The implication of non-classical transformation and how to address

I read a recently published paper about genome transplantation. In their report, genome transformation is applicable although with low frequency. They reported that only circular genome can be successfully transformed. But the mechanism of this type of transplantation is completely unkown. I was surprised to found that Dr. Smith is within the authors because I did not find his publications after twentith century. He has done perfect work in transformation of H. influenzae and his publications are thoughtful and insightful.



One teacher in our lab remind me one thing: what is artificial transformation? If there is no way to let DNA enter cell, there is no way for DNA entering. If there is a window there, the outer stress might make the window become a door. My question is that whether the mechanism of plasmid transformation is just the the window of so called 'artificial transformation'. People make this widow become bigger and then the transformation efficiency enhanced so the window was reformed to the door. Natural plasmid transformation has been widely found (here I mean the plasmid without DUS, if the plasmid contain DUS the transformation form changed to chromosomal transformation). Both H. influenzae and N. gonorrhoeae have such kind of transformation. Although it is not very clear whether this type of transformation exists in B. subtilis, the existance of recA-independent plasmid transformation implied that this type of transformation might also apply to gram positive bacteria. However, it is difficult to study this type of transformation at this moment because we do not know whether genes are involved in the regulation (since all competence genes are not required and we might not be able to use genetic methods). In addition, the low transformation frequency make it difficult to observe single competent cells.

Nevertheless, one can completely change the plasmid transformation to chromosomal transformation if the DUS sequence is found. The question is whether DUS sequence really exists in E. coli. Although there are reports which shows negative evidences from bioinformatics, still it is hard to say whether DUS sequence is really abscent in E. coli genome or whether it will appear in another form. In H. pylori, it is not known that whether special DNA uptake sequence is required for natural transformation and the mechanism of transformation in H. pylori is quite novel. We do not know whether the chromosomal transformation of E. coli make use of another novel transformation mechanism.

The following work seems to be a big project. But we need to design several simple experiments to reveal some important aspects and impact firstly. I will discuss with my mentor in detail about what and how I should address to next week.