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Muller se ratel en virusse

Muller se ratel en virusse


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Ly virusse aan Muller se ratel? Kan dit die huidige koronaviruspandemie aansienlik beïnvloed?


Soos met die meeste dinge in die natuurlike wêreld, is daar nie regtig 'n enkele eenvoudige antwoord op hierdie vraag nie! Dit hang grootliks af van die ekologiese konteks en die bevolkingsdinamika.

Basies, in organismes met hoë mutasietempo's (soos RNA-virusse), stel Muller's Ratchet voor dat die gemiddelde fiksheid in 'n bevolking altyd sal afneem. In klein bevolkings is mutasievrye individue skaars, en hulle sal verlore gaan deur genetiese drywing. In 1990 het Chao gewys dat skadelike mutasies teen 'n voldoende hoë tempo gegenereer word om Muller se ratel in 'n RNA-virus te bevorder.

In die algemeen kan egter aangevoer word dat Muller se ratel ondoeltreffend is in virale populasies omdat populasies nooit 'klein' is nie, en wegdrywing is gewoonlik baie swak (of seleksie is sterk, met ander woorde). Chao merk ook op dat die effektiewe bevolkingsgrootte in die natuur, 8x10^9, dikwels irrelevant is of Muller's Ratchet aktief is of nie, want virusse gaan dikwels deur die bottelnek van 'n enkele individu. Daarbenewens kan gereelde herkombinasie van virusse soos MIV ook onderhewig wees aan Muller se Ratchet Yuste et al (1999). Die resultate van Chao is veralgemeen na baie ander virusse.

Hierdie studies is egter laboratoriumgebaseer en het nie betrekking op jou vraag oor wat met SARS-CoV-2 'in die natuur' kan gebeur nie. RNA-virusse toon die hoogste mutasiekoerse in die natuur (Sanjuan et al 2010). Dit kan lei tot Muller's Ratchet in klein bevolkings waar seleksie swak is en wegdrywing prominent is, maar kan lei tot hoë vlakke van aanpassing in groot bevolkings. Dit is nie net die sensusbevolkingsgrootte wat belangrik is nie, maar die effektiewe bevolkingsgrootte, wat beskou kan word as 'n maatstaf vir die hoeveelheid genetiese diversiteit binne 'n bevolking. As 'n bevolking vinnig vanaf 'n enkele oorsprong uitbrei, soos wat na verwagting met die SARS-CoV-2-uitbraak gebeur het, sal die sensusbevolkingsgrootte groter wees as die verwagte diversiteit. Novella (1995/1996) het aangetoon dat daar 'n wisselwerking is met die grootte van die bottelnek en die fiksheid van die oorlewende klone; wanneer 'n meer fikse virusse deur die bottelnek gaan, is dit meer geneig om Muller's Ratchet te vermy. Dus in die geval van SARS-CoV-2, of die virus aan Muller's Ratchet onderhewig sou wees of nie, sal afhang van beide die variasie en fiksheid van mutasie van die virusse wat van die intermediêre dier na mense gespring het.

Met die risiko om dinge te oorkompliseer, speel bevolking-/afnamestruktuur ook 'n rol. As die virus in verskillende dele binne 'n struktuurpopulasie ontwikkel, kan virusse binne 'n deme populasiespesifieke mutasies ontwikkel. As daar dan geenvloei tussen die demes is, kan daar seleksie bestaan ​​tussen die verskillende mutasies, wat die gemiddelde fiksheid oor demes verhoog (Mirales et al 2009) en die Ratchet vermy.


Muller se ratel is meer relevant/belangriker in organismes met klein effektiewe bevolkingsgroottes. Terwyl die effektiewe bevolkingsgrootte van die wêreldwye SARS-COV-2-bevolking kleiner is as (miljarde kopieë per persoon ['n tipiese opsporingsdrempel is 10^4 kopieë/milliliter bloed]) x (miljoene besmette mense), is dit baie waarskynlik so groot te wees dat Muller se ratel irrelevant is.


Ander antwoorde dek goed Muller se ratel van die wêreldwye virusbevolking.

