Bacteria, formation of complex multicellular life and moving

[William Gaatjes]

I was thinking this morning about research that bacteria have collective behaviour to control their environment.
This a bit of a daring thought :
Since the formation of multicellular lifeforms and improved ways of movement, i am wondering if bacteria would stimulate this evolution in an indirect way with the use of natural selection. Notice, i do not mean bacteria steered this intelligently, but through evolution because it is the best coarse to take in the following situation. I am not talking about intelligent conscience bacteria. I am talking about the result of complex collective behaviour. Because the advantage would be to have a means to move faster away from a threat like heat or chemicals. Such situations could occur near volcanoes. And it seems that the ground around erupting volcanoes( on land but also in the sea) is always very nutricious for plants and bacteria. A fast way to move around would be handy. As predators evolve, this would speed up evolution to move faster and faster away from the predator.

Any thoughts ?

 

[cKGunslinger]

The problem with natural selection is that it has to reduce down, and at the cellular level , you hit the issue of irreducible complexity.

No one part of any movement-inducing mechanism would be particularly advantageous (evolutionary-speaking,) so there would be no reason that any of those mechanism would have time to stick around and eventually assemble into some flagellum-like motor.

This doesn't necessarily point to intelligent design, as some claim, but it does point out some weaknesses in pure evolutionary theory - a weakness that Darwin himself anticipated and had no answer for.

Evolution, to me, seems like Newtonian physics. It's a pretty good working solution and gets us a 99% answer, but exhibits real issues the smaller you get.

So while I get your point in this case, I always bring the conversation down one level - how did the bacteria itself develop its collective behavior and motility?

 

[Gibsons]

IMO, it's a misconception that the first cells were bacteria. There's certainly evidence that the first living things had some very significant differences from current bacteria. Or to be properly HT, the earliest things that we can trace current lineages to.

The bacterial flagella (as we know it) isn't necessarily derived from the mechanisms used by the first unicellular organisms. They might've used something else, maybe something that's not even around anymore or that has a very different function now.

As for going multicellular, one simple thing to think about - given two rod shaped cells that swim based on some sort of polar motor, give them a way to stick together (not hard, proteins tend to be sticky anyway), and they can then swim faster and more efficiently than one alone, just by reducing total surface area. Now, they need to have the motors not interfere with each other and they need to stick together in the right way, but that doesn't seem difficult.

 

[William Gaatjes]

The problem with natural selection is that it has to reduce down, and at the cellular level , you hit the issue of irreducible complexity.

No one part of any movement-inducing mechanism would be particularly advantageous (evolutionary-speaking,) so there would be no reason that any of those mechanism would have time to stick around and eventually assemble into some flagellum-like motor.

This doesn't necessarily point to intelligent design, as some claim, but it does point out some weaknesses in pure evolutionary theory - a weakness that Darwin himself anticipated and had no answer for.

Evolution, to me, seems like Newtonian physics. It's a pretty good working solution and gets us a 99% answer, but exhibits real issues the smaller you get.


So while I get your point in this case, I always bring the conversation down one level - how did the bacteria itself develop its collective behavior and motility?

First let me disclaim that this is my opinion based on what i have read and concluded from that information.


I have read something about how the flagella have been created. And is quite spectacular because the engine is actually an rotating biological system doing 360 degrees rotation. Imagine if our joints where able to do 360 rotations with out causing damage.

I have some information here :

http://www.cartage.org.lb/en/themes...cellstructure/CiliaFlagella/CiliaFlagella.htm


http://www.nanonet.go.jp/english/mailmag/2004/011a.html

Nature created a rotary motor with a diameter of 30 nm. Motility of bacteria, such as Salmonella and E. coli with a body size of 1 ~ 2 microns, is driven by rapid rotation of a helical propeller by such a tiny little motor at its base. This organelle is called the flagellum, made of a rotary motor and a thin helical filament that grows up to about 15 microns. It rotates at around 20,000 rpm, at energy consumption of only around 10-16 W and with energy conversion efficiency close to 100%;. Prof. Namba’s research group is going to reveal the mechanism of this highly efficient flagellar motor that is far beyond the capabilities of artificial motors.

The flagellum is made by self-assembly of about 25 different proteins. The rotor ring made of protein FliF is the first to assemble in the cytoplasmic membrane. Then, other protein molecules attach to the ring one after another from the base to the tip to construct the motor structure. After the motor has been formed, the flagellar filament, which functions as a helical propeller, is assembled. Precise recognition of the template structure by component proteins allows this highly ordered self-assembly process to proceed without error. The flagellar filament is made of 20,000 to 30,000 copies of flagellin polymerized into a helical tube structure. Flagellin molecules are transported through a long narrow central channel of the flagellum from the cell interior to the distal end of the flagellum, where they self-assemble in a helical manner by the help of a cap complex. The cap is pentameric complex made of HAP2 and has a pentagonal plate and five leg domains, whose flexible stepping movements accompanied by rotation of the whole cap is the key mechanism to promote the efficient self-assembly of flagellin molecules by preparing just one binding site of flagellin at a time and guiding the binding.

