As Many Exceptions As Rules: September 2014

Wednesday, September 24, 2014

Chase The Good, Evade The Bad

Biology concepts – motility, flagella, bacteria, chemotaxis, magnetotactic, monotrichous, amphitrichous, lophotrichous, peritrichous, run and tumble, coccus

The Princess Bride had everything – good guys, bad guys,

rodents of unusual size, ex-professional wrestlers. Vizzini

was supposed to be brilliant, so why didn’t he cure his own

speech impediment? Inconceivable!

Proximity is a good relative indicator of danger or benefit. As Vizzini said to Wesley in The Princess Bride, “As a student you must have learned that man is mortal and you would therefore put the poison as far from you as possible.” We tend to move toward things we need or want, and away from those things that could harm us – except for doughnuts of course.

A couple of weeks ago we started to talk about flagellar movement and the how a bacterium will “run” up a positive gradient or “down” a negative gradient. More detail will show us how amazing this chemotaxis (chemo = chemical, and taxis = arrangement) is.

The “run” in run and tumble movement is in a particular direction, while the tumble is a mess, just turning randomly before the run continues in another direction. What directs a run or a tumble? Well, they’re either running toward or running away from something.

There are receptor proteins on the surface of bacteria that sense different things. Some sense food; if food is to the left, receptors on the left will start to pick up more signals. As long the concentration keeps going up, the cell is directed to continue a run (positive chemotaxis). If the concentration starts to decrease (less signal for receptors), then a tumble is in order.

Random walking by run and tumble in bacteria.

Since the tumble is a random turn, the result doesn’t necessarily turn the bacterium toward food. If the concentration doesn’t start to increase as the next run starts, another tumble will commence and maybe then the organism will be faced the right direction (see animation). This works for twitches, glides, and rolls as well, and is particularly effective even if part of it is random.

Chemotaxis works the other direction as well. If a negative chemical is sensed, such as a predator or toxin, a run will continue as long as the concentration of the chemical keeps going down (negative chemotaxis). If the concentration stays the same or increases, a tumble will hopefully reorient the direction of movement down the gradient.

Remember that the movements for runs and tumbles are controlled by the flagella. Not surprisingly, there are several different flagellar possibilities. Having one flagella is called monotrichous (mono = one, and trichous = hair), it’s usually at the long end of a bacterium.

A new paper has started to describe the symbiotic relationship
between the bobtail squid and Vibrio fischeri. The bacterium is

bioluminescent, and lights up the squid when it is in the

moonlight so it doesn’t cast a shadow from below (predators

would find it that way). It turns out that flagella of the bacteria

give off LPS a toxin, and the concentration tells the squid when

to alter the biochemistry of its light organ to accommodate the

needs of the bacteria. They work together to keep them both alive.

For example, many Vibrio organisms are monotrichous. They have one flagellum located on one end of their cell body, and it propels tem forward or in a tumble. One organism, Vibrio cholerae, is especially important to humans as it causes the disease cholera. This organism has a sheathed flagella (cell membrane covers the flagellin protein polymer on the outside). It has been hard to study this since unsheathed mutants are nonfunctional. See the caption at right for more.

Lophotrichous bacteria (lopho = crested or tufted) have tufts of multiple flagella at one (polar lophotrichous) or both ends of the organism. Spirillum volutans is lophotrichous - but not always. When it divides, each of the progeny has just one tuft of flagella, since each daughter gets one end of the parent. As they grow longer and older, they develop the second tuft of flagella at the opposite end.

S. volutans was first described in 1900's. The unusually large

flagella made them visible by light microscopy, the only type they

had at the time. Most other flagella had to wait for electron

microscopy to be discovered. S. volutans is a spirillum, shaped sort

of like a spirochete, and the flagella make the body spin in the

opposite direction, just like the spirochetes. But the spirochete has

the flagella on the inside, and the spirillum has them on the outside.

I wonder if one evolved from the other.

The question then is how S. volutans regulates movement with a tuft at each end. An older study showed that there is a head type tuft and a tail tuft in terms of sensing chemicals. When the tufts reverse their rotation, the tail tuft becomes the head tuft. There are chemicals that can make each tuft rotate as the head, and then the organism doesn’t go anywhere. This could become important for stopping disease development.

