MyTH: Week 3 bacterial species is Caulobacter crescentus

This is a physical model of a bacterial flagel...
This is a physical model of a bacterial flagellum. It was imaged and modeled at Brandeis University in the DeRosier lab and printed at the University of Wisconsin – Madison. It was fabricated on a ZCorp Z406 printer from a VRML generated at Brandeis. (Photo credit: Wikipedia)
Caulobacter crescentus
Caulobacter crescentus (Photo credit: Microbe World)

It’s time again for the weekly My Tiny Highlight (MyTH). This week we will explore one of my favorites, Caulobacter crescentus. C. crescentus is a unique bacterium that has made it the focus of a lot of research due to its lifestyle and easy observable changes in cell shape. Part of the C. crescentus life cycle is spent freely swimming in its aquatic habitat using a single flagellum. These are called swimmer cells. At some point in development, the swimmer cell ejects the flagellum from itself and begins growing a stalk on the opposite cell pole as the flagellum. As the stalk continues growing, the cell produces a VERY stickly glue called holdfast at the tip of the stalk which is used to attach to a surface and is called a stalked cell. The cell undergoes division assymetrically; meaning, the two daughter cells produced are not identical (as is the case for most bacteria). One daughter becomes a swimmer cell due to new flagellum synthesis on one pole while the other remains stalked.

Thinking about split personality, how can one cell contain both a flagellum and a stalk simultaneously; both being functional? This is the focus of years of research. One answer refers to my favorite molecule discussed in earlier MyTH posts, the bacterial second messenger cyclic-di-GMP. Cyclic-di-GMP is constantly being made and degraded in C. crescentus. However, the production and degradation are sequestered to opposite poles of the cell via precise protein localization. The enzyme needed to produce c-di-GMP is at the stalked pole while the enzyme to degrade c-di-GMP is at the swimmer pole. Although there are no physical compartments within this bacterial cell, the concentration of c-di-GMP is not uniform throughout. The proteins that interact with c-di-GMP are predominantly at the stalked pole and allow for the stalk to elongate and leave the flagellated pole alone. Brilliant!

caulo

 

 

C. crescentus is also of importance for its ability to clean up contaminated surface and subsurface groundwater because it is resistant to the effects of heavy metal exposure. Also, examination of the genome was used to determine the ancestry of C. crescentus. It contains gene clusters similar to Pseudomonas species and others that are predominantly found in the soil. This fact along with the presence of genes necessary to breakdown plant-derived carbon molecules suggests C. crescentus originated on land (or under it) before winding up in its present day niche.

English: Graphical representation of Caulobacter crescentus (Photo credit: Wikipedia)

MyTH: Week 2 bacteria focus organism: Azospirillum brasilense

Welcome to week two of My Tiny Highlight (MyTH). This week I will focus my attention on a bacterium not many people know about, Azospirillum brasilense or A. brasilense. I know quite a bit about this one since it was the model organism used for my dissertation (sorry, under embargo…no link). The genus Azospirillum is found in almost all soils across the globe. A. brasilense, as you may be able to decipher from its name, was discovered in Brazil and is found associated with roots of different cereals (wheat, corn, even rice). Like most bacteria, A. brasilense is good to have around. It was thought for a long time that this organism provided the plants it colonizes with a usable form of nitrogen since A. brasilense is able to fix nitrogen (turn nitrogen gas found in the atmosphere into useful ammonium). However, A. brasilense is greedy and has two ways to uptake ammonium into the cell if it happens to leak out somehow. So how is A. brasilense beneficial to a plant?

Glad you asked. Azospirilla have the capacity to produce plant hormones, specifically auxins. Auxins are a class of plant hormones derived from the amino acid tryptophan. In plants, among other things, auxins increase nutrient uptake. More nutrients for the plant means increased plant growth and by consequence more nutrients and growth for A. brasilense. So, instead of increasing its own nutrient uptake (which increases the need for energy to be spent), A. brasilense ‘tricks’ the plant into doing it by just producing plant hormones. Brilliant!

