tag:blogger.com,1999:blog-32079676.post115618114777165302..comments2024-02-13T21:22:02.522-08:00Comments on RRResearch: The ligase puzzleRosie Redfieldhttp://www.blogger.com/profile/06807912674127645263noreply@blogger.comBlogger4125tag:blogger.com,1999:blog-32079676.post-1156401840470475322006-08-23T23:44:00.000-07:002006-08-23T23:44:00.000-07:00Arghh, here I go again and then I am going to bed....Arghh, here I go again and then I am going to bed. I have Blogorreah. If it costs more ATPs to initiate uptake of several fragments through the IM than it does to have a ligase "ligate once and fall over" then that would favour ligases in the periplasm.LindsayAWilsonhttps://www.blogger.com/profile/09666151957693399667noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-1156400635460334272006-08-23T23:23:00.000-07:002006-08-23T23:23:00.000-07:00Why did I write that without really sitting and th...Why did I write that without really sitting and thinking first? It sounds silly now. I guess another possible benefit of a ligase would simply be in providing a long, continuous DNA fragment for the IM machinery to pull through, rather than it having to reinitiate uptake of many, short fragments, which might be more hit and miss. This is really bringing home to me that I can't yet picture the uptake machinery...LindsayAWilsonhttps://www.blogger.com/profile/09666151957693399667noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-1156398771124677832006-08-23T22:52:00.000-07:002006-08-23T22:52:00.000-07:00I haven't really thought about this before and you...I haven't really thought about this before and you've made it sound really interesting. The only way I can imagine a ligase being needed is if uptake of the DNA from the external environment and transport of DNA into the cytoplasm is coupled and part of one continuous process. Then, a break in the DNA in the periplasm could disrupt DNA uptake from outside - I am imagining threading a bit of string through some double glazing - if the strong snaps in the double glazing cavity, it's a bummer, unless you have some little machine in the cavity that can mend the string. I have a vague idea that models of DNA uptake propose that the driving force to pull the DNA into the periplasm lies within the outer membrane, and that would work against an idea of some sort of pulling power coming from proteins situated in the inner membrane. However, I don't think that would preclude some kind of intimate interaction between OM and IM proteins that might require an intact DNA strand suspended across the two for maximum efficiency? <BR/><BR/>My only other thought is how did authors know those bands always came from assembly of two small bands into one big band, and not digestion of one big band into some smaller bands? I suspect a cursory glance at just one paper will answer that question! Another job for Thursday...LindsayAWilsonhttps://www.blogger.com/profile/09666151957693399667noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-1156215089428519692006-08-21T19:51:00.000-07:002006-08-21T19:51:00.000-07:00Wow, that is really interesting. What would a lig...Wow, that is really interesting. What would a ligase be needed for in DNA uptake? Were all of the experiments done in KW20 strains? I wonder if all strains require the ligase for efficient transformation....90% microbehttps://www.blogger.com/profile/10288595333674587852noreply@blogger.com