If a bacterium has one flagellum at each end it is considered amphitrichous (amphi = both). A good example is Campylobacter jejuni, the causative organism of the most common type of gastroenteritis (diarrhea). C. jejuni causes more disease each year than Shigella and salmonella combined, about 3 million cases – mostly from poorly cooked chicken.

A 2014 study on C. jejuni flagella show that it has necessary genes that are not found in other types of bacteria. Campylobacter flagella are some of the most complex and the motility they control is very important for pathogenesis. This flagellar system is just another example of how flagella can’t be seen as evidence for intelligent design.

Peritrichous (peri = around) bacteria are hippies. They have flagella that stick out in all directions; no sense of order or grooming. The quintessential peritrichous organism is E. coli. All the flagella turn the same direction in a run, but when just one or a few switch direction, they start a tumble. Since these organisms sense chemicals from all directions, they switch from runs to tumbles quicker and more often. As a result, peritrichous organisms are often faster in both + and – chemotaxis.

Selenomonad bacteria are bean shaped, with a long axis. But their

tuft of flagella is located on the long side, not on an end. So why

do they travel along their long axis? It might have something to

do with the degree of turn in their hook, or the curve of the

bacterial cell.

Notice that we've been talking about bacteria that have a long axis and a short axis. Their flagella are usually on their end(s). But there are exceptions. Selenomonad bacteria are polar lophotrichous, but the flagella aren’t on a long end. It’s weird, because they still move along their long axis. You need to figure out how they do that.

And what about the cocci? A coccus type microorganism is round (coccus = berry in Greek). Most cocci are immotile, they get moved around instead of moving around. But it hasn’t hurt them, as cocci are found everywhere the other shaped bacteria are found.

Being round may have something to do with their immotility. Round objects aren’t best designed for movement in a single direction. Think about it, almost all animals are motile (except some sponges and the Tribbles on Star Trek), but have you ever seen a spherical animal?

Things that are longer than wide are usually best equipped for linear movement. And if you aren’t going to move linearly (up or down a gradient), what’s the point of moving at all? Therefore, most cocci are flagella-less. Fortunately for us, there are exceptions to the exceptions. Some cocci do have flagella and are motile. Often, the flagellated cocci are polar lophotrichous - like a bald guy with a ponytail.

I was surprised to find that the term “coccus” doesn’t just apply to bacteria, archaea can be coccal as well. This may not seem like a big deal, but remember that archaea and bacteria are as divergent from one another as we are from bacteria. The point is that “coccus” is just a description of a shape, it doesn’t have to mean bacteria. Coccolithophores are eukaryotic phytopklankton, and the genus “coccus” plants are berry-forming vines or shrubs.

On the top is an electron microscopic image of the magnetosome

chain inside a magnetotactic bacterium. See how they line up along

a field line? The bottom cartoon is one hypothesis of why they

developed this skill. Perhaps they can find the right concentration of

oxygen to sulfur by traveling just along the field line, not in three

dimensions. This is sort of like the electrical cable bacteria we talked

about last week.

Pyrococcus furiosus (rushing fireball) is a lophotrichous archaea with up to 50 flagella. They swim very fast when in their optimum temperature water, around 100˚C, hence their name. A 2006 paper showed that the flagella aren’t just for swimming, but also for cell-cell adhesion and adhering to surfaces, but more about this in the future.

In terms of the flagellated cocci, the most interesting exceptions are the magnetotactic cocci. Magnetotactic bacteria come in many shapes and sizes, and examples can be found in many different bacterial family trees.

What these differently shaped magnetotactic bacteria have in common is that they contain tiny magnetic organelles (yes, bacteria can have organelles, see this post). There are basically two types of magnetic organelles, based on what metal they contain, but both are generated by the bacterium sequestering the metal and then storing it in a granule.

Because they contain magnets, magnetotactic bacteria line up along the magnetic field lines of the Earth. This was noticed as early as 1963 when an Italian scientist studying some bacteria on slides noticed that certain types of them always pointed north/south.

