Your science project seems really interesting. In fact, this question about what cellular substance controls pigmentation has become more difficult than I anticipated. I have tried to educate myself on the subject as much as possible, but I think I am going to need to go to a better source. So I will give you the information that I have found so far. But if you are interested in me investigating this question further, I will need to talk to a microbiologist here at the university.

There is one scientific paper that helped to provide me with some information. Here is the reference if you want to read it for yourself. The reading is not that difficult just slightly technical but I think you will find it interesting.

Haddix, P.L. and Werner, T.F (2000) Spectrophotometric Assays of GeneExpression: Serratia marcescens Pigmentation. Gene Expression-Bioscene vol. 26 (4) 3-13.

Here is what I was able to pull apart from the paper without getting to technical. The paper above does state that temperature does effect prodigiosin expression. Such that at higher temperatures a physiological response is invoked rather than a genetic change in prodigiosin expression.

Besides temperature, pH and nutrients are important in prodigiosin expression (pigment expression). For instance, Serratia marcescens cannot survive nor grow at a pH < 4.5 nor at a temperature > 45C. There must be an abundant of nutrients in the environment for Serratia marcescens to survive as well.

If you are interested in me contacting someone here at the university to investigate your question further, I would be happy to help you out further.

The temperature changes the rates of chemical reactions, with high temperature causing reactions to be faster. Some chemical reactions are affected more by temperature than others, however.

The bacterium has a protein that causes a reaction that is particularly fast at high temperature. This reaction probably prevents a gene from being expressed, a gene that makes the red pigment. This is my best guess, anyhow.