Top 5 useful facts about the MDS42 strain

Friday 6 January 2017

Top 5 useful facts about the MDS42 strain

MDS42, also known as the Blattner strain, is a strain made in 2006 by deleting 13% of the genome of E. coli K-12 MG1655. Unfortunately, as tools go, it rivals IKEA in cryptic instruction manuals.

MDS42 is derived from MG1655, the wild type E. coli K-12 (see my other post about how 'wild' it is),  by removing insertion sequences (IS), prophage and pseudogenes. One of the groups that created was led by Fred Blattner (who is mentioned in another post!) from Wisconsin, so it is sometimes called the Blattner strain or Wisconsin strain.
It grows well in minimum media —like a B strain as it can use the glycoxylate shunt, which is broken in other K-12 strains— and virtually does not break toxic (non-lethal) plasmids. Okay, cloning errors by Gibson or ligation happen but it is not the strain's fault. The strain has three issues however: (i) nobody seems to quite agree about its competency, (ii) the distributing company Scarab genomics has prohibitive prices for industrial uses and (iii) it has really shocking documentation.

Most commercial strains do have terrible documentation, especially for genotypes.
This is either a sloppy transmission error or secrecy. BL21(DE3) for example have a lambda phage relative called DE3 inserted into the genome. The int gene was knocked out by replacing it with lacI and lacZ. In turn the lacZ was knocked out by gp01 from T7. NEB gets it right, but Lucigen has the gene as ind and not int.
NEBTurbo strain has the same genotype as DH5α, but is clearly not thi-1 or pyrE rate-limited —I suspect it is wt recA, which is worrying, but I have not checked.
In the case of MDS42 it is a messy layout of data. Okay, there are lot of junk genes nobody cares about, but somethings are rather major. There are two ways to find info on it, the supplementary table of the 2006 paper or the genome sequence. So here are some useful bits of info:

Arabinose. It is derived from MG1655, not BW25113 (Keio mother strain), so can it utilise rhamnose, arabinose and lactose? It cannot use lactose, but it can arabinose and rhamnose. It also is galK positive (i.e. no galactose/2-deoxygalactose selection and counterselection).

Clonetegratable. It still has all the phage attP sites, so clonetegration works.

Non-motile, but slightly slimy. It lacks the flagellum (∆flg, ∆fli, ∆flh), type I pilus (∆fim) and antigen 43 (∆flu), O-antigen cryptic genes (∆rfb) and colanic acid production (∆wca), but has curli fimbriae (csg), cellulose synthase (bcsA) and poly–1,6-N-acetyl-d-glucosamine synthases (pga). Whether any of these are mutated in the meta variants is not stated. It still also has lipopolysaccharide (LPS), which is absent in the ClearColi strain, which is really sick and clumpy —the genes of the latter are msbA148 ΔgutQ ΔkdsD ΔlpxL ΔlpxM ΔlpxP ΔpagP ΔeptA. The lack of flagella means it is non-motile.

Unrestritive. It has the dam and dcm methylases, but not hsd or mrr restriction system. Like a W3110, basically. So dpnI digestion will work and it accepts all plasmids.

Smells different. Pseudomonas aeruginosa smells like bubblegum and Geobacillus thermoglucosidasius like toast.... and E. coli smells acrid, lavatorial and sweaty, with a hint of floral at the same time even in M9 —LB is more fruity than floral I'd say. Not that one should smell strains, but K-12 strains smell worse than B-strains, possibly due to the fact they are more catabolic, so more indole (toilet/floral), cresol (pig) mixed acid fermentation (sour, various enzymes) —luckily E. coli lacks BCAA decarboxylase or it would smell like a hangover. Which reminds me of the shame that the E. coli strain that smells like banana made by the MIT 2008 iGEM team was never finished...

