[HN Gopher] Everything You Ever Wanted to Know about E. Coli (2008)
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Everything You Ever Wanted to Know about E. Coli (2008)
Author : angrygoat
Score : 36 points
Date : 2024-08-12 13:00 UTC (3 days ago)
(HTM) web link (www.scientificamerican.com)
(TXT) w3m dump (www.scientificamerican.com)
| pazimzadeh wrote:
| The article touches on the versatility of E. coli, but doesn't
| explicitly mention the extreme diversity within what we call E.
| coli.
|
| Even just within the subset of E. coli which causes UTI's, 25-40%
| of the genome varied between strains.
| (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5653229/)
|
| This diversity wasn't really appreciated in 2008 when many E.
| coli genomes hadn't been sequenced yet.
| lysozyme wrote:
| Good point! And a related topic, we call the organism that
| lives happily in our gut _E. coli_ and we also call the
| organisms that cause disease the same name. What's the
| difference?
|
| It turns out that the _Escherichia coli_ (to spell out its
| Latin binomial) that cause disease are in some sense "diseased"
| themselves: the genes that enable them to be pathogenic, or
| make them pathogenic, I should say, are originally from a
| phage, a type of virus that infects bacteria [1]. In a manner
| that is not the same as, but conceptually similar to how HIV
| inserts its genes into the human's genome, phages insert their
| genes (termed the "prophage") into the bacterial genome.
|
| In addition, most strains of pathogenic _Escherichia_ are also
| holding on to an entirely separate, small, circular "genome"
| called a plasmid, also of exogenous origin, that contains
| additional genes that make them pathogenic.
|
| So in addition to wide genome variation within the "species"
| (which is not really the same thing for bacteria as for
| mammals, mind you) of _Escherichia coli_ , many subtypes have
| additional genetic material from endogenous sources that
| substantially changes their observed characteristics
| (phenotype).
|
| 1. https://en.m.wikipedia.org/wiki/Escherichia_coli_O157:H7
| thelaxiankey wrote:
| Also happen to be in microbiology, but pretty far from the
| medical side of things.
|
| Do you have a citation on the fact that 'most' pathogenic
| strains have a plasmid making them so? Some guys in our lab
| have been playing around with plasmid copy number lately (in
| a largely 'basic science' kind of way) -- this could give
| some nice context for that work.
| koeng wrote:
| I use E.coli on a pretty daily basis for cloning. It's alright,
| and there is so much work that has gone into it as a chassis
| organism, but overall there are definitely better organisms out
| there if we just took the time to figure them out (Vibrio
| natriegens and Bacillus subtilis are two examples).
|
| We absolutely do not have a clear idea of how E.coli works. Hell,
| we don't even know how almost 1/3 of the genes work on JCVI-Syn3a
| works, a minimal genome we synthetically created. Far fewer in
| E.coli.
| pazimzadeh wrote:
| Better how? Cloning strains are particularly boring...what are
| you expecting to happen?
| koeng wrote:
| I'm expecting that it should grow 2x the speed, sporulate if
| needed, have natural competence systems for large
| modifications / genome engineering (lambda red aint there),
| have some environmental resistances that are uncommon in
| typical contaminants, have better protein secretion directly
| out of cloning strain, hell just an expression AND cloning
| strain, better stability in typical strains that dont require
| STBLE or whatever, better positive and negative selection
| markers, Vitamin B1 synthesis pathway for minimal medias,
| E115K fix in purB for DH5alpha so that they don't grow like
| crap on M9, the list just goes on.
| pazimzadeh wrote:
| What is the doubling time for the E. coli you are working
| with?
|
| E. coli will never form a spore (unless you engineer that
| somehow?), why would you want E. coli to sporulate? Some of
| the things you mention can be done by clinical strains.
| Couldn't you just make the E115K purB mutation if you want
| that? I agree that lambda red is limited.
| koeng wrote:
| Normal E.coli doubling time, which means about half the
| speed of Vibrio natriegens. I use NEB turbos sometimes,
| but they still don't bring down the liquid culture time
| down from overnight to within a day, mostly.
|
| I would want E.coli to sporulate because then shipping
| and distribution of strains is a lot easier. This was a
| problem back when I was shipping at FreeGenes and still
| is a problem. I used Bacillus subtilis to make the
| sporenet protocol which worked, but the vector backbone
| switching was pretty painful.
|
| Clinical strains == not necessarily GRAS. Also, they're
| clinical, so regulated by MTAs, which are a big no-no.
|
| I could make the E11K purB mutation, but why would I go
| through the effort in an inferior species of bacteria
| when I can invest my time into something like Vibrio
| natriegens? The payoff is better at the end.
| pazimzadeh wrote:
| If all you're interested is cloning/expression, then I
| guess that makes sense, although I've not heard anyone
| complain that 20 min is a slow doubling time. can't you
| just inoculate your starting culture with a larger amount
| or something? I often find myself starting cultures late
| in the day so that they don't overgrow the next day
| (although I am not doing expression work).
|
| Vibrio natriegens seems great for your purposes. I'm
| curious if there is a tradeoff to its super fast growth.
| Does it have a greater mutation rate?
| mncharity wrote:
| _Many_ numbers for E. coli:
| https://bionumbers.hms.harvard.edu/search.aspx?trm=coli
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