the movement. However, after a small tumble time, they will spin forward direction and the bacterium will take off running forward again, probably in a new direction. The purpose the run and tumble is to move toward something good (source of food) or away from something bad (predator or chemical). More on this in a couple of weeks.

Of course, there are exceptions. Some marine bacteria (those that swim in salt water) have one flagellum and can reverse direction by rotating their flagellum the opposite direction. This works for a while and actually works better for reversing motion than having several flagella would. However, a new study shows that they don’t reverse for long, they quickly execute a trick called a flick. Their flagellum flicks in one direction, turning them so that when they run again, it will be in a new direction.

The researcher’s paper shows that this "reverse and flick" is a very efficient way of turning. Some of these bacteria can move up gradients toward food faster than bacteria that use the run and tumble method. "Reverse and flick" is a good strategy, just like the “bend and snap maneuver from the movie Legally Blonde.

The axial filaments of spirochetes are really several flagella
that lie in a ribbon. They work together to rotate under the
“skin” of a bacterium, which causes a helical wave that
propels the organism along. Scientists didn’t have this
mechanism for a long time because when they prepared
bacteria for electron micrograph, the flagella would pile up
on one another and the coordinated rotation hypothesis just
wouldn’t work that way. It was a preparation artifact that s
topped our learning for a couple of decades.
Spirochete bacteria use flagella to move as well, but they use them differently. We talked about this a bit last week. Spirochetes have internal flagella (called endoflagella) that run the length of their corkscrew shape in their periplasm (between inner and outer membranes).

According to a 2005 paper, these 7-11 flagella lie in a ribbon that wraps around the cell body. By rotating counterclockwise, the flagella put a torque into the cell body that makes it spin the opposite direction, this drives the spirochete forward. See the image to the right and this movie to get a better picture.

If most bacteria use flagella to move, you just know that some have to be finding a different way. Twitching is a kind of bacterial motility that doesn’t need flagella at all. Even though I could probably come up with several movie references for twitching, I will refrain. Twitching makes use of small appendages that project from bacteria cells called pili (pilus is the singular, it comes from Latin for hair). We have talked about them before in terms of trading DNA back and forth in lateral gene transfer, but here that are used to move the bacteria along.

Pseudomonas aerguinosa bacteria are famous for twitching, but a surface has to be involved, it isn’t possible in a liquid medium only. The proteins in type IV pili are coiled like a slinky. They stretch out, attach to a surface, and then retract forcefully. This jerks the bacterium forward. This was discovered in the very late 1990’s, but they didn’t know how they turned until 2011.

Have you ever had a twitch in your eyelid? You swear everyone
can see it. It occurs because of a spasm in the palpebral
portion of the occularis occuli muscle. That short fast
movement looks a little like the twitch of bacteria, except
they do it by snapping back a pilus instead of contracting
a muscle.
A 2011 PNAS paper showed that they slingshot themselves. Some pili stretch out and attach. Others stretch out in another direction and then instead of retracting to pull the bacterium in that direction, they release at the tip. This shoots the organism in the other direction. It’s the moral equivalent of a tumble, just not using flagella.

Another kind of surface motility is called gliding. This type of motion is more of a mystery than twitching ever was. There’s more than one way to glide. The first example of gliding can really be considered elegant twitching. It uses type IV pili that stretch out and then retract, but it is much smoother than the jerky movement created when twitching.

Another type of gliding is used by some cytophagia (cell-eating) and flavobacterial organisms. This movement might work a little like a conveyor belt, where proteins attach to the surface and then move along the cell’s surface from front to back. As the proteins are moved backwards, the cell moves forward. Many show a helical track along the surface of the bacterium, so that as the proteins dislocate toward the back, the cell goes both forward and rotates around its long axis – efficient, but they may get dizzy. A 2014 minireview paper shows that very different bacteria use the same mechanism, but the proteins and force for motility are different.

Slimer from Ghostbusters left slime where he had been, but I don’t
know that he used it to push him along – he flew. Bacteria that use
slime have to be on a surface. Is it just me, or does Slimer look a lot
like the snot monsters from the Mucinex commercials? Bacterial
slime is a little like snot, but is made of most sugars, not mucin proteins.
In a third form of gliding, the bacterium produces a slime that it then travels over, sort of like a snail or slug, maybe more like Slimer in Ghostbusters. In this form of gliding on a surface, a mix of polysaccharides is secreted from pores in the cell wall and membranes of the bacterium. The force of the release in one direction pushes the cell in the other direction. Think of it as very slow motion rocket propulsion.

Finally, one of the fastest bacteria on surfaces is called Mycoplasma mobile. It may use a mechanism of motility previously unseen and evolutionarily stunning. A 2005 paper showed that if you lyse the M. mobile with a detergent, but provide the resulting fragments with the proper ions, they will still move along a surface. This suggested that the mechanism was ion gradient driven and confined to the membrane.

More recent studies (here and here) suggest that the protein mechanism in the membrane might look very similar to the cytoskeleton of a eukaryotic cell. This would be either an evidence of an endosymbiotic origin of the cytoskeleton or that very different organisms had the same great idea, called convergent evolution. Either way, it’s cool.

Myxococcus gets around. When alone, he forms a slime trail
that actually pushes him forward. When he is with his buds,
he might push out pili and retract them to pull himself
forward, he might use a conveyor belt system to spin himself
along, or he might use both. The signals that control which
he uses still need to be worked out – anyone out there
feel up to that task?
All these mechanisms just go to prove that bacteria have more ways of moving than we could ever dream up on our own. They have propellers, finger proteins to pull them along, conveyor belts, cytoskeletons, and even snot rockets. It must be important to get from on place to another if they have developed so many mechanisms. Some even combine their modes of transportation.

Several strains of bacteria together known as Myxococcus use different types of gliding at different times. When M. xanthus is with other bacteria of his kind, they move using something called social gliding, which is of the conveyor belt type OR the elegant twitching type. But when he’s alone, he performs adventurous gliding, which uses slime extrusion. Humans call this social climbing, but sliminess is certainly involved in both.

Speaking of social motility - bacteria working with other bacteria; this just happens to be our topic for next week.

Balish MF (2014). Giant steps toward understanding a mycoplasma gliding motor. Trends in microbiology, 22 (8), 429-31 PMID: 24986074

Kinosita Y, Nakane D, Sugawa M, Masaike T, Mizutani K, Miyata M, & Nishizaka T (2014). Unitary step of gliding machinery in Mycoplasma mobile. Proceedings of the National Academy of Sciences of the United States of America, 111 (23), 8601-6 PMID: 24912194

Jin F, Conrad JC, Gibiansky ML, & Wong GC (2011). Bacteria use type-IV pili to slingshot on surfaces. Proceedings of the National Academy of Sciences of the United States of America, 108 (31), 12617-22 PMID: 21768344

Stocker R (2011). Reverse and flick: Hybrid locomotion in bacteria. Proceedings of the National Academy of Sciences of the United States of America, 108 (7), 2635-6 PMID: 21289282

For more information or classroom activities, see:

A great site from Harvard University with movies of many types of bacterial motility:

Bacterial motility -

Run and tumble –

Pili –

Gliding –

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
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 -