Why Should You Care How Bacteria Fight Viruses?

Regular readers have been learning a great deal about the human immune system thanks to our ongoing series on allergies by Julia van Rensburg. But did you know that bacteria have an immune system of sorts, too? Yes, even germs get germs!* Bacteria are susceptible to a group of viruses called bacteriophages, or phages for short. Phages resemble early spacecraft and “land” on the surface of bacteria in order to inject their DNA/RNA, much like a syringe ejects its contents.

Houston, we have a problem! A phage has just injected its DNA into our cell!

Bacteria, which have been on Earth for some 3.5 billion years, have had plenty of time to evolve defense mechanisms against predatory phages. Just like human viruses, phages are a most unwelcomed guest. They barge into the cell unannounced, “borrow” cellular components without asking, and then use them to make baby viruses until the cell becomes so engorged with viral progeny that it explodes, releasing the huge viral family so that it can invade more bacteria and repeat the process all over again. Phages that burst the bacterium like this are called “lytic”, but there are other types that don’t blow the house up. These are referred to as “lysogenic” phages and can insert their genetic material into the bacterial genome, becoming a permanent resident of that bacterium. Even more sinister, the incorporated viral genome is copied like all the other bacterial genes when the bacterium divides, so it is inherited by the daughter cell!

Lytic phages will replicate until they blow the infected bacteria apart. In contrast, lysogenic phages can stick around forever, even getting passed on to future generations since the viral genome was inserted into the bacterial genome.

So that sucks – imagine if you had uninvited viral DNA shoved into your DNA – such viruses basically transform you into a GMO. Sorry to inform you, but up to 8% of your genome is already littered with lots of viral DNA. If you oppose GMOs, I hope you can still stand to be in your own skin!

Presently, we don’t know how to remove foreign DNA from our own. But bacteria have figured out a way to get rid of incoming phage DNA, which provides the basis for a type of bacterial immune system.

 

Some combinations work great together, like chocolate and peanut butter. But getting viral DNA stuck into your own DNA, a strategy used by many viruses including HIV, is not a welcome combination.

In 1987, scientists uncovered unusual repeat sequences in the genome of E. coli bacteria, which were later named “clustered regularly interspaced short palindromic repeats”, or CRISPR. In the early 2000s, scientists identified bacterial proteins interacting with CRISPR sequences (now called CRISPR-associated (Cas) proteins) and discovered that they provide resistance to phage infection. Through the efforts of many laboratories, it is now known that bacteria can use a phage invasion as a vaccination by incorporating some of the foreign DNA between CRISPR repeat sequences. This provides the bacteria with a “catalogue” – a memory system, if you will – of foreign DNA that it can pass along to future generations.

But CRISPR is not just a storage system. The bacteria can retrieve these sequences and hook them to Cas9, a nuclease enzyme that can cut DNA. When foreign DNA enters that bacteria, its CRISPR-Cas9 system can specifically target the invasive element and neutralize it.


Foreign DNA, such as that injected by a phage, can be neutralized by CRISPR/Cas9, which serves as a type of bacterial immune system. Bacteria can store foreign DNA sequences in its genome and express them as crRNAs that bind to Cas9. If the bacterium encounters foreign DNA that matches any of the sequences stored in its CRISPR array, the crRNA will deliver Cas9 to that invading sequence to chop it up.

Pretty clever for tiny bacteria, huh? But here is where things get really interesting, or worrisome, depending on your appetite for paranoia. Scientists have adapted CRISPR/Cas9 to work in all sorts of cell types, including human. Cas9 acts as DNA shears that can cut wherever we tell it to by directing it with a “guide RNA” (analogous to how a crRNA operates in bacteria). This provides us with an unprecedented means to easily “edit” the genome of virtually any living thing, including stem cells and embryos. Furthermore, Cas9 has been modified to do more than just cut DNA; versions exist now that can insert new DNA sequences or switch out bad (mutated) DNA with good DNA.

In the hit TV show, Orphan Black, a group of clones discover that their DNA has been “barcoded” to designate them as intellectual property by their maker. Theoretically, CRISPR technology could have been used to tag DNA in this fashion.

The power of genome editing can be used for good. Several diseases, such as cystic fibrosis and sickle-cell anemia, are caused by a single mutation in one gene. CRISPR/Cas9 is a plausible tool that may be able to repair this defect. However, tinkering with one gene can have unforeseen repercussions on other genes, so this exciting technology could have adverse effects. In March, 2015, a group of scientists proposed a ban on editing the human genome, arguing that a greater understanding of how CRISPR/Cas9 works is required before we even consider applying it clinically.

