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    Social Skills Are Key To Bacterial Evolution
    By Catarina Amorim | December 13th 2012 05:03 AM | 6 comments | Print | E-mail | Track Comments
    About Catarina

    After many years as a scientist (immunology) at Oxford University I moved into scientific journalism and public understanding of science. I am...

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    Bacteria have lived for millions of years in our planet where, with an impressive capability to adapt, they now colonize virtually every environment, including us. But as tiny one-cell organisms they had to learn to work together to be powerful enough to act on the environment and other organisms. And now, new research has discovered that their evolution is triggered exactly by these interactions, as scientists from Centre for Environmental Biology at the University of Lisbon in Portugal and the Institute Pasteur in Paris show that bacteria’s genes for secreted proteins - the ones that mediate the interactions with the outside - evolve faster than any others in the genome. 

    The fast changing pace of these secreted proteins also suggests that they are the basis for bacterial adaptation, and should be the first stop for researchers looking for new ways to fight bacterial infection, exploit their resources or simply trying to understand these organisms better. 

    Scanning electron micrograph of an antibiotic resistant Staphylococcus bacteria by Janice Haney Carr with the higher resolution of transmission electron microscopy would be seen the thickening of the cell wall that is responsible for the reduced susceptibility to antibiotics

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    It has become clear, that though we can be killed by bacteria we cannot live without them either. From stimulating our immune system, provide vitamins that we cannot synthesize, affect diabetes and obesity to even protect us against other pathogens, bacteria can be both for or against us. The increasing awareness of this always-present relationship has turned more urgent than ever the need to understand better these microorganisms so we could tip the balance in our favor when necessary.  

    And the core of any bacterium's life is the secretome – bacteria’s secreted proteins that mediate their relationship with the outside world and have functions as diverse as capturing food, changing the environment to suit bacteria’s needs or interacting with other organisms. What is particularly interesting with this approach to the outside is that is has a crucial problem – once secreted these proteins become “public goods” available to be exploited by any organism in the vicinity. And if the “freeloaders” cannot be stopped, the bacteria producing proteins can be driven to extinction and replaced by the cheaters.

    A strategy to avoid this - seen for example in Escherichia coli a common bacterium in humans – is to make the secretome genes highly mobile using horizontal gene transfer, a non-sexual process where genes “jump” from one individual to another. As the secretome genes (also called social genes due to their role in bacteria-bacteria interaction) spread to other bacteria, the population producing proteins increases reducing freeloaders’ numbers until their stealing no longer matters. 

    But genes with high mobility also have high chances of being lost or changed as they leave a genome to enter other. And this - together with the evolutionary competition (where a species evolve as result of having to escape or pursue other) occurring between bacteria and their hosts, parasites or predators – made researchers Teresa Nogueira, Marie Touchon and Eduardo P. C. Rocha  think that social genes should be under strong evolutionary pressure to change rapidly and, as such, vital in bacteria’s evolution.

    To test this hypothesis they looked at more than 400 bacterial genomes, many pathogenic for humans, first grouping them according to their genetic similarities and common ancestors, to then compare their genes according to the localization (inside and outside of the cell) of their proteins. They found that although only a small part of the bacterial genome produced secreted proteins, its size was relatively constant and not dependent of the bacterial genome size with this consistency suggesting an important role for the organism.

    Next, thry searched for the social genes within the genome and, confirming their suspicions, these were located in its most mobile parts: the accessory genome (a supernumerary part of the genome where there are no genes essential for survival) and the plasmid (a piece of extra DNA outside of the chromosomes).

    Not only that but they also found that social genes existed only in some bacteria species within a group indicating they had appeared recently (otherwise they would have had time “jump” into the other species), supporting the idea that these were genes changing rapidly. But were they changing faster than the rest of the genome?

    To answer that the researchers looked for orthologous proteins (proteins in different species that originated from a common ancestor), comparing their rate of change in the secretome with the rest of the genome. Again, not only secreted proteins had higher rates of change, but they also showed a type of change, called non-synonymous substitutions, that is known to lead to proteins with new biological functions.

    In conclusion, social/secretome genes not only are localized in the most mobile parts of the genome, but they also show signs of accelerated change and of having evolved to produce new proteins recently supporting the idea that they are crucial in bacterial adaptation.

     “Remarkably what our work shows,” says Nogueira, “is that cell localization shapes genome evolution. Bacteria evolution is triggered by the interaction with neighboring bacteria, by what they are producing and releasing to the surroundings (the secretome). Most importantly, this also means that the repertoire of genes coding for secretome can be seen as a therapeutic target for the control of bacterial infection. And with resistance to antibiotics already considered one of the greatest threats of modern health, all help is welcome.”

