Ac­tive Lysogeny Reg­u­la­tory Switches

Scars That Can Make Genes Whole

by Daniel P. Haeusser

Scars are not in­juries… A scar is a heal­ing. Af­ter in­jury, a scar is what makes you whole.
—China Miéville, The Scar

Last year Small Things Con­sid­ered was hurt by the loss of one of our reg­u­lar con­trib­u­tors, Mar­vin Fried­man, who had a strong pas­sion and joy for mi­cro­bi­ol­ogy and this blog. I found my­self look­ing through some of his fea­tured pieces in re­mem­brance and was in­trigued by one that dis­cussed de­ve­lop­mentally reg­u­lated prophage ex­ci­sion. This re­mark­able case in­volves re­con­sti­tu­tion of a com­­pe­tence gene es­sen­tial for bac­te­r­ial phago­so­mal es­cape dur­ing mam­malian cell in­fec­tion by Lis­te­r­ia mono­cy­to­genes.

Fig­ure 1. The Red Queen Hy­poth­e­sis – named in re­fer­ence to a scene from Carroll's 'Through the Look­ing-Glass', this de­scribes an evo­lu­tion­ary sys­tem of species in­ter­ac­tion where con­tin­u­ing a­dap­ta­tion is needed for one species to main­tain its rel­a­tive fit­ness in re­la­tion to an­other, co- evolv­ing species, such as in preda­tor-prey in­ter­ac­tions. The in­ti­macy of lysogeny re­pre­sents a sit­u­a­tion where mu­tu­ally be­ne­fi­cial traits, like a regu­latory switch, could be se­lected for rather than sim­ply in­creased an­tag­o­nis­tic traits. Source

I won­dered how many other cases are now known of such a com­pelling story of ben­e­fi­cial co-evo­lu­tion. Mi­cro­biologists have dis­cov­ered both vi­able phage and scars of DNA rem­nants from an­ces­tral phage in­serted within host genes. These cod­ing in­ter­rup­tions pre­vent gene func­tion, but in some cases host de­vel­op­men­tal path­ways have evolved to con­trol­lably ex­cise these se­quences, these scars, to make a gene whole once more. (Please note this is quite dis­tinct from CRISPR sys­tems, which Merry nicely sum­ma­rized here.) A 'Per­spec­tive' pa­per by Feiner et al. from Oc­to­ber pro­vides an ex­cel­lent up­date on this form of bac­terium-phage in­ter­ac­tion that the au­thors term an 'ac­tive lysogeny reg­u­la­tory switch'.

Preda­tors, Prey, and Co­op­er­a­tion

The pre­da­tion by phage on bac­te­ria for vi­ral repli­ca­tion ex­erts a pres­sure on the cell for the se­lec­tion of de­fense mech­a­nisms that, in turn, ex­ert pres­sure back on the phage to adapt, in a clas­sic Red Queen sit­u­a­tion (Fig­ure 1). But, as the au­thors point out (with British spelling): "Lysogeny has a unique role within the bac­­terium-phage arms race in that it favours the de­vel­op­ment of sym­bi­otic in­ter­ac­tions be­cause the fu­sion of phage and bac­te­r­ial genomes, even if tem­po­rary, pro­vides an eco­log­i­cal win­dow for the evo­lu­tion of mu­tu­ally ben­e­fi­cial func­tions."

Lyso­genic con­ver­sion, a sit­u­a­tion where chro­mo­so­ma­lly in­te­grated phages ex­press genes that in­crease bac­te­r­ial fit­ness, is one ex­am­ple of ben­e­fi­cial co­ex­is­tence. Can­tacuzene & Bon­cieu and Fro­bisher & Brown dis­cov­ered it in 1926 and 1927, re­spec­tively, with ex­per­i­ments on Strep­to­coc­cus that bear sim­i­lar­i­ties with those that led to Griffith's trans­form­ing prin­ci­pal in 1928. Feiner et al. high­light sev­eral of the ex­am­ples of vir­u­lence-af­fect­ing lyso­genic con­ver­sions dis­cov­ered since then. Yet, one imag­ines that ex­am­ples not linked to patho­gen­e­sis must surely also ex­ist, re­main­ing to be un­cov­ered.

Fig­ure 2. The ac­tive lysogeny reg­u­la­tory switch as de­scribed by Feiner et al. Ac­tive lysogeny is a sit­u­a­tion where a phage in­te­grated into a bac­te­ri­al host chro­mo­some serves (at least in part) as a ge­netic reg­u­la­tory switch for the ex­press­ion of con­di­tion­ally im­por­tant bac­te­r­ial genes at that in­tegration site. In their Per­spec­tive the au­thors additio­nally dif­fer­en­ti­ate be­tween re­ver­sible and non-rever­si­ble forms of this re­gu­la­to­ry switch. Source

In­ser­tion of a tem­per­ate phage into a host chro­mo­some will be dele­te­ri­ous if the phage genome in­ter­rupts a func­tio­nally es­sen­tial se­quence. How­ever, in­ser­tion that in­ter­rupts a host se­quence that is only con­di­tion­ally vi­tal per­mits evo­lu­tion of an­other ben­e­fi­cial co­ex­is­tence where phage ex­ci­sion (and re-in­ser­tion in some cases) could be gov­erned by the same cel­lu­lar sig­nals that ac­ti­vate re­la­ted con­di­tional gene reg­u­la­tion. Sev­eral such ac­tive ly­so­ge­ny reg­u­la­tory switches (Fig­ure 2) have now been de­scribed, be­yond the L. mono­cy­to­gens–phage in­ter­ac­tion that Mar­vin wrote about.

