Tal­mu­dic Ques­tion #91

Eu­kary­otes, typ­i­cally have the lux­ury of time and the sep­a­ra­tion of pow­ers... aka the nu­cleus and the un­cou­pling of tran­scrip­tion and trans­la­tion. Like gov­ern­ments they can work out when and if they need some­thing done, in this case the ex­pres­sion of a par­tic­u­lar gene, and like the Con­gress of the US, the ge­netic pro­gram of eu­kary­otes can pre­scribe an om­nibus spend­ing bill cov­er­ing all as­pects of their im­me­di­ate needs through the cleaver tran­scrip­tion of a uni­ver­sal tran­scrip­tion fac­tor. For the prokary­otes, be­cause of the ab­sence of the sep­a­ra­tion of pow­ers, the link­age of tran­scrip­tion & trans­la­tion and be­cause time is of­ten of the essence they re­quire com­pact genomes that can get the to­tal job done with the as­sent of one pro­moter. No time to cau­cus, no time for de­bate, they need the job done and achieve re­sults quickly. Eu­kary­otes con­trol the ma­jor­ity of their tran­scrip­tion via pos­i­tive con­trol, while the prokary­otic world con­trols 75% of its ex­pres­sion via neg­a­tive con­trol. So this is long way of say­ing eu­kary­otes have the abil­ity to sweat the de­tails while the prokary­otes just have time to sweat. The net con­se­quence as the first com­menter sug­gested, is that the genome of eu­kary­otes is a mega-operon, like a fed­eral gov­ern­ment... all things to all?
Elio replies: How timely! And how clever! You have a way with sim­i­les (or is it analo­gies?), as you el­e­gantly dis­play from time to time in our pod­cast This Week in Mi­cro­bi­ol­ogy (TWiM). Thanks for shar­ing this in­sight.

I agree that there are some won­der­ful evoca­tive com­ments here. But I would add this. In the Epu­lop­is­cium story, Elio has writ­ten pre­vi­ously about the is­sue of nu­cleoids need­ing to "ser­vice" a vol­ume of cy­to­plasm (to fol­low the whole sep­a­ra­tion of pow­ers metaphor). Large cy­to­plas­mic vol­umes ne­ces­si­tate large num­bers of nu­cleoids, be­cause of the sheer vis­cos­ity of the nu­clear ma­te­r­ial and—the ugly lit­tle se­cret in mol­e­c­u­lar biology—how the ar­eas of reg­u­la­tory "need" are se­lec­tively made avail­able for Cen­tral Dogma ma­chin­ery, while keep­ing other por­tions of the genome com­pact. This makes sense for "gi­ant" mi­crobes like Epu­lop­is­cium, hence the myr­iad nu­cleoids present (again, Elio pre­sented that very ef­fec­tively here at STC a while back).
My feel­ing is that even in the sim­plest of or­gan­isms, this is a deep is­sue. And in eu­kary­otes, it is even more rel­e­vant.
So I agree that neg­a­tive reg­u­la­tion is a crit­i­cal level in prokary­otes, per­haps due to the im­me­di­acy of en­vi­ron­men­tal im­pacts on the cell (but is that not also true in sin­gle celled eu­kary­otes?). But I am al­ways amazed at the in­ter­lock­ing pat­terns of re­lated reg­u­lons, even in bac­te­ria un­der a co­l­i­cen­tric mi­cro­scope.
Still, I like to think that eu­kary­otes have the reg­u­la­tory sys­tem they do be­cause dif­fer­ent cell types need to reg­u­late genes in many dif­fer­ent ways—not like a switch, but like a dial. But again—what about the sin­gle celled eu­kary­otes?
I fear I suf­fer from mul­ti­cel­lu­lar­ce­ntrism, iron­i­cally. A won­der­ful Tal­mu­dic Ques­tion, in­deed.
Elio replies: I am re­minded of a Gilbert and Sul­li­van quote: "Things are sel­dom what they seem,
Skim milk mas­quer­ades as cream; ..." I won­der who's do­ing the mas­querad­ing here and ap­pre­ci­ate how you ex­tended the ar­gu­ment. Nice com­ment.

Does the pres­ence of relict operon-like fea­tures in some mi­to­chon­dr­ial DNA (but not in the host nu­cleus) sup­port the idea that cer­tain eu­kary­otic traits of the host lin­eage pre­date ac­qui­si­tion of the an­ces­tral mi­to­chon­dr­ial en­dosym­biont?

I think one of the chal­lenges dur­ing eu­kar­i­o­gen­e­sis was to con­trol the traf­fic of mo­bile el­e­ments from en­dosim­by­onts to nu­cleus. So the in­ter­fer­ence meth­ods de­vel­oped to con­front this col­lat­eral ef­fect of eu­kar­i­o­gen­e­sis, ended with hor­i­zon­tal gene tran­fers and also ex­tin­guished the ac­tiv­i­ties of oper­ons...