Last week, there was an overnight sampling effort in order to observe the daily patterns of transcription. Specifically, we are looking at the gene encoding actinorhodopsin. A rhodopsin is a protein that pumps ions across a membrane using light energy. Actinorhodopsin specifically pumps protons. By setting up a higher concentration of protons on one side of the membrane, the cell can power another protein called ATPase, which makes ATP, one of the major energy carrier molecules in a cell. While the actinorhodopsin does harvest light energy, this is a different process from photosynthesis.
The actinorhodopsin we’re interested in comes from a bacterium called acI. This group is cool because it is found in nearly every body of freshwater and often in high abundance. However, it is also tiny – even more so than most bacteria – and has an extremely small genome. The actinorhodopsin could be how acI survives so well in so many environments. To observe how the transcription of actinorhodopsin changes on a daily scale, we collect RNA four times over 24 hours. We would expect that the gene of interest is transcribed more during the daytime if it truly does encode an actinorhodopsin.
For more information on acI, check out this paper: