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Tiny genome may be melting away, study suggests

Researchers have identified the smallest known cellular genome, and say it may suffer a strange fate.

Oct. 12, 2006
Special to World Science  

Biologists have long won­dered what is the small­est num­ber of genes re­quired for an or­gan­ism to sur­vive. Iden­ti­fy­ing this “min­i­mal ge­nome,” some re­search­ers think, could re­veal the most bas­ic re­quire­ments of life, and thus pro­vide a more fun­da­men­tal un­der­stand­ing of it.

A bac­te­ri­o­cyte, a type of mo­di­fied fat cell in cer­tain in­sects that con­tains sym­bi­o­tic bac­te­ria. Bac­te­ri­ocytes of Pa­chyp­syl­la ve­nus­ta, shown ab­ove, con­tain Car­so­n­el­la bac­te­ri­a. The mi­crobes ap­pear as dark blue, tu­bu­lar struc­tures. The light­er circ­les are cell nu­clei of the host or­ga­n­ism. (© Sci­ence)

Now, sci­en­t­ists say they’ve found the ti­ni­est known ge­nome of a liv­ing thing, along with two huge sur­pri­ses.

First, the ge­nome is just one third the size of the “smal­lest” known be­fore. But pos­si­bly strang­er, they claim, it ap­pears too pu­ny to al­low its own­er, a bac­te­ri­um, to live on as a spe­cies much long­er. 

Like a cash-strapped com­pa­ny that has to merge with a rich­er firm to keep go­ing, they say, the mi­crobe and its genes seem to be lit­er­al­ly fus­ing in­to a larg­er crea­ture, be­com­ing cogs in its cel­lu­lar ma­chi­n­er­y.

“The race to find the small­est mi­cro­bi­al ge­nome has tak­en an amaz­ing turn,” wrote Siv An­ders­sen of Upp­sa­la Uni­ver­si­ty, Swe­den, in a com­men­tary in the Oct. 13 is­sue of the re­search jour­nal Sci­ence.

Researchers stu­dy­ing small ge­nomes have faced sur­prises be­fore. 

Pre­vi­ous work, for in­stance, found that a bac­te­ri­al ge­nome could be ar­ti­fi­cial­ly pared down to mi­nus­cule sizes; but then the bug could sur­vive on­ly on the mi­cro­bi­al equiv­a­lent of life sup­port, bathed in a care­ful­ly se­lected nu­tri­ent mix. That the crea­ture could live on­ly in ar­ti­fi­cial set­tings sug­gest­ed to some that the “min­i­mal ge­nome” con­cept was a bit fuzzy.

The new find­ings may fur­ther mud­dle things. 

The an­nounced new record-holder for ti­ni­est ge­nome is the bac­te­ri­um Car­sonella rud­dii, which lives in an in­sect, and has a se­quenced ge­nome—or com­plete set of DNA—with about 182 func­tion­al genes. These cor­re­spond to 160,000 “let­ters” of ge­net­ic code; pre­vi­ous es­ti­mates had placed the min­i­mal ge­nome at about 400,000.

“It’s un­be­liev­a­ble, real­ly,” said Nan­cy A. Moran of the Uni­ver­si­ty of Ar­i­zo­na in Tuc­son, Ariz., one of the sci­en­tists who con­ducted the new re­search. “It’s be­lieved that more genes are re­quired for a cell to work.” The find­ing pro­vides new in­sights in­to bac­te­ri­al ev­o­lu­tion, Moran and col­leagues wrote, also in the Oct. 13 Sci­ence.

The microbe lives within an Ar­i­zo­na in­sect, Pa­chyp­syl­la ve­nus­ta, that like many in­sects feeds on plant sap. This is­n’t very nu­tri­tious. To live, such in­sects of­ten re­ly on res­i­dent bac­te­ri­a that make and share key nu­tri­ents with them. The host and mi­crobes de­pend on each oth­er to live, a re­la­tion­ship called en­do­sym­bio­sis. The bond is so close and an­cient that the mi­crobes live with­in spe­cial in­sect cells that have ev­olved to house them, called bac­te­ri­o­cytes. 

The bac­te­ri­a thus live in a shel­tered world with a sim­ple, pre­dict­a­ble di­et and lifestyle. So they get by with sim­ple ge­net­ic in­struc­tions. If they or their an­ces­tors had any ex­tra, un­need­ed genes, these would ge­ner­al­ly have been lost over the course of ev­o­lu­tion.

The re­search­ers col­lect­ed Pa­chyp­syl­la ve­nus­ta bugs from hack­ber­ry trees on their uni­ver­si­ty cam­pus and around town. They ex­tracted the Car­sonella DNA and se­quenced it, and got a jolt. “It lost genes that are con­sid­ered ab­so­lute­ly nec­es­sar­y. Try­ing to ex­plain it will prob­a­bly help re­veal how cells can work,” said Moran.

The sci­en­tists spec­u­late that in the bac­te­ri­um’s ev­o­lu­tionary past, some of its genes moved in­to the in­sect’s own ge­nome, be­gin­ning a pro­cess of gene takeo­ver.

An­i­mal and plant cells have spe­cialized in­ter­nal struc­tures called or­ganelles, ti­ny sacs of ma­chin­ery used for var­i­ous pur­poses. Strong ev­i­dence sug­gests many of these or­ganelles are de­scen­dants of sym­bi­ot­ic bac­te­ri­a that once lived free, but grad­u­al­ly be­came in­cor­po­rat­ed in­to the cell. A trans­fer of genes from the bac­te­ri­um to the host is of­ten part of the pro­cess. 

Car­sonella may likewise be turn­ing in­to an or­gan­elle, the re­search­ers wrote.

In a sec­ond study pub­lished in the same is­sue of the jour­nal, re­search­ers with Va­lèn­cia Uni­ver­si­ty in Va­lèn­cia, Spain, de­scribed find­ing a si­m­i­lar endosym­bi­ot­ic bac­te­ri­um, Buch­n­era aphi­di­co­la, whose ge­nome is about 5 per­cent larg­er than that of Car­so­nel­la. 

Buch­n­era may be on its way to to­tal ex­tinc­tion, the au­thors ar­gued, be­cause it has lost many func­tions that would let it help its host. Oth­er bac­te­ri­a co­hab­it­ing in the same in­sect seem to have have tak­en over the func­tions, they wrote.

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