Medisyne-geïnduseerde Muller's ratel (ook bekend as mutasie-insmelting) kan egter oorweeg word op die vlak van die virale populasie wat een pasiënt besmet het. 'n Onlangse publikasie Oorweeg mutasie-insmelting as 'n potensiële SARS-CoV-2-behandelingstrategie praat oor die moontlike indusering van mutasie-ineenstorting op die virale populasie binne-pasiënt.

Let daarop dat dit nie navorsing is nie, maar 'n kommentaarstuk! Skrywers hersien die teorie en empiriese bewyse wat hulle laat dink dat mutasie ineenstorting het die potensiaal om 'n koronavirusbehandeling te word.


Ondersoek na die evolusionêre model van Muller's Ratchet

Ewewig van mutasie en seleksieprosesse: 'n Bevolking kan verdeel word in groepe individue wat verskillende getalle nadelige mutasies dra. Groepe met min mutasies word geamplifiseer deur seleksie maar los lede na ander groepe deur mutasie. Groepe met baie mutasies reproduseer nie soveel nie, maar kry lede deur mutasie. Richard Neher/MPI vir Ontwikkelingsbiologie

Twee nuwe studies wat ondersoek het die proses staan ​​bekend as Muller se ratel, wat 'n kwantitatiewe begrip van die ratel se prosesse gee en wys waarom bevolkings nie noodwendig tot uitsterwing gedoem word nie ten spyte van die voortdurende toestroming van skadelike mutasies.

Van protosoë tot soogdiere het evolusie al hoe meer komplekse strukture en beter aangepaste organismes geskep. Dit is des te meer verstommend aangesien die meeste genetiese mutasies nadelig is. Veral in klein ongeslagtelike bevolkings wat nie hul gene herkombineer nie, kan ongunstige mutasies ophoop. Hierdie proses staan ​​bekend as Muller se ratel in evolusionêre biologie. Die ratel, voorgestel deur die Amerikaanse genetikus Hermann Joseph Muller, voorspel dat die genoom onomkeerbaar agteruitgaan, wat bevolkings in 'n eenrigtingstraat laat uitsterf. Richard Neher van die Max Planck Instituut vir Ontwikkelingsbiologie het in samewerking met kollegas van die VSA wiskundig gewys hoe Muller se ratel werk en hy het ondersoek ingestel waarom bevolkings nie noodwendig tot uitsterwing gedoem is nie ten spyte van die voortdurende toestroming van skadelike mutasies.

Die oorgrote meerderheid van mutasies is nadelig. "As gevolg van seleksie reproduseer individue met meer gunstige gene meer suksesvol en nadelige mutasies verdwyn weer," verduidelik die bevolkingsgenetikus Richard Neher, leier van 'n onafhanklike Max Planck-navorsingsgroep by die Max Planck Instituut vir Ontwikkelingsbiologie in Tübingen, Duitsland. In klein populasies soos 'n ongeslagtelike voortplantende virus vroeg tydens infeksie is die situasie egter nie so duidelik nie. "Dit kan dan toevallig gebeur, deur stogastiese prosesse alleen, dat skadelike mutasies in die virusse ophoop en die mutasievrye groep individue uitsterf," sê Richard Neher. Dit staan ​​bekend as 'n klik van Muller se ratel, wat onomkeerbaar is - ten minste in Muller se model.

Muller het sy model oor die evolusionêre betekenis van skadelike mutasies in 1964 gepubliseer. Tot op hede het 'n kwantitatiewe begrip van die ratel se prosesse egter ontbreek. Richard Neher en Boris Shraiman van die Universiteit van Kalifornië in Santa Barbara het nou 'n nuwe teoretiese studie oor Muller se ratel gepubliseer. Hulle het 'n vergelykbare eenvoudige model gekies met slegs skadelike mutasies wat almal dieselfde effek op fiksheid het. Die wetenskaplikes het seleksie teen daardie mutasies aanvaar en ontleed hoe fluktuasies in die groep van die sterkste individue die minder fikses en die hele bevolking beïnvloed. Richard Neher en Boris Shraiman het ontdek dat die sleutel tot die begrip van Muller se ratel in 'n stadige reaksie lê: As die aantal fiksste individue verminder word, neem die gemiddelde fiksheid eers na 'n vertraging af. "Hierdie vertraagde terugvoer versnel Muller se ratel," sê Richard Neher oor die resultate. Dit klik meer en meer gereeld.

