Breaking down the wall: Illustration of the cellulosome as an impressive bacterial machine to degrade plants…think Legos

cellulosome, bacteria, bioenergy
Components of a major cellulosome of Clostridium thermocellum

I have heard of the cellulosome for quite some time. It discribes a extracellular ‘factory’ of enzymes some bacteria (or fungi) are equipped with to degrade the components of the plant cell wall. These enzymes are held by a scaffold structure projecting out of the cell. Several bacterial species to date are known to encode some sort of cellulosome. Here, I will focus on a model species, Clostridium thermocellum.  I never really thought twice about cellulosomes until recently when researching for an upcoming project. Now, however, I have a great appreciation and respect for this massive, impressive apparatus.

The backbone of sorts for the cellulosome is the scaffoldin CipA. CipA is a monstrous protein with many domains, most of which necessary to attach the enzymes needed to break down plant cell walls. CipA contains 9 cohesins, domains used to securely allow different proteins to interact. The enzymes ( I will describe soon) contain dockerin domains that interact with cohesins. CipA also contains a carbohydrate binding module (CBM) which allows it to directly interact with cell walls.

Many of the cohesins are used to attach carbohydrate degrading enzymes, usually of two classes: endoglucanases and exoglucanases.  These work in concert to breakdown cellulose and other carbohydrate polymers. Apart from the catalytic portions of these proteins are dockerin, needed to bind to CipA, and other domains like the Ig domain or X domain.

These enzymes ‘fit’ onto the scaffold protein like Legos. This makes them very modular. Now consider other scaffold proteins have a different type of cohesin (cohesin II) that can be used to attach other scaffold proteins thus making polycellulosomes. For example, Cthe_0736 is a scaffold protein with 7 type II cohesins. This means Cthe_0736 can have 6 other scaffold proteins attached to it meaning this polycellulosome could contain up to 63 individual enzymes which is potentially common considering isolated cellulosomes vary in molecular weight considerably.

illustrated bacteria, cellulosome, microbiology
Illustration of a polycellulosome attached to cell (blue) on substrate (brown)
animated bacteria, cellulosome, microbiology, bioenergy
Closer look at the polycellulosome

In a later post, I will go into a little detail on how these cellulosomal enzymes actually are able to degrade anhydrous polymers of carbohydrate.

June 18 News: Autism Is Twice As Likely In Children Living Near High Air Pollution Areas | ThinkProgress

June 18 News: Autism Is Twice As Likely In Children Living Near High Air Pollution Areas | ThinkProgress.

Great article and more science to add to the growing knowledge of autism mechanisms.

Gotta give it up to algae; I wouldn’t want to live in wastewater: Illustrated Chlamydomonas

bacteria, microbiology, animated bacteria, chlamy
Graphic illustration of Chlamydomonas reinhardtii, a model organism for fatty acid production to replace transportation fuels.

Illustration of the world of synthetic biology: a new phase in science

animated bacteria, bioenergy, synthetic biology graphic
With novel technologies, it is becoming commonplace to manipulate microbes to acquire desired effects. Shown is a bacterium with foreign gene pathways (glowing) that enable this cell to efficiently produce a desired product.

First, there was biology which began in earnest in the 19th century. Then came molecular biology in the 1920s and the foundation of mutagenesis set forth by Herman Muller in 1927. Then, genetic engineering was first applied in 1972 the lab of Paul Berg. Finally, humans had the ability to manipulate living organisms in a specific, directed way. Fast forward 38 years to the announcement by J. Craig Venter that the first synthetic organism was created with a completely synthetic genome. However, Mother Nature is very particular about what exactly humans can do with respect to organismal manipulation. The naive thought that simple addition of genes from one organism into a more suitable organism would lead to theoretical, effective production of desired chemicals was soon the way of the albatros.