Since we're talking about cocci at the moment, you may ask how something that is spherical can line up in a direction. Well, some of them are flagellated, so you can see a direction, some of them string together to form streptococci (strepto = line) along a magnetic line, and some that don’t attach to each other will still line up by the hundreds according to magnetic lines introduced by a strong, close magnet.

A recent study has found what might be the first peritrichous coccus, and it's magentotactic as well. This paper refers to them as MMP – multicellular magnetotactic prokaryotes. These particular microorganism are always found in strings of a dozen to three dozen and have flagella sticking out on all sides.

So last week and above we see that some bacteria can generate an

electrical current in oxygen and sulfur. A new study shows that

altering magnets can turn magnetotactic bacteria, which might

then be like the logic gates or 0/1 switches of a computer. I think

someone should be looking into building a completely bacterial

computer, with bacteria supplying the power and the circuitry.

Also a novelty, these new bacteria are the first magnetotactic bacteria known to have both types of magnetic granules; all others have one type or the other. The question - why have either type? What good does it do a bacterium to be aligned along the magnetic fields of the planet?

All the known magnetotactic bacteria, including all the coccal examples, are flagellated; therefore, it must be important for them to be motile. What’s the point of lining up with magnetic field lines if you just sit there, it should be involved in helping you get somewhere faster or better or putting you in a position to take advantage of something - so they’re all flagellated. The current hypothesis is that lining up with the field takes one plane of movement decision away from them, so they can move quickly toward food or oxygen. Sounds plausible.

Next week – not every flagellum is the same, so we need another name. Ever hear of an undulipodium?

Gao B, Lara-Tejero M, Lefebre M, Goodman AL, & Galán JE (2014). Novel components of the flagellar system in epsilonproteobacteria. mBio, 5 (3) PMID: 24961693

Zhang R, Chen YR, Du HJ, Zhang WY, Pan HM, Xiao T, & Wu LF (2014). Characterization and phylogenetic identification of a species of spherical multicellular magnetotactic prokaryotes that produces both magnetite and greigite crystals. Research in microbiology PMID: 25086260

Brennan CA, Hunt JR, Kremer N, Krasity BC, Apicella MA, McFall-Ngai MJ, & Ruby EG (2014). A model symbiosis reveals a role for sheathed-flagellum rotation in the release of immunogenic lipopolysaccharide. eLife, 3 PMID: 24596150

Khalil, I., & Misra, S. (2014). Control Characteristics of Magnetotactic Bacteria: Magnetospirillum Magnetotacticum Strain MS-1 and Magnetospirillum Magneticum Strain AMB-1 IEEE Transactions on Magnetics, 50 (4), 1-11 DOI: 10.1109/TMAG.2013.2287495

For more information or classroom activities, see:

A great video of chemotaxis, a neutrophil chasing a bacterium. One using chemotaxis to find, the other using it try and escape.

http://www.dnatube.com/video/4380/Neutrophil-Chemotaxis-Chasing-a-Bacterium

Magnetotactic bacteria –

http://commtechlab.msu.edu/sites/dlc-me/curious/caOc96SC.html

http://www.calpoly.edu/~rfrankel/mtbcalpoly.html

http://www.komeililab.org/videos.html

http://www.strangehorizons.com/2001/20010702/living_lodestones.shtml

https://www.youtube.com/watch?v=8N1U75qCg00

http://www.mpg.de/7592726/magnetotactic_bacteria-magnetite-nanoparticle

Bacterial flagellar chemotaxis –

http://jmbe.asm.org/index.php/jmbe/article/view/216/html_81

https://www.bio.cmu.edu/courses/03441/TermPapers/99TermPapers/TwoCom/chemotaxis.html

