Joseph Campbell did a lot of work on archetypes, epics and myths.  He also fully believed that each of us has a singular purpose, and strongly encouraged us to “follow your bliss“.  He is speaking about DHARMA.  Dharma is kind of like your purpose/gift… the thing that only you can offer the world.  Although, its even bigger than that:  its the way that you should act… its your duty.  What is your dharma?   Everything in your life should line up with your dharma and support the journey that you are on.

Dear Diary…

This week, we talked about gene expression and regulation in bacteria.  We used the construction of the flagella as our model for how DNA is EXPRESSED (transcribed and translated into functional protein) and how it is REGULATED (turning expression of genes on or off).

We started off with Transcription…  the creation of mRNA from a DNA.  The sigma factor assists the RNA polymerase enzyme in finding the promoter.  The promoter has two important sequences for this, the Pribnow site and the -35 site.  Variations in these two sites lead to promoters WEAKLY binding Sigma/RNA pol, and promoters STRONGLY binding sigma/RNA pol.  Once the polymerase gets going, the sigma factor falls off and the RNA pol continues along the DNA, transcribing, until it reaches a termination signal.  This can be mediated either by RHO protein, or without RHO protein, as shown in the video.

Simultaneously, the new RNA is being translated by the ribosomes (Checkout that website!) since there is no physical separation between the DNA and the cytoplasm, as there would be if there was a nucleus. The translation process in eukaryotes is shown in the movie below… what would be the differences in prokaryotic translation?

https://www.dnalc.org/resources/3d/16-translation-advanced.html

Next, we looked at the structure of the flagella and how it is constructed, from the bottom up.  The rings are made and embedded in the membranes, then the hook and the filament are constructed next… feast your eyes!

The genes encoding all of the flagellar parts are activated sequentially, and all of them can be controlled by systems of both ACTIVATION or REPRESSION.  In addition, many of these flagellar genes can be found clustered behind a single promoter, composing an OPERON.  Genes in an operon are all transcribed into a single polycistronic mRNA, and then translated into multiple individual proteins.

In class, we went deeper into WHY operons exist in bacteria and not eukaryotes, and WHY eukaryotic mRNA are incapable of being polycistronic.  Do you remember the reason?  Why can’t polycistronic RNAs be made in eukaryotes?

We also examined several examples of ACTIVATION and REPRESSION.

• DNA sequences are either ACTIVATOR or OPERATOR sequences
• Proteins are either ACTIVATOR or REPRESSOR proteins
• Effectors are either INDUCERS or Co-REPRESSORS

How do we know which is which?  What is happening to the gene when the DNA, protein or effector is BOUND?  If the gene is EXPRESSED when the DNA/Protein/effector is bound then it is called  ACTIVATOR SEQ, ACTIVATOR and INDUCER (respectively).  If the gene is not expressed when the DNA/protein/effector is bound, then we call it an operator seq/repressor/co-repressor (respectively).  Please be aware that Inducers can function in BOTH the systems of Activation AND Repression.

In activation systems, the inducer binds to the activator protein, and together they bind to the activator sequence, turning gene expression ON.

In repression systems, the inducer binds to the repressor protein, causing it TO FALL OFF of the operator sequence.  This causes a gene that was previously repressed, to turn ON.

Design a system of activation or repression.  Imagine if a bacterium received a signal from neighbors that there was enough of them to start a biofilm.  How would that autoinducer “turn on” the genes that were necessary for making a biofilm?  You would be including things like activator proteins, activator sequences and inducers…. OR…. repressors, operator sequences and co-repressors (or inducers, depending on how the system works). 

Another cool way that biofilms are connected to quorum sensing:  When bacteria are already in a biofilm, quorum sensing is ENHANCED because they are all clustered together and the autoinducers cannot drift away.  So its like turning the volume up on their communication!

If you need more practice on this, here’s another exercise:

 

 

We then discussed flagellar movement… which is a little silly.

Flagella rotate counterclockwise to drive the bacteria to “run”  forward.  And they rotate clockwise to cause the bacteria to tumble randomly in space.  This allows them to change directions, only the direction is completely random.

Super sophisticated.

Lastly, we discussed quorum sensing.  The idea that bacteria can sense the quantity and identity of AUTOINDUCERS.  These are small molecules that bacteria secrete into the surrounding environment… more bacteria, more autoinducers.  When the bacterial population hits a critical mass, or quorum, the community may change their behavior to all act simultaneously…. like turn on light production (in the Bobtail squid) or secrete toxins to cause disease (like in your guts).

Bonnie Bassler’s group pretty much discovered this whole process:

Things to focus on for this week:

• Understand how transcription is initiated and what the role of the RNA pol, sigma factor and promoter is.
• Identify some major differences between eukaryotic and prokaryotic gene expression
• Name the three players in gene regulation, and be able to identify which one is which (inducer, co repressor, activator, operator, etc) if given an example.
• Describe some situations where a bacterium would turn a gene on, or turn a gene off… where does the signal to do so come from?
• Be able to locate and name the major parts of the flagella
• Be able to draw a diagram showing how quorum sensing works and what the result might be when a bacteria sensing a growing amount of autoinducer
• Can you draw the bacterial flagella, labeling the three main parts?
• Describe how the flagella is powered to move
• What is the difference between a monocistronic and polycistronic mRNA, and why do bacteria have them and eukaryotes do not?
• How do bacteria direct their movement towards (or away) from a stimulus?  Understand how “runs” and “tumbles” are used and how the flagella can direct these two different types of movement.

Any questions?  Leave ’em below!