Even though the filament is a polymer of chemically identical molecules, it conforms a supercoiled structure. By using electron cryomicroscopy and X-ray fiber diffraction, Prof. Namba’s group has discovered that the flagellar filament consists of 11 strands of protofilaments with two slightly different conformations, named L and R types. The repeat distance observed in the structure of the L-type protofilament is 5.27 nm, while it is 5.19 nm in the R-type, the difference being only 0.08 nm. The mixture of protofilaments with the different lengths produces the helical tube structure of the filament.

Bacterial cells swim actively by rotating a bundle of flagella. The motor switches its direction every few seconds to change the swimming direction of the cells for bacteria to seek better environments. Reversal of the motor rotation causes a structural change of the flagellar filament from the left-handed to the right-handed helical form. This makes the flagellar bundle fall apart, propelling force imbalanced, leading to changes of the swimming direction. The switch that triggers this change in the helical form of the filament has been found in the atomic structure of flagellin obtained by X-ray crystallographic analysis. When the twisting force produced by quick reversal of the motor rotation is transmitted to the protofilaments, part of flagellin undergoes a slight change in its conformation, thereby making a few of the 11 protofilament strands transform from the L-type into the R-type. As a result, normally left-handed flagellar filament turns into right-handed helical forms. Prof. Namba’s group tried to understand the switching mechanism responsible for these structural changes. To analyze the structure in atomic detail by X-ray crystallography, flagellin had to be crystallized. However, its strong tendency of polymerization made the crystallization difficult. It took ten years for them to finally crystallize flagellin and analyze the structure to find out the switch mechanism, for which a super brilliant X-ray beam from SPring-8 beamlines was essential.

Prof. Namba first saw an electron micrograph of the bacterial flagellum and its motor when he was a graduate student. He was surprised to see such complex and sophisticated structure exist in living organisms. It impressed him deep enough to switch his research from muscle to flagella after a while. “Looking at the shape of the flagellar basal body, it is obviously designed to rotate. Looking at a picture of the flagellar motor on the wall every day, I feel up towards revealing the mystery by any means.” The design concepts of protein molecules to realize various functional mechanisms by their three-dimensional architecture are quite different from those we design by our engineering technique with bulk materials. Folding of single polymer chain into some three-dimensional structures gives a huge amount of freedom and flexibility in both function and structure. Individual atoms are used as functional parts, and this is the essential feature that makes biological macromolecules distinct from artificial machines at present. The design concepts have to be well understood and learned for future nanotechnology applications. So far, for the flagellar motor, the deeper our insights get into the mechanism, the deeper the mystery becomes. Now the mystery of conformational switching of the filament has been solved, and in terms of the number of protein molecules, the filament makes up 99% of the entire flagellum, it does not mean 99% of the mystery is solved. It is the motor mechanism that is even more difficult to understand.

When Prof. Namba’s group attached a 40 nm fluorescence bead to the flagellar motor and observed the motor rotation, the group was surprised to see large and rapid fluctuations of the rotation speed. The key to revealing the mystery of the motor must be hidden behind the thermal fluctuation of the protein structure, which is still so far from understanding. “The atoms constituting proteins do fluctuate but the average positions of individual atoms are very precisely determined with an accuracy of sub-angstrom level. That is why individual proteins can properly identify partner molecules to bind and get assembled into the higher order structures of living organisms. The fluctuations of protein structure, that’s what makes living organisms function in such sophisticated and well regulated ways. I am willing to dedicate my entire life to the hard work unveiling the mysterious world of protein structure and function.”

But the origin of flagella and cilia and the rotary engine is in my opinion an event where a phage virus and a bacteria got into a strange situation. A virus locked into the exoskeleton of a bacteria. During division something happened causing the dna to be mutated. This leak in the exoskeleton eventually evolved into some electrically polarized paddle movement, only later to be replaced by a rotary engine. This happened in a fluid because the rotary engine was more efficient then having a paddle. And the peddle was already an advantage over moving while using electrostatic atomic noise. It is all based on being the first to the food. Afcourse, there was no intelligence as such behaving in such a way is the only way to survive. That is until the life form get's to abundant as an collective and starts to become like a predatory virus. Destroying everything in it's path only to destroy itself in the end. It is all about balance. Furthermore, simple electrostatics is enough to move. As Gibsons possible example . Take for example the H2O molucule . It is electrically polarized. If i remember correctly all of the biological molecules are polarized when used and are made neutral when not used. At least that is how it should go. In reality there is broad band spectrum radiation everywhere messing around and even gravity fluctuation have to some degree an effect. However when these factors are not around, life would NOT exist. Rules of the current universe.