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3867774/

http://www.lessoncorner.com/Science/Biology/Microbiology/Bacteria

https://www.youtube.com/watch?v=Qk4vazjnCqU

https://www.youtube.com/watch?v=1wW2CZz6nM4

http://chemotaxis.biology.utah.edu/Parkinson_Lab/projects/ecolichemotaxis/ecolichemotaxis.html

https://www.google.com/?gws_rd=ssl#q=bacterial+chemotaxis&start=10

Flagellar arrangements-

http://www.life.umd.edu/classroom/bsci424/BSCI223WebSiteFiles/Flagella.htm

http://www.professorcrista.com/files/animations/posted_animations/flagella_arrange.html

http://web.biosci.utexas.edu/psaxena/MicrobiologyAnimations/Animations/BacterialMotility/PLAY_motility.html

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=18&ved=0CFoQFjAHOAo&url=http%3A%2F%2Ffaculty.sgc.edu%2Fcperkins%2F2215%2Fchapt04_lecture.ppt&ei=EP4IVJH4JdepyAS7-YH4DQ&usg=AFQjCNGYBgZE1QCxrlEYFCAL7n2zv8zW8A&sig2=vPDoBCikGwarZ8uFQjJQVw

http://microbeonline.com/bacterial-flagella-structure-importance-and-examples-of-flagellated-bacteria/

http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit1/prostruct/flag.html

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 –

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&ved=0CDUQFjAC&url=http%3A%2F%2Fibiochina.org%2Ftools%2Fbonnie-bassler%2Fbassler_lecture_notes_1.pdf&ei=ZnD7U-nYNcGfyASai4GYCw&usg=AFQjCNHRtcex_VMpi8T3JnXlVTtuypV2og&sig2=MMQOWP1Kh_v-XIpZC1dkwg&bvm=bv.73612305,d.aWw

http://www.hhmi.org/biointeractive/bacterial-quorum-sensing

http://www.pbslearningmedia.org/resource/oer08.sci.life.gen.bassler/talking-bacteria/

https://www.youtube.com/watch?v=YJWKWYQfSi0

http://www.hhmi.org/biointeractive/molecular-cascade-bacterial-quorum-sensing

http://highered.mheducation.com/olcweb/cgi/pluginpop.cgi?it=swf::500::500::/sites/dl/free/0073375225/594358/QuorumSensing.swf::Quorum%20Sensing

http://sciblogs.co.nz/infectious-thoughts/tag/quorum-sensing/

http://www.dnatube.com/video/12256/Biochemical-cascade-mechanism-how-bacterial-quorum-senses

http://www.ibiology.org/ibioseminars/microbiology/bonnie-bassler-part-1.html

http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit3/bacpath/quorum_sensing.html

http://www.pbs.org/wgbh/nova/body/bassler-bacteria.html

http://www.siemensstemacademy.com/index.cfm?event=showSearchResults&c=37&collname=EE92B302-1F29-3B68-E636-F81E6B003479&criteria=%20communicate&pageIndex=1&recordsPerPage=10

Biofilms –

http://www.bioone.org/doi/abs/10.1525/abt.2012.74.5.4?journalCode=ambt

http://www.colgateprofessional.com/patient-education/articles/what-is-biofilm

http://www.esep.umces.edu/modules/lf_lesson_plan/admin/index.php?adminaction=view&lp_id=96

http://vimeo.com/30571458

http://www.biofilm.montana.edu/category/resources/biofilm-structure

http://www.learner.org/courses/biology/archive/animations/hires/a_microb2_h.html

http://www.microbioncorp.com/biofilms/

http://www.authorstream.com/Presentation/Protikha-1610465-biofilm-sudesna/

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CCcQFjAB&url=http%3A%2F%2Ffaculty.weber.edu%2Fmzwolinski%2FMicrobialEcology%2FLabs%2FBiofilms.doc&ei=4277U-GFCIahyASF74KICg&usg=AFQjCNHOj6butQbupZuf0JRRP8RVgFBqXA&sig2=hW44Wd562kobz8Soz6vTiw&bvm=bv.73612305,d.aWw

http://thehomeschoolscientist.com/biofilm-experiment/

http://www.stemmom.org/2012/07/biofilm-lab-controlling-growth-on.html

http://www.flinnsci.com/store/Scripts/prodView.asp?idproduct=21841

http://www.microbelibrary.org/library/resources/3867-a-laboratory-class-exploring-oral-biofilms-and-the-contamination-of-toothbrushes

