Functional control by codon bias in magnetic bacteria

Directed and controlled motion of small (micron sized and smaller) objects in fluid systems is an active area of research in biomedical nanotechnology. Magnetotactic bacteria undergo a kind of directed and control motion called magneto-aerotaxis by utilizing nanopropellers (flagella) and nanomagnets. While studying the role of nanomagnets in magnetic-bacterial motility to investigate nano-scale control of motion, we have serendipitously discovered a major protein specific codon bias residing in the Magnetospirillum magnetotacticum genome. While primary sequences of flagellar, iron uptake and the house-keeping RNA polymerase proteins are identical in magnetic bacteria compared to E coli and mammalian cells, there is no genetic similarity for flagellar and iron uptake proteins. In contrast, the house-keeping RNA polymerase in magnetic bacteria shows complete genetic similarity also. Surprisingly, the lack of any genetic homology in flagellar and iron uptake proteins, in spite of identical primary amino acid sequences in different organisms, is a consequence of a protein specific codon bias, thereby resulting in non-identical gene sequences. This codon bias is directly correlated with differences in protein functions specific to magnetic bacteria. Based on our findings, we propose a bold Functional Control by Codon Bias (FCCB) hypothesis suggesting that protein function is controlled by codons responsible for its primary sequence in addition to the primary sequence itself. The remarkable feature of our proposal is that even if primary sequences of two proteins are identical, utilization of different codons to express those sequences directly affects the function of the proteins.