Gene editing using CRISPR/Cas9 can be used to modify the genome of virtually any creature. One recent application is the creation of wheat that is resistant to a fungus that causes mildew.

Here is a video that shows how CRISPR/Cas9 works and some of the applications it may have down the road:

 

 

Contributed by:  Bill Sullivan

Follow Bill on Twitter.

*It should be noted that not all bacteria are “germs”; in fact, many species of bacteria inhabit our bodies to constitute our “microbiome” and provide important services to us. Learn more about your microbiome here.
 

Sander JD, & Joung JK (2014). CRISPR-Cas systems for editing, regulating and targeting genomes. Nature biotechnology, 32 (4), 347-55 PMID: 24584096

Garneau, J., Dupuis, M., Villion, M., Romero, D., Barrangou, R., Boyaval, P., Fremaux, C., Horvath, P., Magadán, A., & Moineau, S. (2010). The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA Nature, 468 (7320), 67-71 DOI: 10.1038/nature09523

Horie, M., Honda, T., Suzuki, Y., Kobayashi, Y., Daito, T., Oshida, T., Ikuta, K., Jern, P., Gojobori, T., Coffin, J., & Tomonaga, K. (2010). Endogenous non-retroviral RNA virus elements in mammalian genomes Nature, 463 (7277), 84-87 DOI: 10.1038/nature08695

Horvath, P., & Barrangou, R. (2010). CRISPR/Cas, the Immune System of Bacteria and Archaea Science, 327 (5962), 167-170 DOI: 10.1126/science.1179555

Baltimore, D., Berg, P., Botchan, M., Carroll, D., Charo, R., Church, G., Corn, J., Daley, G., Doudna, J., Fenner, M., Greely, H., Jinek, M., Martin, G., Penhoet, E., Puck, J., Sternberg, S., Weissman, J., & Yamamoto, K. (2015). A prudent path forward for genomic engineering and germline gene modification Science, 348 (6230), 36-38 DOI: 10.1126/science.aab1028

Frankenfood or Monster Myth?

Mary Shelly was wedded to Percy Shelley, one of the

great poets of the early 19^th century. But she was fair

writer on her own. Note the bolts on the monster’s

neck. These were added by make-up artist Jack P.

Pierce. He said they were electrodes, not bolts, even

though Mary Shelly never actually wrote that

the good doctor used electrodes on the body.

Can you think of anything scarier for Halloween than an irresponsible scientist letting his creation loose on the world? Now imagine that his creation is something that violates our human sense of decency and reverence for the dead. Well, that’s the story behind Mary Shelly’s Frankenstein.

The movies and stories about Frankenstein’s monster usually highlight the way in which the monster was created and his ugliness and hatred, but that isn’t what the book is about. It’s a story of responsibility in science and toward others.

The Age of Enlightenment had just ended when Frankenstein was written, and the Romantic period was in full bloom. A switch from science to emotion meant that the facts and discoveries about the world now needed to be examined, not just accepted. Here was where Mary found her message – a person must be responsible for the things he/she creates – be it physical things, knowledge, or opinion.

Electrical impulses make muscles move. Adding salt to

freshly skinned frog legs is a lot like hitting the with a

mild jolt of electricity. This is like Galvani demonstrated

with the corpse of the murderer and the image Mary

Shelly evoked in her novella.

The science of the monster’s reanimation was not the focus, but Mary had good knowledge of the latest science of the day, and this is what informed her making of the monster.

Just before 1800, Luigi Galvani had published on the ability of electricity to excite the muscles of dead animals – the innate electrical force of living tissue came to be known as “galvanism.” In 1803, Galvani applied an electrical charge to the corpse of executed murderer Thomas Forster, and the body jolted and moved – a good visual for Mary.

One indication that a story is a classic is whether its themes are applicable to different eras. Frankenstein may be even more applicable to our times than it was to Mary’s. Current debates boil over the uses and limitations of science.

The issue most often compared to Frankenstein’s monster is genetically modified organisms (GMOs). Have you heard of the term, “Frankenfoods?” This is the name that opponents of GMOs and particularly GM foods use to taint the agricultural biotechnology industry.

The fears are that by tampering with nature and introducing genes into organisms, we are creating monsters that might have unexpected effects on us. It’s a good marketing campaign idea, and it has taken off.

