All the World Is Not E. coli

by Elio

Like most peo­ple in­ter­ested in bac­te­r­ial phys­i­ol­ogy, I spent much of my life with the nearly reli­gious per­sua­sion that the start­ing con­di­tion for study­ing growth is when cells and their constitu­ents all in­crease in uni­son. In prac­tice, such "bal­anced growth" is achieved when bac­te­ria grow ex­ponentially at low con­cen­tra­tions. Much was learned from this stance, es­pe­cially when it came to un­der­stand­ing the mech­a­nism of reg­u­la­tion of gene ex­pres­sion. One of the main points has been that syn­the­siz­ing the prin­ci­pal sorts of macro­mol­e­cules pro­ceeds at the same in­di­vid­ual rate re­gardless of the growth rate. You need to make more pro­teins? Bring up more ri­bo­somes! See here for a re­view ar­ti­cle.

Elec­tron mi­cro­graph of Methanococ­cus mari­paludis' show­ing promi­nent ar­chaella fea­tures. Cour­tesy of Dr. Ken F. Jar­rell and Shin-Ichi Aizawa. Mag bar of 500nm. Source

But a nag­ging ques­tion re­mained, what does this have to do with the real world? Out­side the cozy con­fines of Sal­monella or E. co­li in the lab­o­ra­tory, mi­crobes sel­dom find them­selves un­der bal­anced growth con­di­tions. Along with the un­der­stand­ing that mi­crobes of our planet are much more abun­dant than clas­si­cally thought came the re­al­iza­tion that most of them are starv­ing or nearly so. This ob­vi­ously fol­lows from the fact that the largest nat­ural en­vi­ron­ments, such as the oceans or the sub­soils, are "thin soups" or, to use science talk, olig­otrophic.

How can we study the phys­i­ol­ogy of such a huge va­ri­ety of mi­crobes that live un­der so many dif­fer­ent con­di­tions? Alas, we must pick and choose exam­ples, hop­ing that the choices are ger­mane. One such newly re­ported study car­ries the ti­tle: "An al­ter­na­tive re­source al­lo­ca­tion strat­egy in the chemolithoau­totrophic ar­chaeon. Methanococ­cus mari­paludis." It is au­thored by in­ves­ti­ga­tors from Stan­ford and the Scripps Re­search In­sti­tute, the se­nior (last) au­thor be­ing Al­fred Spormann. They conclud­ed that "In con­trast to re­ly­ing on gene reg­u­la­tion like meta­bol­i­cally ver­sa­tile, het­erotrophic model bac­te­ria such as Es­cherichia coli, Methanococ­cus mari­paludis re­sponds to en­ergy lim­i­ta­tion by re­dis­trib­ut­ing en­ergy for cel­lu­lar main­te­nance and chang­ing cata­bolic and ri­bo­so­mal ac­tiv­i­ties."

What does this mean? In brief, it sug­gests that there is a grand al­ter­na­tive to the con­ven­tional be­lief. Whereas E. coli al­ters the amount of its ri­bo­somes (its pro­tein syn­thetic ma­chin­ery) with the growth rate but keeps the ac­tiv­ity of its ri­bo­somes pretty con­stant, M. mari­paludis sim­ply changes its ri­bo­some ac­tiv­ity. These two con­trast­ing tac­tics im­ply the ex­is­tence of at least two dif­fer­ent phys­i­o­log­i­cal strate­gies for cop­ing with chang­ing en­vi­ron­ments, one within the world of nu­tri­tional af­flu­ence, the other, un­der con­di­tions of famine.

A word about Methanococ­cus mari­paludis. It's a methanogenic, strictly anaer­o­bic ar­chaeon first de­scribed in 1983 from a salt-marsh sed­i­ment in South Car­olina. Its species name means 'sea marsh.' It makes methane from car­bon diox­ide us­ing hy­dro­gen as the re­duc­ing agent. It has be­come a pop­u­lar model species be­cause it grows rel­a­tively fast and can be read­ily ma­nip­u­lated ge­net­i­cally. It is pop­u­lar among as­tro­bi­ol­o­gists be­cause it can grow on "Mars Soil Sim­u­lant."