http://www.biofilm.montana.edu/

http://www.mdsg.umd.edu/topics/k-12-lesson-plans/biofilms-and-biodiversity

Bacterial swarming -

https://www.youtube.com/watch?v=q27Jn3h4kpE

http://www.rowland.harvard.edu/labs/bacteria/movies/

http://nautil.us/blog/the-pretty-bacterial-dance-that-may-help-prevent-infections

http://www.samachar.com/Bacteria-swarms-could-inspire-new-generation-of-smart-robots-llxaMCihdij.html

http://www.popsci.com/science/article/2010-06/scientists-crack-chemical-code-controls-bacterial-swarm

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=38&ved=0CGMQFjAHOB4&url=http%3A%2F%2Fcnls.lanl.gov%2Fq-bio%2Fwiki%2Fimages%2Fb%2Fbe%2F10_097_abstract.pdf&ei=TXT7U-DjEMeoyASF3YLoAw&usg=AFQjCNGW7ss0YYx34gYyuk5_-er038SxeQ&sig2=5B7SQCgS_wGxIqBw7hvTCA&bvm=bv.73612305,d.aWw

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:
http://www.rowland.harvard.edu/labs/bacteria/movies/

Bacterial motility -

http://education-portal.com/academy/lesson/flagellum-bacterial-cell-function-definition-quiz.html#lesson

http://www.microbiologybytes.com/video/motility.html

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0CCQQFjAB&url=http%3A%2F%2Fwww.flinnsci.com%2FDocuments%2FdemoPDFs%2FBiology%2FBF0508.00.pdf&ei=aLXzU7SMLJCdygSNrILABw&usg=AFQjCNH6_ocjQR1Svs5oHKPi8x_IarceAw&sig2=LXjUVTWKscHTu1o16S3wFg&bvm=bv.73231344,d.aWw

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=5&ved=0CDsQFjAE&url=http%3A%2F%2Fwww.ableweb.org%2Fvolumes%2Fvol-24%2F8-christopher.pdf&ei=aLXzU7SMLJCdygSNrILABw&usg=AFQjCNFHnyMvjUO_8io5fL21UtqNqCrvBA&sig2=n6AsvprT8R2PvVDQkUkqDw&bvm=bv.73231344,d.aWw

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=7&ved=0CEoQFjAG&url=http%3A%2F%2Fwww.professorcrista.com%2Ffiles%2Flab_PDFs%2FLE7_Microbial_Motility.pdf&ei=aLXzU7SMLJCdygSNrILABw&usg=AFQjCNGH2YMZPwyhNVseGZs-uRxZNfI5Gw&sig2=JHbC_8LUs92NI1o0Jwoe5Q&bvm=bv.73231344,d.aWw

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CB0QFjAA&url=http%3A%2F%2Fmicrobes.arc.nasa.gov%2Fdownload%2Fpdf%2FCyanobacteria_Races.pdf&ei=zLXzU9-iMIH3yQSA1IHYAg&usg=AFQjCNHixMa3A4kF5SkFmWvqEY9zngr70A&sig2=D32jBxU691BIDChFGYNotQ&bvm=bv.73231344,d.aWw

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=11&ved=0CFcQFjAK&url=http%3A%2F%2Fjmbe.asm.org%2Findex.php%2Fjmbe%2Farticle%2FviewFile%2F625%2Fpdf&ei=zLXzU9-iMIH3yQSA1IHYAg&usg=AFQjCNHI17pWcqQpuoq9WS-k3hAltGIxwQ&sig2=LjwaPotaTtgaowL-39e6mw&bvm=bv.73231344,d.aWw

http://www.scienceprofonline.com/microbiology/bacterial-colony-morphology-identification-unknown-bacteria.html

http://faculty.ccbcmd.edu/~gkaiser/Cool%20Things%20PDC_2014/contactcell_flag.html

http://web.biosci.utexas.edu/psaxena/MicrobiologyAnimations/Animations/BacterialMotility/PLAY_motility.html

http://highered.mheducation.com/sites/007337525x/student_view0/exercises_35-90/bacterial_locomotion.html