The auxin indoleacetic acid
The auxin indoleacetic acid (Photo credit: Wikipedia)

Wait…it gets better. Maybe you have heard of quorum sensing (check here). Bacteria produce and release a chemical signal that is recognized by other cells and gives them instructions (go away or come here and settle down). Some recent research (personal observation) suggests auxins are quorum signals in A. brasilense telling other cells to come join in and settle down. Since A. brasilense is almost always motile, moving around in search of the best environment for the cell, a signal telling these cells to stop is amazing.

 

tlp1 pRKdeltapilZ 6

 

Picture of A. brasilense colony on agar plant and not color enhanced. They actually are pink/orange from production of carotenoids.

Azospirillum brasilense

 

Electron micrograph of A. brasilense.

Watch short movie of A. brasilense swimming in liquid media Here

One amazing behavior in A. brasilense is a phenomenon called aerotaxis. It is similar to chemotaxis, the movement of cells along gradients of a chemical. However, as you might predict, aerotaxis is movement of a cell long a gradient of air. A. brasilense prefer an environment with a low oxygen concentration (~0.4% compared to atmospheric oxygen concentration of 21%). From the meniscus, they will form a thin band of cells at the concentration of oxygen they like in a small capillary filled with liquid (see below).

Azospirillum brasilense capillary aerotaxis

 

Image of A. brasilense cells in a small glass capillary. A aerotactic band of cells (whitish in color) forms a certain distance from the meniscus (left side of image).

 

 

This is all I can provide at this time. I may update this post at a later time. Hope you enjoy the MyTH series! Next week, I will highlight one of my personal favorites. Stay tuned!

 

Hooray for Failure! It’s Science’s way of telling you you’re not being creative enough

English: A diagram of a typical prokaryotic ce...
English: A diagram of a typical prokaryotic cell. This diagram, made in Adobe Illustrator, is an improved version of a similar diagram, Image:Prokaryote cell diagram.svg, which was also made by LadyofHats. Besides general appearance changes, this version adds plasmids and pili, and notes that DNA is circular. Latina: Diagramma cellulae naturalis prokaryoticae. Adobe Illustratore factaerat. (Photo credit: Wikipedia)
Schematical structure of a molecule of cyclic ...
Schematical structure of a molecule of cyclic di-GMP. The guanine (blue), ribose (red) and phosphate (green) have been bonded through dehydration. (Photo credit: Wikipedia)

I’m not a scientist at the bench anymore. My wife told me I had to stop playing and get a real job (a.k.a. graduate). However, I have very fond memories of my days studying chemotaxis. I will discuss that tomorrow in the second installment of My Tiny Highlight (MyTH) series. Bacteria, despite all modes of intimidation, do not follow our commands. They dance to the beat of a different drum, internal programming.  Following the scientific method is easy but hard. You can make observations all you want (in my case 6 and half years and over 40 hours of video), but describing why things with the cell are happening or how they happen is a process. Finding explanations for what you observe and designing experiments to test them teaches humility because inevitably the cells will prove you wrong.

There is not much bravado in science. Failure is much more common than success and I would not have it any other way. I learned ten times more from failure than success. My dissertation project was split into two main goals dealing with two different proteins within a single bacterium, let’s call them protein1 (due to embargo and not published yet) and Tlp1 (since one paper is already published). It took 4 years of mostly failure with P1 to open my eyes and look outside the box. Breakthrough! Tlp1 was more straight forward, at least I thought at first. I still failed to explain my observations for a few years. Once I started visualizing the inside of the cell, with all its organized chaos, I started to be more creative in my hypotheses. Ultimately, we discovered a sort of paradox to everything found in the literature about the bacterial second messenger cyclic-di-GMP (c-di-GMP). I can’t wait for it to be published.

Grad school taught me a lot. I learned that if you love what you do, it doesn’t seem like work. Most of all, I learned that failure is a good thing because it takes us outside the box which is usually where the correct answers are.