This is when scientists had to take a step back and rethink their strategy. They had to consider gene regulation (positive and negative feedback), build-up of secondary metabolites, toxicity of produced end products, etc. It wasn’t enough to add genes coding for enzymes necessary for desired chemical production. Through the advancements of bioinformatics, computation biology, and a nascent field called systems biology, scientists are just now starting to see the fruits of their labor.

Humor me; type in “engineering bacteria” into Google News. Take a look at the headlines that pop up in your browser. Look at the amazing advancements that are happening currently and imagine what is to come…

How Do Bacteria Make Decisions? Part 3

Time for Part 3 in the series examining how bacteria make decisions. Parts 1 and 2 focused on chemotaxis. Today, we will focus on how bacteria decide which genes need to be expressed and which need to be repressed. One of the most prevalent ways a bacterium decides this is by using a two component system, or TCS. TCSs are relatively simple compared to chemotaxis. As you would suspect from the name, TCSs are pathways consisting of only two protein members, the sensor histidine kinase and the response regulator. Histidine kinases are a major protein family in bacteria because they are able to sense many different factors in the bacterium’s environment including nutrients, toxins, fellow bacteria, etc. In case you are wondering, chemotaxis is a modified form of a TCS in which the histidine kinase CheA is regulated by the activity of a separate protein, the methyl-accepting chemotaxis protein.

What if you are a bacterium and you have been using a certain type of carbon source to generate energy and suddenly that carbon source isn’t as prevalent? In this case, you would want to shut down the enzyme factories that were converting the previous food source into energy and begin preparing new enzyme factories to convert other food sources into energy as you prepare for starvation. If these conditions persist, you might want to decide to hibernate in the form of a spore or cyst until conditions around you improve. Or, if other food sources are sensed in the environment, any special enzymes that would be needed to convert them into energy would need to be synthesized from their respective genes. All of these scenarios are controlled by TCSs. The conditions are used as input for the cell to decide the best strategy to survive and thrive. Histidine kinase activation leads to a hand-off event from the kinase to the response regulator of a molecule which acts as a green light for the response regulator to proceed with its job. This job may be to turn on gene expression to produce proteins needed in the cell. The response regulator’s job may be to shut down gene expression for proteins no longer needed by the cell. It is a carefully orchestrated balancing act evolved over millions of years to make sure only the proteins/enzymes needed by the cell at a given time are present assuring highly valuable energy molecules are not wasted.

Yet another way bacteria are Nature’s smallest 5000 ring circus.

“Write what you know about” – Mark Twain

Good advice from a great communicator. From now on, the majority of posts will relate in some way to bacteria, especially microbial genomics. Most of the remainder of posts will be related to science communication and education.

Why bother spreading the love for the little creatures? I believe this quote from microbialgenomics.energy.gov sums it up:

By some estimates, microbes make up about 60% of the earth’s biomass, yet less than 1% of microbial species have been identified. Because most do not cause disease in humans, animals, or plants and are difficult to culture, they have received little attention. Identifying and harnessing their unique capabilities will offer us new solutions to longstanding challenges in environmental and waste cleanup, energy production and use, medicine, industrial processes, agriculture, and other areas. Scientists also are starting to appreciate the role played by microbes in global climate processes, and we can expect insights about both the biological underpinnings of climate change and the contributions of microbes to earth’s biosphere. Their capabilities soon will be added to the list of traditional commercial uses for microbes in the brewing, baking, dairy, and other industries.

There is so much we don’t know about microbes. However, we are beginning to understand their enormous adaptability. Whether it is 30,000 feet above the ground or two miles beneath it, bacteria can inevitably survive. I will now focus on getting the word out about the little guys who can’t speak for themselves.

Microbes can be used in soil cleanup
Microbes can be used in soil cleanup (Photo credit: Wikipedia)

‘Zoomable’ map of poplar proteins offers new view of bioenergy crop

‘Zoomable’ map of poplar proteins offers new view of bioenergy crop.