Science Buddies: "Ask an Expert"

I am thinking of doing a project on the relationship between DNA methylation in bacteria and the amount of colony growth. I need alot more information on what specific genes or proteins the DNA methylation will regulate, which in turn affect the bacteria's growth. Also, what nutrients are turned into methyl groups, which then allow the DNA methylase to function? Any advice/ articles would help. I dont' know how I will be able to do this without a lab... purchasing the materials won't be a problem however.

Hello Yas2,

DNA methylation and bacterial growth is a very interesting area with lots of aspects that remain to be discovered! In terms of how DNA methylation affects gene regulation, more extensive studies have been done in eukaryotic cells than in bacterial cells. Much of what is known about DNA methylation in bacteria is how the bugs use methylation to distinguish their own DNA from foreign DNA (such as those from viruses that infect the bacteria). However, there has been recent interest in how bacteria can also use DNA methylation to regulate their gene expression, although much is left to be learned.

To start you off, here's a review on what is currently known about DNA methylation in bacteria and how it affects gene regulation (http://perspectivesinmedicine.cshlp.org ... 10272.long). The review article is pretty technical, so please let me know if it is too difficult to understand--you can definitely do some searches on your own to find other sources! As for whether a lab is necessary for you to do your project, it really depends on the resources necessary to address your question experimentally. However, I would say that if you want to alter DNA methylation in bacteria to see how that would affect growth, that definitely requires the use of sophisticated molecular techniques that would require a lab and a mentor to guide you. Why don't you do a bit of reading on this topic, come up with some questions that intrigue you, and we can help you brainstorm some ideas to see how much is required of you experimentally to test your hypothesis!

Best of luck,
Connie

Hi Connief,
Thank you so much for your advice! I have done some reading, and unfortunately a lot of the information is very technical and a bit hard for me to understand. I want to study the following: the role of dam methylase in the regulation of DNA replication in bacteria. From my reading, I have understood the following:

Immediately after replication, the site of origin is hemimethylated and sequestered (by SeqA) for a period of time. Only after this, the site of origin is released and must be fully methylated by Dam methylase before DnaA binding occurs. DnaA is a protein that binds to the origin site in order to initiate transcription.

Therefore, SeqA is the main culprint in the process. My question is, what conditions (nutrients, temperature, ect.) can be manipulated in order to control the amount of Seq A protein?
If I manage to create low levels of SeqA, can this cause uncontrolled DNA replication?
Will uncontrolled DNA replication cause the bacteria to malfunction and stop growing, or will it cause uncontrolled cell division?

Also, another route would be to control the amount of methyl available to the Dam. If the Dam methylase is unable to do it's job, then DnaA shouldn't be able to bind to the origin site, and therefore the DNA cannot be replicated. Will this process stop bacterial growth?

I was thinking of using E. coli, as it is mentioned a lot in the literature and seems to be a well known for its Dam methylase.

I suppose I will need a mentor and a lab in order to control the function of either Dna methylase or the SeqA protein. I can try to email the professors and researchers at my nearby university (which happens to be UCI). Do you have any advice in terms of finding a mentor?

Thanks sooo much for all the help. I really appreciate it .
Yasmine

Hi Yasmine,

It's very great to see that you have already done so much reading on this topic! And it's totally fine that you don't understand some of the details because oftentimes, scientific articles are a bit technical and it takes a while to get used to reading and understanding them--you are getting a great headstart already.

Your topic is very interesting. As for what conditions to manipulate to control the amount of SeqA protein, this may be hard to do unless there are things known about what certain environmental stimuli control how often SeqA is made. You would probably have to try searching for papers in regards to the regulation of SeqA gene expression, although it is possible that not much is known about this. One way to control SeqA levels is to delete the gene in E. coli--that is, the bacterium will no longer make any SeqA. That way, you can assess what effects SeqA can have on bacterial replication. Likewise, you can delete the Dam methylase gene in E. coli to see how that would affect replication/growth. If you want to do these two things, you will need a mentor and a lab to guide you.

To find a mentor, you can definitely try e-mailing professors at a local university like you had mentioned; for your case, it'd be UCI. I would take a look at UCI's microbiology department (http://www.microbiology.uci.edu/research.asp) to see if there is anyone working on the same topic. If not, you can try looking for professors that work on bacterial replication or professors that work on methylation and see if they would be able to help you with your project idea. For example, this professor here (http://faculty.sites.uci.edu/mcclelland-lab/) doesn't necessarily work on bacterial methylases, but he does do work on the bacterium Salmonella and on DNA methylation in mammalian genes, so perhaps that lab could help you with your ideas. I would e-mail the professors introducing yourself, that you're interested in doing a science project on your particular topic, and ask them if they would kindly be able to help you brainstorm ideas and set up the experiments. That way, you would be able to get feedback from them, and perhaps you can come up with even more ideas to test. One of the most important things is to show that you're enthusiastic about science and that you're really excited about your project!

I hope that helped. Please let me know if you have anymore questions.

Best of luck,
Connie