    Journal article

    Nogueira T, Touchon M, Rocha EPC, Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria,  (2012) PLoS One 7(11): e49403. doi:10.1371/journal. pone.0049403  http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0049403 

    Comments

    Bonny Bonobo alias Brat
    Very interesting article Catarina. In the opening paragraph you say that :-
    Bacteria have lived for millions of years in our planet where, with an impressive capability to adapt, they now colonize virtually every environment, including us. But as tiny one-cell organisms they had to learn to work together to be powerful enough to act on the environment and other organisms. And now, new research has discovered that their evolution is triggered exactly by these interactions...that bacteria’s genes for secreted proteins - the ones that mediate the interactions with the outside - evolve faster than any others in the genome. 
    Earlier today I watched a minutephysics or was it a 'Smarter every day' YouTube answering the question 'Is there poop on the Moon?' and the answer was a resounding 'yes'. Not only poop and the trillions of bacteria it contains but also urine, food waste, used towels and paper, cameras, batteries and much more were left behind by the astronauts. At the end of the YouTube video the presenter goes to a science museum and cuts open one of the 60 year old poop bags that did return from the space mission to investigate its contents. It would be interesting to know what was happening to the trillions of bacteria that we have left behind on the moon wouldn't it? Have they managed to start to colonize the moon yet or have they just formed bacterial endospores? Wiki describes how resilient these endospores can be :-
    Certain genera of Gram-positive bacteria, such as Bacillus,  Clostridium,  Sporohalobacter,    Anaerobacter and Heliobacterium, can form highly resistant, dormant structures called endospores.
    Endospores show no detectable metabolism and can survive extreme physical and chemical stresses, such as high levels of UV light, gamma radiation, detergents, disinfectants, heat, freezing, pressure and desiccation.[72] In this dormant state, these organisms may remain viable for millions of years,[73][74] and endospores even allow bacteria to survive exposure to the vacuum and radiation in space.[75] According to scientist Dr. Steinn Sigurdsson, "There are viable bacterial spores that have been found that are 40 million years old on Earth — and we know they're very hardened to radiation."
    Could the rudiments of bacterial life now be evolving on the Moon thanks to man's visits there?
    My article about researchers identifying a potential blue green algae cause & L-Serine treatment for Lou Gehrig's ALS, MND, Parkinsons & Alzheimers is at http://www.science20.com/forums/medicine
    amorca

    Hummm, I don't really know that much of bacteria Helen  but from what I know they need water to reproduce so I don't think there are much chances of them being around as there is no water on the moon, at least on the surface.
    Bonny Bonobo alias Brat
    Actually Catarina, according to many sources, including the universetoday website there is water on the moon :-
    Three different spacecraft have confirmed there is water on the Moon. It hasn’t been found in deep dark craters or hidden underground. Data indicate that water exists diffusely across the moon as hydroxyl or water molecules — or both — adhering to the surface in low concentrations. Additionally, there may be a water cycle in which the molecules are broken down and reformulated over a two week cycle, which is the length of a lunar day. This does not constitute ice sheets or frozen lakes: the amounts of water in a given location on the Moon aren’t much more than what is found in a desert here on Earth. But there’s more water on the Moon than originally thought. Read more at :-   http://www.universetoday.com/41212/yes-theres-water-on-the-moon/#ixzz2FOPiVz6y
    My article about researchers identifying a potential blue green algae cause & L-Serine treatment for Lou Gehrig's ALS, MND, Parkinsons & Alzheimers is at http://www.science20.com/forums/medicine
    amorca

    That's where my "on the surface" comment came from. 
    But I am not sure if that composition will work for bacteria - when we talk about their needs the word used is "moist". And they come from earth so not sure how happy they will be with a different chemical source of water. They can adapt but they need to reproduce a few times first.But to be honest Helen all this is purespeculation, I don't know enough of bacteria to bee able to make an educated prediction
    Bonny Bonobo alias Brat
    I don't know enough of bacteria to bee able to make an educated prediction
    I'm not sure that anyone knows enough yet about bacteria's ability to adapt and reproduce on other planets to be able to make educated predictions. Hopefully I'm wrong!
    My article about researchers identifying a potential blue green algae cause & L-Serine treatment for Lou Gehrig's ALS, MND, Parkinsons & Alzheimers is at http://www.science20.com/forums/medicine
    Bonny Bonobo alias Brat
    Also, according to this NASA article 'space historians will recall that the journey to the stars has more than one life form on its passenger list: the names of a dozen Apollo astronauts who walked on the moon and one inadvertent stowaway, a common bacteria, Streptococcus mitis, the only known survivor of unprotected space travel.' :-
     As Marshall astronomers and biologists met recently to discuss biological limits to life on Earth, the question of how an Earth bacteria could survive in a vacuum without nutrients, water and radiation protection was less speculative than might first be imagined. A little more than a month before the forthcoming millennium celebration, NASA will mark without fanfare the thirty year anniversary of documenting a microbe's first successful journey from Earth.

    The Surveyor probes were the first U.S. spacecraft to land safely on the Moon. In November, 1969, the Surveyor 3 spacecraft's microorganisms were recovered from inside its camera that was brought back to Earth under sterile conditions by the Apollo 12 crew.

    The 50-100 organisms survived launch, space vacuum, 3 years of radiation exposure, deep-freeze at an average temperature of only 20 degrees above absolute zero, and no nutrient, water or energy source. (The United States landed 5 Surveyors on the Moon; Surveyor 3 was the only one of the Surveyors visited by any of the six Apollo landings. No other life forms were found in soil samples retrieved by the Apollo missions or by two Soviet unmanned sampling missions, although amino acids - not necessarily of biological origin - were found in soil retrieved by the Apollo astronauts.)

    How this remarkable feat was accomplished only by Strep. bacteria remains speculative, but it does recall that even our present Earth does not always look as environmentally friendly as it might have 4 billion years ago when bacteria first appeared on this planet.

    My article about researchers identifying a potential blue green algae cause & L-Serine treatment for Lou Gehrig's ALS, MND, Parkinsons & Alzheimers is at http://www.science20.com/forums/medicine