Europe and Russia have banned all GM foods, out of fears that they may contain toxins or mutagens that would harm the consumers. One fear is that DNA from the genetically modified organisms would be transferred to the eater and combine with their own DNA. That is a scary idea.

The problem is, you take up DNA from the food you eat every day, although not whole genes as the fearmongers warn. Digestion breaks down DNA, so we take up mostly nucleotides and short stretches of nucleic acid. No recorded evidence exists of uptake of an entire gene.

Dr. Frankenstein used all natural body parts, no artificial

sweeteners, additives or preservatives, and good old-

fashioned electricity. If he was sold in the market, the

monster could be labeled as organic! No genetic

modification here.

Websites and books talk about the dangers of GM foods, but it hasn’t shown up in the scientific literature. Most of the papers that have announced negative ramifications have later been retracted. I’ll give a typical example.

In 2012, a researcher named Seralini from the U. of Caen announced that an herbicide used with GM foods (glyphosate in Roundup) caused tumors. He didn’t just publish it - he had a press conference with the concurrent release of his book on the subject and videos in three different languages. It turns out that he also had a company that was preparing to market a product as a “protectant” against glyphosate. The study was subsequently retracted, but a modified version with a conclusion that “more study is needed” was re-published in a lesser journal, but without peer-review.

Other studies on the dangers of GM foods have been correlative, meaning that when you see “A”, you often see “B.” But that doesn’t mean that A causes B, or that B causes A. Remember this, correlation does not imply causation. This is also seen when assessing the rise in gluten allergy. Gluten allergy goes up at the same time more GM wheat is being used. GM wheat must cause gluten allergy. Nope. Several recent studies (like here and here) show that GM has no more endogenous allergens than wild type wheat.

The truth - we need more studies. There are real issues to be dealt with, like does introduction of a particular gene cause plant toxins to be increased – this could be bad for us. The idea is the same as in Mary Shelly book – we must be responsible for those things we make. No GMO or GM food should go to market without extensive testing.

The testing to date shows that there are no health risks associated with GM foods. Longitudinal studies from 2014, 2013, and 2012 of live stock feeds showed that animals fed GM crops over five generations showed no ill health effects and their meat was exactly like that of animals fed conventional feed. By the middle of 2013, over 600 studies showing that GM foods carried no health risks had been peer-reviewed and published.

Synthetic biology has arrived. Vanilla is a very expensive

crop to produce. But a gene has been constructed and

vanillin is now produced in yeast. They ferment sugar and

produce vanillin. This is more natural than artificial vanilla,

and contains many of the metabolites that make vanilla

taste like vanilla.

The problem with hidden agendas like Seralina's goes both ways; a 2014 editorial on the safety of GM foods was written by a Monsanto employee, the company that markets GM corn and soybeans. Society must be diligent and demand top-notch, transparent science. This was one of Shelly’s themes, Dr. Frankenstein conducted his work in private, with no comment from society about whether it should be done at all.

The next generation will have more issues to deal with, like synthetic biology (not merely taking a gene from one organism and putting it another, but constructing a gene or genes from scratch and then inserting them). We need a science literate population that can judge and reason for themselves. And that’s why we learn biology.



Contributed by Mark E. Lasbury, MS, MSEd, PhD
As Many Exceptions As Rules



Lupi R, Denery-Papini S, Rogniaux H, Lafiandra D, Rizzi C, De Carli M, Moneret-Vautrin DA, Masci S, & Larré C (2013). How much does transgenesis affect wheat allergenicity?: Assessment in two GM lines over-expressing endogenous genes. Journal of proteomics, 80, 281-91 PMID: 23403254
 
Herman RA, & Ladics GS (2011). Endogenous allergen upregulation: transgenic vs. traditionally bred crops. Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association, 49 (10), 2667-9 PMID: 21784119

Van Eenennaam AL, & Young AE (2014). Prevalence and impacts of genetically engineered feedstuffs on livestock populations. Journal of animal science, 92 (10), 4255-78 PMID: 25184846

Snell C, Bernheim A, Bergé JB, Kuntz M, Pascal G, Paris A, & Ricroch AE (2012). Assessment of the health impact of GM plant diets in long-term and multigenerational animal feeding trials: a literature review. Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association, 50 (3-4), 1134-48 PMID: 22155268

McCall WV, Andrade C, & Sienaert P (2014). Searching for the mechanism(s) of ECT's therapeutic effect. The journal of ECT, 30 (2), 87-9 PMID: 24755719