Respiration is the way in which all organisms consume and break down certain compounds to make energy, in the form of ATP. Aerobic respiration is when oxygen is converted into water, in order to make energy. This is what mammals like humans do. Many microorganisms, like bacteria and archaea, also use up oxygen to make energy like we do. However, we use different proteins to perform the same reaction from some of the microbes. Humans use an enzyme (this is a protein that catalyzes a chemical reaction) called a heme-copper oxidase. Some microbes use a different enzyme called cytochrome bd oxidase. This is the protein I work on.
Figure 1. Crystal structure of cytochrome bd oxidase from Geobacillus thermodenitrificans ( PDB id: 5DOQ, representation made using VMD)
Does the ability of the enzyme, cytochrome bd, to help microbes make ATP vary depending upon conditions?
Figure 2. Respiratory chain of Escherichia coli showing multiple oxygen using enzymes – cytochrome bd-I, cytochrome bd-II and cytochrome bo3
A study from 2009 (Bekker et al., JBC) had suggested that only one of the two forms of cytochrome bd, bd-I could help make ATP while the other, bd-II could not. They investigated this by making E.coli strains with either of the enzymes genetically deleted, leaving the strain capable of only using the remaining enzyme (since the genes are completely removed from the genome, these bacterial strains are called knock-outs). They then saw which of the strains could grow better, indicating which of the proteins helped make more ATP, which is essential for growth. While this was a sound experiment, this tested the whole bacteria itself instead of the proteins individually. Within a bacterium, there are many complicated factors which could affect growth.
We tested the individual proteins and specifically their ability to help make energy. (Borisov et al. PNAS (2011)) We inserted the protein into a liposome (arrangement of lipids in a similar manner to cellular membrane) which simulates its native environment. Using fluorescent dyes which accumulate in the liposome, we monitored the change in electric potential as a change in the wavelength of light which the dye absorbs when potential is generated. According to our experiments, it was clear that bd-II was capable of generating energy in the same way as bd-I. Which follows logically from the idea that it is very likely that proteins which have similar structures and similar functionally important amino acids function similarly.