Fig­ure 2. High-level overview of pro­teome com­position at dif­fer­ent growth rates. Pro­teins are or­ga­nized into func­tional sec­tors, show­ing data from chemo­stat-grown cells (filled di­a­monds) and an ex­po­nen­tial phase batch cul­ture sam­ple (open di­a­monds). (B) Pro­teome al­lo­ca­tion to sub­sys­tems com­pris­ing >2% of the to­tal pro­teome in at least one sam­ple. Dot­ted lines show lin­ear re­gres­sions. Source

The au­thors of this pa­per car­ried out an ex­haus­tive sys­tems-level in­ves­ti­ga­tion of the phys­i­ol­ogy of this or­ganism grow­ing over a wide range of rates of en­ergy li­mitation. Us­ing a chemo­stat, they grew their cul­tures at rates 1 to 39% of the max­i­mum (which is a dou­bling time of 2 to 3 hours). Un­like E. coli, the pro­teome did not change ap­pre­cia­bly with the growth rate, nei­ther did the cell con­tent of DNA and RNA, nor did the size of the cells. Ri­bo­so­mal RNA con­sti­tuted a con­stant frac­tion of all RNA and, again un­like what hap­pens in the world of E.coli, it did not di­min­ish upon amino acid star­va­tion (no strin­gent re­sponse). Con­trari­wise, the frac­tion of ri­bo­some in polysomes de­creased at slower growth rates, sug­gest­ing that the ef­fi­ciency of the work­ing ri­bo­somes de­creased un­der these con­di­tions, which is not how E. coli reg­u­lates its biosyn­thetic busi­ness. They also es­ti­mated the ex­tent of main­te­nance en­ergy, the amount of sub­strate used for the up­keep of cell func­tions and found that it was higher at high growth rates.

Fig­ure 3. Ri­bo­some ac­tiv­ity. Polysome frac­tion (black di­a­monds) cor­re­lated log­a­rith­mi­cally with di­lu­tion rate (show­ing data from chemo­stat-grown cells (fil­led di­a­monds) and an exponen­tial phase batch cul­ture sam­ple (open dia­monds). Shaded ar­eas de­pict 5% con­fi­dence level in­ter­vals. Source

What does all this mean? It sug­gests that in the mi­cro­bial world there are two very dif­fer­ent strate­gies for cop­ing with dif­fer­ent nu­tri­tional con­di­tions in the en­vi­ron­ment. In one, the "E. coli va­ri­ety," the growth rates dic­tates the size of the biosyn­thetic ma­chin­ery but keeps its ac­tiv­i­ties con­stant. In the other, the M. mari­paludis one, the bio­synthetic ma­chin­ery re­mains con­stant, but its ac­tiv­i­ties vary. As the au­thors say: "The M. mari­paludis strat­egy does not re­quire com­plex reg­u­la­tory fea­tures that are com­monly found in mi­crobes se­lected for com­pe­ti­tion for fast growth (link)." This strat­egy has been found in some other methanogenic ar­chaea. The au­thors spe­culate that, among other things, this tac­tic may al­low for faster re­sump­tion of growth when food be­comes again avail­able. This may in­deed be char­ac­ter­is­tic of or­gan­isms adapted to com­pete with oth­ers in nu­tri­tion­ally fal­low en­vi­ron­ments.

A word about two of us STC blog­gers. This sub­ject is near the hearts of both Roberto and Elio. Ro­berto was one of the first to in­ves­ti­gate what hap­pens when E. coli en­ters the sta­tion­ary phase of growth, Elio, stud­ied the de­pen­dence of macro­mol­e­c­u­lar syn­the­sis and cell di­vi­sion on the growth rate. We are both happy to learn of a grand al­ter­na­tive.

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