Genotype. Its full genotype is:
E. coli K-12 F- λ- ∆abgA ∆abgB ∆abgR ∆abgT ∆afuB ∆afuC ∆alpA ∆ampH ∆amyA ∆appY ∆argF ∆bfd ∆bfr ∆borD ∆cheA ∆cheB ∆cheR ∆cheW ∆cheY ∆cheZ ∆chiA ∆codA ∆codB ∆cpsB ∆cpsG ∆cspB ∆cspF ∆cspI ∆cynR ∆cynS ∆cynT ∆cynX ∆dbpA ∆dicA ∆dicB ∆dicC ∆dicF ∆eaeH ∆elbA ∆emrE ∆endA ∆essD ∆essQ ∆etp ∆fcl ∆feaB ∆feaR ∆fecA ∆fecB ∆fecC ∆fecD ∆fecE ∆fecI ∆fecR ∆fhuA ∆fhuB ∆fhuC ∆fhuD ∆fimA ∆fimB ∆fimC ∆fimD ∆fimE ∆fimF ∆fimG ∆fimH ∆fimI ∆flgA ∆flgB ∆flgC ∆flgD ∆flgE ∆flgF ∆flgG ∆flgH ∆flgI ∆flgJ ∆flgK ∆flgL ∆flgM ∆flgN ∆flhA ∆flhB ∆flhC ∆flhD ∆flhE ∆fliA ∆fliC ∆fliD ∆fliE ∆fliF ∆fliG ∆fliH ∆fliI ∆fliJ ∆fliK ∆fliL ∆fliM ∆fliN ∆fliO ∆fliP ∆fliQ ∆fliR ∆fliS ∆fliT ∆fliY ∆fliZ ∆flu ∆flxA ∆galF ∆gatA ∆gatB ∆gatC ∆gatD ∆gatR ∆gatY ∆gatZ ∆glcA ∆glcB ∆glcC ∆glcD ∆glcE ∆glcF ∆glcG ∆glf ∆gmd ∆gnsB ∆gspA ∆gspC ∆gspD ∆gspE ∆gspF ∆gspG ∆gspH ∆gspI ∆gspJ ∆gspK ∆gspL ∆gspM ∆gspO ∆hokC ∆hokD ∆hokE ∆hsdM ∆hsdR ∆hsdS ∆hslJ ∆iadA ∆icdC ∆ileY ∆insA-1 ∆insA-2 ∆insA-3 ∆insA-4 ∆insA-5 ∆insA-6 ∆insA-7 ∆insB-1 ∆insB-2 ∆insB-3 ∆insB-4 ∆insB-5 ∆insB-6 ∆insB-7 ∆insC-1 ∆insC-2 ∆insC-3 ∆insC-4 ∆insC-5 ∆insC-6 ∆insD-1 ∆insD-2 ∆insD-3 ∆insD-4 ∆insD-5 ∆insD-6 ∆insD-7 ∆insE-1 ∆insE-2 ∆insE-3 ∆insE-4 ∆insE-5 ∆insF-1 ∆insF-2 ∆insF-3 ∆insF-4 ∆insF-5 ∆insG ∆insH-1 ∆insH-10 ∆insH-11 ∆insH-2 ∆insH-3 ∆insH-4 ∆insH-5 ∆insH-6 ∆insH-7 ∆insH-8 ∆insH-9 ∆insI-1 ∆insI-2 ∆insI-3 ∆insJ ∆insK ∆insL-1 ∆insL-2 ∆insL-3 ∆insM ∆insN-1 ∆insN-2 ∆insO-1 ∆insO-2 ∆intA ∆intB ∆intD ∆intE ∆intF ∆intG ∆intQ ∆intR ∆intS ∆intZ ∆isrA ∆isrC ∆kil ∆kptA ∆lacA ∆lacI ∆lacY ∆lacZ ∆lar ∆ldhA ∆lit ∆lomR ∆maoC ∆mcrA ∆mcrB ∆mcrC ∆mhpA ∆mhpB ∆mhpC ∆mhpD ∆mhpE ∆mhpF ∆mhpR ∆mhpT ∆micC ∆mmuM ∆mmuP ∆mntH ∆mokC ∆motA ∆motB ∆mpaA ∆mppA ∆mrr ∆nfnB ∆nhaA ∆nhaR ∆ninE ∆nmpC ∆nohA ∆nohB ∆nudD ∆nupC ∆ogrK ∆ompN ∆ompT ∆paaA ∆paaB ∆paaC ∆paaD ∆paaE ∆paaF ∆paaG ∆paaH ∆paaI ∆paaJ ∆paaK ∆paaX ∆paaY ∆perR ∆pin ∆pinH ∆pinQ ∆pinR ∆pitB ∆pppA ∆prpB ∆prpC ∆prpD ∆prpE ∆prpR ∆racC ∆racR ∆recE ∆recT ∆relB ∆relE ∆rem ∆renD ∆rfbA ∆rfbB ∆rfbC ∆rfbD ∆rfbX ∆rhsA ∆rhsB ∆rhsC ∆rhsD ∆rhsE ∆rusA ∆ryeE ∆rzoD ∆rzoR ∆rzpD ∆rzpR ∆sbmA ∆sgcA ∆sgcB ∆sgcC ∆sgcE ∆sgcQ ∆sgcR ∆sgcX ∆sieB ∆sokC ∆stfE ∆stfQ ∆stfR ∆tap ∆tar ∆tauA ∆tauB ∆tauC ∆tauD ∆tfaD ∆tfaE ∆tfaQ ∆tfaR ∆tfaS ∆trkG ∆tsr ∆tynA ∆uspE ∆uspF ∆wbbH ∆wbbI ∆wbbJ ∆wbbK ∆wbbL ∆wcaA ∆wcaB ∆wcaC ∆wcaD ∆wcaE ∆wcaF ∆wcaI ∆wcaJ ∆wcaK ∆wcaL ∆wcaM ∆wza ∆wzb ∆wzc ∆wzxC ∆yafW ∆yafX ∆yafY ∆yafZ ∆yagA ∆yagB ∆yagE ∆yagF ∆yagG ∆yagH ∆yagI ∆yagJ ∆yagK ∆yagL ∆yagM ∆yagN ∆yagP ∆yagQ ∆yagR ∆yagS ∆yagT ∆yagU ∆yagV ∆yagW ∆yagX ∆yagY ∆yagZ ∆yahA ∆yahB ∆yahC ∆yahD ∆yahE ∆yahF ∆yahG ∆yahH ∆yahI ∆yahJ ∆yahK ∆yahL ∆yahM ∆yahN ∆yahO ∆yaiL ∆yaiO ∆yaiP ∆yaiS ∆yaiT ∆yaiV ∆yaiW ∆yaiX ∆yaiY ∆yaiZ ∆ybbC ∆ybbD ∆ybcC ∆ybcD ∆ybcK ∆ybcL ∆ybcM ∆ybcN ∆ybcO ∆ybcQ ∆ybcS ∆ybcV ∆ybcW ∆ybcY ∆ybdF ∆ybdG ∆ybdJ ∆ybdK ∆ybfB ∆ybfC ∆ybfD ∆ybfL ∆ybfO ∆ybfQ ∆yccC ∆yccZ ∆ycdP ∆ycdQ ∆ycdR ∆ycdS ∆ycdT ∆ycdU ∆ycfK ∆ycgE ∆ycgF ∆ycgG ∆ycgH ∆ycgX ∆ycgZ ∆ycjG ∆ycjY ∆ycjZ ∆ydaC ∆ydaE ∆ydaF ∆ydaG ∆ydaL ∆ydaM ∆ydaN ∆ydaO ∆ydaQ ∆ydaS ∆ydaT ∆ydaU ∆ydaV ∆ydaW ∆ydaY ∆ydbA ∆ydbC ∆ydbD ∆ydbH ∆ydbJ ∆ydbK ∆ydbL ∆ydcC ∆ydcD ∆ydcE ∆yddH ∆ydfA ∆ydfB ∆ydfC ∆ydfD ∆ydfE ∆ydfG ∆ydfH ∆ydfI ∆ydfJ ∆ydfK ∆ydfO ∆ydfP ∆ydfQ ∆ydfR ∆ydfT ∆ydfU ∆ydfV ∆ydfW ∆ydfX ∆ydfZ ∆yeaJ ∆yecC ∆yecS ∆yedD ∆yedE ∆yedF ∆yedK ∆yedL ∆yedM ∆yedN ∆yedO ∆yeeA ∆yeeP ∆yeeR ∆yeeS ∆yeeT ∆yeeU ∆yeeV ∆yeeW ∆yeeX ∆yegP ∆yegQ ∆yegR ∆yegS ∆yegZ ∆yejO ∆yfdG ∆yfdH ∆yfdI ∆yfdK ∆yfdL ∆yfdM ∆yfdN ∆yfdO ∆yfdP ∆yfdQ ∆yfdR ∆yfdS ∆yfdT ∆yfeA ∆yfeO ∆yffL ∆yffM ∆yffN ∆yffO ∆yffP ∆yffQ ∆yffR ∆yffS ∆yfjH ∆yfjI ∆yfjJ ∆yfjK ∆yfjL ∆yfjM ∆yfjN ∆yfjO ∆yfjP ∆yfjQ ∆yfjR ∆yfjS ∆yfjT ∆yfjU ∆yfjV ∆yfjW ∆yfjX ∆yfjY ∆yfjZ ∆ygaF ∆ygaQ ∆ygaR ∆ygaT ∆ygeL ∆ygeM ∆ygeN ∆ygeO ∆ygeP ∆ygeQ ∆yghD ∆yghE ∆yghF ∆yghG ∆yghJ ∆yghO ∆yghQ ∆yghR ∆yghS ∆yghT ∆ygiL ∆yhcA ∆yhcD ∆yhcE ∆yhcF ∆yhhH ∆yhhI ∆yhhY ∆yhhZ ∆yhiS ∆yibA ∆yibG ∆yibJ ∆yjgW ∆yjgX ∆yjgZ ∆yjhA ∆yjhB ∆yjhC ∆yjhD ∆yjhE ∆yjhF ∆yjhG ∆yjhH ∆yjhI ∆yjhP ∆yjhQ ∆yjhR ∆yjhS ∆yjhT ∆yjhU ∆yjhV ∆yjhW ∆yjhX ∆yjiA ∆yjiC ∆yjiD ∆yjiE ∆yjiG ∆yjiH ∆yjiJ ∆yjiK ∆yjiL ∆yjiM ∆yjiN ∆yjiO ∆yjiP ∆yjiQ ∆yjiR ∆yjiS ∆yjiT ∆yjiV ∆yjiW ∆yjiX ∆yjiY ∆yjiZ ∆yjjM ∆yjjN ∆ykfA ∆ykfB ∆ykfC ∆ykfF ∆ykfG ∆ykfH ∆ykfI ∆ykgA ∆ykgB ∆ykgC ∆ykgD ∆ykgE ∆ykgF ∆ykgG ∆ykgH ∆ykgI ∆ykgJ ∆ykgK ∆ykgL ∆ykgM ∆ykgN ∆ykgO ∆ykiB ∆ylbG ∆ylbH ∆ylcE ∆ylcG ∆ymcA ∆ymcB ∆ymcC ∆ymcD ∆ymdE ∆ymfD ∆ymfE ∆ymfG ∆ymfH ∆ymfI ∆ymfJ ∆ymfK ∆ymfL ∆ymfM ∆ymfN ∆ymfO ∆ymfP ∆ymfQ ∆ymfR ∆ymfS ∆ymfT ∆ymgA ∆ymgB ∆ymgC ∆ymgD ∆ymgF ∆ymgG ∆ymjC ∆ynaA ∆ynaE ∆ynaI ∆ynaJ ∆ynaK ∆ynbA ∆ynbB ∆ynbC ∆ynbD ∆ynbE ∆yncI ∆yncM ∆ynfN ∆ynfO ∆ynfP ∆yoeA ∆yoeF ∆ypdJ ∆ypeC ∆ypjA ∆ypjB ∆ypjC ∆ypjF ∆ypjJ ∆ypjK ∆ypjL ∆ypjM ∆yqaC ∆yqaD ∆yqiC ∆yqiG ∆yqiH ∆yqiI ∆yrhA ∆yrhB ∆yrhC

This list was generated by copypasting the supplementary table and munging it in python3
>>> x='''copypasted_table'''
>>> x2=[p.split() for p in x.split('\n') if len(p)>20]
>>> x3=[x2[i][1] for i in sorted(range(len(x2)), key=lambda k: x2[k][1])]
>>> print('∆'+' ∆'.join(x3))

1 comment:

  1. Hi Matteo,

    I stumbled across this post looking for something else, and decided to read it. Nice summary, and I for one don't take offense to the IKEA comparison. The MDS strain constructions were a convoluted process, to say the least.

    As for smelling cultures, I always thought Pseudomonas aeruginosa smelled more like grapes. And if you think K-12 strains smell bad, track down the E. coli F strain used as a host for 'phage T5 back in the 1970s.

    Thanks for an enjoyable diversion; I'll bookmark your blog for future visits.