MyTH: A new weekly series about one bacterial species. First Post: Escherichia coli

This thought came to my head as I couldn’t sleep last night. My Tiny Highlight (MyTH) will be weekly and will showcase interesting or useful bacteria. For the first installment, I will focus on the gold standard of biology; Escherichia coli or E. coli. E. coli was discovered in 1885 by a German doctor in feces of healthy people. He called it Bacterium coli commune because it was found in the colon. The classification system of bacteria was much different before the ability to sequence DNA as novel bacteria were initially classified and named by their shape and motility. The name later changed to Bacillus coli before finally being reclassified and named Escherichia coli after the original discoverer. How would you like it if someone named a bacteria from feces after you?

E. coli receives a bad reputation thanks to pathogenic strains that force recalls of all kinds of food products. However, those strains are very uncommon as E. coli is one of the most abundant species found in the GI tract of mammals. Also, without this bacterium, many of the scientific discoveries of the past 50 years would not be possible including solving protein 3D structures, mass production of insulin, and understanding signal transduction; the process of a cell sensing surrounding signals or cues and responding to them in a way that is favorable for the cell. One reason E. coli was such a well suited model organism is the doubling time or time to divide one cell into two daughter cells. A doubling time of only 20 minutes means in less than 48 hours, the mass of E. coli cells would roughly be equal the the mass of Earth and have the combined volume equalling a 1 meter thick layer of bacteria covering the entire surface of Earth (including oceans). This is incredible and gives E. coli a major advantage over slower growing bacteria.

I want to discuss, briefly, a major influence of mine. Julius Adler was born in Germany and became a lover of Nature as a child. He was fascinated with butterflies. adler

His lifelong passion has been behavior of living things. Luckily, he spent most of his professional career studying chemotaxis in E. coli although he now studies fruit flies. Adler is known as the father of chemotaxis, or the movement of a cell in response to sensing chemical signals. His landmark early papers in the journal Nature about chemotaxis in E. coli in 1966 and his later paper on the chemoreceptors, the proteins that interact with the surrounding chemicals, in E. coli laid the foundation that maid the chemotaxis system of E. coli the best characterized signaling pathway in Biology. In regards to chemotaxis, however, E. coli is on the simplistic side of the scale. For example, E. coli has 5 chemoreceptors and 1 chemotaxis operon, or a stretch of genes that are transcribed into RNA together but lead to distinctly different proteins that usually interact with each other. Through the explosion of genome sequencing, scientists can scan newly sequenced bacteria genomes for chemotaxis genes. The average number of chemoreceptor genes is roughly 5 times more than E. coli (~25) and it is more common for bacteria to harbor multiple chemotaxis operons suggesting most bacteria have evolved to use chemotaxis for regulate more than the motility behavior in these cells.

Let’s think a minute about why E. coli is ‘stupid’ compared to other bacteria. By ‘stupid’ I mean, they have less capacity to integrate signals from their surroundings into a cell response. Why doesn’t E. coli have 25 chemoreceptors, for example? For the answer, we just need look at where this microbe is found. The GI tract of mammals is fairly constant meaning there is less need to scavenge for a new home or adjust to changes in temperature or nutrients. We as mammals have no problems eating meaning E. coli has no problem eating as well. How about the other sequenced bacteria? They predominantly live in more variable environments like soil or oceans where is would be to their advantage to be able to sense a lot of chemicals or nutrients in their surroundings. Therefore, through evolution, they have acquired new abilities to sense through duplicating genes and mutating DNA favorably. Changing only a few nucleotide bases (A,C,G,T) could mean acquiring the ability to physically interact with different environmental chemicals that could serve as an energy source. Nature is awesome and she knows how to keep us, as observers, guessing.

You may feel I am biased about chemotaxis ( I am). This was my dissertation work in another bacterium. Check back next week when I will highlight a little known (publicly) soil bacterium, Azospirillum brasilense. If you have any comments, questions, or suggestions PLEASE LET ME KNOW!

 

Recommended reading about Julius Adler.