Virus phages can actually be used as a way of communication. I think that the bacterial language is an evolved effect of waste products and phages. The waste product gives information about the bacteria and the phages give also information about bacteria.

For example bacteria B eats the metabolism by products(waste products) of bacteria A. As such it is for bacteria B advantage to stay close to bacteria A.


About the origin of life :

There is ongoing research about the speed of chemical reaction in biological systems. It will come as no surprise that the speed is based on physical rules. Most of these biological reactions on atomic level seem to reach levels approaching speed of light levels but only on a small scale afcourse when atom's can "see" each other. It is all about self assembly. And self assembly is based on the behaviour of atom's and the preferences of atom's when at a certain energy(excitation) level.

Quantum mechanics and the standard model: It is not a description of how matter(waves) actually function. But it will be very useful to explain how life in nature works( yes even viruses as well). Because life follows certain physical rules. Now quantum mechanics or the standard model will not make superconduction at room temperature or fusion happen. (If these two examples will happen in these fields, it will be of accidental discovery and not based on QM theories). But i have to stress that QM and the standard model describe some aspects and not all. However, atom's have a certain way of behaviour as actually is discovered with all the QM and standard model research. This behaviour is at the current age of the universe everywhere the same as described more or less in QM. This behaviour you can see as rules. And these rules are very favourite towards life. As such, you could say that where there are certain elements and the space time aether has a constant distortion ( meaning over longer periods of time when multiple atom processes take place and have the same result), life will exist. Now where did the atom's come from ? Stars is the answer. Where did the accumulation of matter to form stars from, come from ? Primordial Black holes. Where did the primordial black holes come from ? standing wave Ripples in the space time aether during the inflation, Creating circular(in 3d spherical) wave patterns similar as throwing a rock into a pond. Effectively behaving like a true large scale single particle for a short timespan, only to cease existing again and as such a cooler universe will result and star formation can begin . Where did the big bang come from ? Well, here we enter the realm of philosophy and the naturally human desire of spawning a religion based on an entity with infinite knowledge and existing on infinite positions(this implies automagically that this happens at the same moment in time and at any moment in time, as such making time non existing).This is actually the evolved natural desire of the human mind to accomplish. The human brain likes to be aware of it's surroundings, it feels save and secure if this is the case.



A phage on a bacteria :

Self assembly of the flagellum and the rotary engine :

 

[William Gaatjes]

I just learned about another way movement for a bacteria : The grappling hook method.

The pilus are hair like structures that can be used to to stick to surfaces to transfer dna. But a sequential formation of pilli in a direction can create motion.


http://en.wikipedia.org/wiki/Pilus

IV pili

Some pili, designated type IV pili, generate motile forces.[3] The external termini of the pili adhere to solid substrate, either the surface to which the bacteria are attached or to other bacteria, and subsequent pilus contraction pulls the bacteria forward, not unlike a grappling hook. As type IV pilus-mediated movement is typically jerky, it is called twitching motility, as distinct from other forms of bacterial motility, such as are mediated by flagella. However,some bacteria, for example Myxococcus xanthus, exhibit gliding motility. Bacterial type IV pilins are similar in structure to the component flagellins of Archaeal flagella.[4]

http://www.bookrags.com/research/bacterial-movement-wmi/

Some more about motion :

Bacterial movement refers to the self-propelled movement of bacteria. This movement is also referred to motility. The jiggling movement seen in some nonmotile bacteria that are incapable of self-propelled movement is due to the bombardment of the bacteria by water molecules. This so-called Brownian motion is not considered to represent bacterial movement.


There are several types of bacteria movement. The most common occurs by the use of appendages called flagella. A bacterium can contain a single flagellum, several flagella located at one or both poles of the cell, or many flagella dispersed all over the bacterial surface. Flagella can rotate in a clockwise or counterclockwise direction. When the motion is counterclockwise, even multiple flagella can unite into a flagellar bundle that functions as a propeller. This occurs when the bacterium is moving towards a chemical attractant or away from a repellent in the behavior known as chemotaxis. If the flagella turn in the opposite direction, the coordinated motion of the flagella stops, and a bacterium will "tumble," or move in an undirected and random way.

Spirochaete bacteria have flagella that are internal. These so-called axial filaments provide the rigidity that enables the spiral bacterium to twist around the axis of the filament. As a result, the bacterium literally screws itself through the fluid. Reversal of the twist will send the bacterium in a reverse direction. Examples of bacteria that move in this manner include Treponema pallidum and Rhodospirillum rubrum.