It's a Small World

Phage genome re­arrange­ments that oc­cur spon­ta­ne­ous­ly have long been ob­served. Con­trolled, con­di­tional DNA re­arrange­ments of ac­tive lysogeny, how­ever, were first (to my knowl­edge) noted in 1990 through re­search done by one of my grad school pro­fes­sors, Bar­bara Kunkel, while she worked in the lab of my re­search grand­fa­ther, Rich Losick. This case in­volves the de­ve­lop­men­tal­ly con­trolled ex­ci­sion of the phage-de­rived skin el­e­ment from the sigK gene dur­ing Ba­cillus sub­tilis sporu­la­tion. Since that time we know of a small num­ber of other ac­tive lysogeny cas­es, such as in­volve­ment in con­di­tional sup­pres­sion of the DNA mis­match re­pair sys­tem of Strep­to­coc­cus pyo­genes and in reg­u­la­tion of cyanobac­te­r­ial het­e­ro­cyst dif­fer­en­ti­a­tion for ni­tro­gen fix­a­tion.

How­ever, sporu­la­tion seems to be a re­cur­ring theme among the few ex­am­ples of this type of re­gu­la­to­ry switch. Af­ter the dis­cov­ery in B. sub­tilis, sim­i­lar re­arrange­ments were found in spo­ru­la­tion genes of re­lated spore-form­ing Bacil­lus species and the not-too dis­tant rel­a­tive, Clostrid­ium dif­fi­cile (re­cently re­named as Pep­to­clostrid­ium dif­fi­cile). Se­quence iden­ti­fi­ca­tion of a phage in an­other B. sub­tilis gene, spsM, led to an­other demon­stra­tion of ac­tive lysogeny and es­tab­lished a novel com­po­nent of this model organism's rel­a­tively un­char­ac­ter­ized spore coat. As with the other cases of ac­tive lysogeny in sporu­la­tion, the DNA re­arrange­ment is lim­ited to the ter­mi­nal mother cell, en­sur­ing the phage's con­tin­u­a­tion in the spore.

No­tably though, this last case is the only de­scribed sporu­la­tion reg­u­la­tory switch with a fully func­tio­nal lytic phage el­e­ment. The fact that in most other cases of ac­tive lysogeny the reg­u­la­tory swit­ches dis­play scars of cryp­tic (non-func­­tio­­nal) phage el­e­ments begs the ques­tion of who does ac­tu­al­ly ben­e­fit from these kinds of phage-bac­te­r­ial in­ter­ac­tions?

Co­op­er­a­tion or Tam­ing?

In lyso­genic con­ver­sion there is typ­i­cally no ap­par­ent ben­e­fit to the phage be­yond the sim­ple com­fortable con­tin­u­a­tion of its host. Yet, the empty void of known ben­e­fits for the phage may at­test to lack of specif­i­cally look­ing for this end of the in­ter­ac­tion, surely when com­pared to re­search on bac­te­ri­al vir­u­lence. For the few func­tio­nal phages that serve as reg­u­la­tory switches, one can en­vi­sion that this rep­re­sents co­op­er­a­tion to main­tain the sta­tus quo.

The fre­quency of ge­nomic se­quences aris­ing from phage that have been ef­fec­tively neutered by the host into a cryp­tic scar – tamed into a reg­u­la­tory tool solely for the host's ben­e­fit (see here for an­other ex­am­ple) – sug­gests that mu­tu­ally ben­e­fi­cial co­op­er­a­tion may not be a com­mon end game for phage-host part­ner­ships. Al­though lysogeny is typ­i­cally viewed as ben­e­fi­cial for phage fit­ness, it is clear that the sit­u­a­tion also puts the virus at risk to evolv­ing a lit­tle too com­fort­able an arrange­ment with its host. To be fair, it also should be re­minded that the host is not with­out risk in this ei­ther.

It's a Phage World

The wealth of phage in the en­vi­ron­ment makes it al­to­gether not sur­pris­ing that tem­per­ate ones have evolved ways to in­te­grate into con­di­tional, func­tion­ally im­por­tant host genes through a­dap­ta­tion to be­come reg­u­la­tory switches. Such ad­ap­ta­tion may be re­lated to their vi­tal need to stay in com­mu­ni­ca­tion with host cell stress sig­nal­ing, as is seen with phage and bac­te­r­ial SOS re­sponse (cov­ered here and here).

The 'Per­spec­tive' by Feiner et al. con­cludes with a sec­tion that ex­plores the po­ten­tial for other phage reg­u­la­tory switches in processes such as biofilm for­ma­tion, LPS vari­a­tion, and toxin ex­pres­sion. The dis­cov­ery of ad­di­tional cases, par­tic­u­larly out­side of the well-trod­den field of pa­tho­ge­n­e­sis is as­sured. These iden­ti­fi­ca­tions along with a firmer grasp of their evo­lu­tion and their re­gu­la­tion in syn­chrony with host cell ac­tiv­ity will be ex­cit­ing to see un­fold.

 

Daniel is an As­sis­tant Pro­fes­sor in the Bi­ol­ogy De­part­ment of Can­i­sius Col­lege in Buf­falo, New York. He teaches courses in the fresh­man and sopho­more in­tro­duc­tory se­quence, Gen­eral Mi­cro­bi­ol­ogy, and an in­te­grated En­vi­ron­men­tal & Path­o­genic Mi­cro­bi­ol­ogy course. In his lab he fo­cuses on un­der­grad­u­ate re­search men­tor­ing through projects on bac­te­r­ial cell di­vi­sion and phage fac­tors that sub­vert the bac­te­r­ial cy­toskele­ton. In ad­di­tion to sci­ence, he en­joys read­ing, writ­ing, and film. He can be found on Twit­ter and his book re­views at Read­ing 1000 Lives or on Goodreads.