The bacteria that are known as gliding bacteria exhibit another type of bacterial movement. One example of a gliding bacterium is the cyanobacterium Oscillatoria. Gliding movement is exactly that; a constant gliding of a bacterium over a surface. The basis of this movement is still not clear, although it is known to involve a complex of proteins.

In a human host, disease causing bacteria such as Salmonella typhymurium can move along the surface of the host cells. This movement is due to another bacterial appendage called a pilus. A bacterium can have numerous pili on its surface. These hair-like appendages act to bind to surface receptors and, when retracted, pull the bacteria along the surface. Movement stops when a suitable area of the host cell surface is reached.

The bold part is interesting. Because it has the machinery of the flagella on the inside. If i understand correctly, the entire bacteria changes it's shape to create movement by over and under pressure like a screw in water or a wing of a plane in the air.
Some more information.
http://en.wikipedia.org/wiki/Spirochaete

The cursive text seems to me to imply some form of electrostatic movement. Like a linear motor but with electric charges instead of magnetic fields.

 

[artvscommerce]

The problem with natural selection is that it has to reduce down, and at the cellular level , you hit the issue of irreducible complexity.

No one part of any movement-inducing mechanism would be particularly advantageous (evolutionary-speaking,) so there would be no reason that any of those mechanism would have time to stick around and eventually assemble into some flagellum-like motor.

This doesn't necessarily point to intelligent design, as some claim, but it does point out some weaknesses in pure evolutionary theory - a weakness that Darwin himself anticipated and had no answer for.

Evolution, to me, seems like Newtonian physics. It's a pretty good working solution and gets us a 99% answer, but exhibits real issues the smaller you get.

So while I get your point in this case, I always bring the conversation down one level - how did the bacteria itself develop its collective behavior and motility?

Please read...

"Scientists regard this argument as having been disproved in the light of research dating back to 1996 as well as more recent findings.[60] They point out that the basal body of the flagella has been found to be similar to the Type III secretion system (TTSS), a needle-like structure that pathogenic germs such as Salmonella and Yersinia pestis use to inject toxins into living eucaryote cells. The needle's base has ten elements in common with the flagellum, but it is missing forty of the proteins that make a flagellum work.[61] Thus, this system negates the claim that taking away any of the flagellum's parts would render it useless. On this basis, Kenneth Miller notes that, "The parts of this supposedly irreducibly complex system actually have functions of their own."

 

[William Gaatjes]

Please read...

"Scientists regard this argument as having been disproved in the light of research dating back to 1996 as well as more recent findings.[60] They point out that the basal body of the flagella has been found to be similar to the Type III secretion system (TTSS), a needle-like structure that pathogenic germs such as Salmonella and Yersinia pestis use to inject toxins into living eucaryote cells. The needle's base has ten elements in common with the flagellum, but it is missing forty of the proteins that make a flagellum work.[61] Thus, this system negates the claim that taking away any of the flagellum's parts would render it useless. On this basis, Kenneth Miller notes that, "The parts of this supposedly irreducibly complex system actually have functions of their own."

Thank you. Very interesting. ^_^

Is by any chance this needle like structure related to the structures used by T4 phages or other phages ? Meaning sharing the same proteins and self assembly principle ?

When i read this and understand it correctly, i would think so but i am not sure :

http://www.pnas.org/content/96/17/9845

Salmonella typhimurium employs the specialized type III secretion system encoded in pathogenicity island 1 (SPI1) to translocate effector proteins into host cells and to modulate host cell signal transduction. The SPI1 type III system and the effector proteins are conserved among all salmonellae and are thought to be acquired by horizontal gene transfer. The genetic mechanisms mediating this horizontal transfer are unknown. Here, we describe that SopE, a SPI1-dependent translocated effector protein, is present in relatively few S. typhimurium isolates. We have isolated a temperate phage that encodes SopE. Phage morphology and DNA hybridization, as well as partial sequence information, suggest that this phage (SopE&#934 is a new member of the P2 family of bacteriophages. By lysogenic conversion this phage can horizontally transfer genes between different S. typhimurium strains. Strikingly, most of the isolates harboring SopEΦ belong to the small group of epidemic strains of S. typhimurium that have been responsible for a large percentage of human and animal salmonellosis and have persisted for a long period of time. Our data suggest that horizontal transfer of type III dependent effector proteins by lysogenic infection with bacteriophages (lysogenic conversion) may provide an efficient mechanism for fine-tuning the interaction of Salmonella spp. with their hosts.

I have more here :

http://bilbo.bio.purdue.edu/~viruswww/Rossmann_home/publications/pdfs/425.pdf