"Ons resultate is geldig vir 'n wye reeks toestande en parameterwaardes - vir 'n populasie van virusse sowel as 'n populasie van tiere." Hy verwag egter nie om die model se toestande een-tot-een in die natuur te vind nie. "Modelle word gemaak om die noodsaaklike aspekte te verstaan, om die kritieke prosesse te identifiseer," verduidelik hy.

In 'n tweede studie het Richard Neher, Boris Shraiman en verskeie ander Amerikaanse wetenskaplikes van die Universiteit van Kalifornië in Santa Barbara en Harvard Universiteit in Cambridge ondersoek ingestel na hoe 'n klein ongeslagtelike bevolking Muller se ratel kan ontsnap. "So 'n bevolking kan net vir 'n lang tyd in 'n bestendige toestand bly wanneer voordelige mutasies voortdurend vergoed vir die negatiewes wat deur Muller se ratel ophoop," sê Richard Neher. Vir hul model het die wetenskaplikes 'n bestendige omgewing aanvaar en stel voor dat daar 'n mutasie-seleksie-balans in elke bevolking kan wees. Hulle het die tempo van gunstige mutasies wat nodig is om die balans te handhaaf, bereken. Die resultaat was verbasend: Selfs onder ongunstige toestande is 'n vergelykbare klein proporsie in die reeks van 'n paar persent van positiewe mutasies voldoende om 'n bevolking te onderhou.

Hierdie bevindinge kan die langtermyn-instandhouding van mitochondria verklaar, die sogenaamde kragsentrales van die sel wat hul eie genoom het en ongeslagtelik verdeel. Evolusie word oor die algemeen gedryf deur willekeurige gebeure of soos Richard Neher sê: "Evolusionêre dinamika is baie stogasties."

Beeld: Richard Neher/MPI vir Ontwikkelingsbiologie

Richard A. Neher, Boris I. Shraiman, Fluctuations of fiksheidsverdelings en die tempo van Muller se ratel.
Genetika, Vol. 191, pp. 1283-1293, Augustus 2012. doi:10.1534/genetics.112.141325

Sidhartha Goyal, Daniel J. Balick, Elizabeth R. Jerison, Richard A. Neher, Boris I. Shraiman en Michael M. Desai, Dinamiese Mutasie-Seleksie-balans as 'n evolusionêre aantrekker.
Genetika, Vol. 191, Augustus 2012. doi: 10.1534/genetics.112.141291


Agtergrond

Evolusionêre teorie voorspel dat mutasieverval onvermydelik is vir klein ongeslagtelike bevolkings, mits skadelike mutasiekoerse hoog genoeg is. Daar word van sulke bevolkings verwag om die gevolge van Muller's Ratchet [1, 2] te ervaar waar die mees geskikte klas individue in 'n mate verlore gaan as gevolg van toeval alleen, wat die naasbeste klas laat om uiteindelik dieselfde lot te ly, ensovoorts , wat lei tot 'n geleidelike afname in gemiddelde fiksheid. Die mutasionele ineenstortingsteorie [3, 4] het voortgebou op Muller se Ratchet om 'n sinergisme tussen mutasie en genetiese drywing te voorspel in die bevordering van die uitsterwing van klein ongeslagtelike bevolkings wat aan die einde van 'n lang genomiese vervalproses is. Ongeag die voortplantingsmodus, word verwag dat mitochondriale genome van die meeste dierspesies besonder sensitief is vir Muller's Ratchet as gevolg van hul eenouerlike oorerwing, hoë mutasietempo's en gebrek aan effektiewe rekombinasie [3, 5, 6]. Die genomiese verval-effekte van Muller's Ratchet is waargeneem in laboratorium-evolusie-eksperimente met abiotiese RNA-molekules [7], biotiese RNA-virusse [8], bakterieë [9] en gis [10]. Indirekte bewyse vir die uitwerking van Muller's Ratchet in die natuur het voortgespruit uit studies oor die langtermyn-effekte van verminderde bevolkingsgroottes op genetiese diversiteit en fiksheid by amfibieë [11], groter prairie hoenders [12, 13] en Nieu-Seeland avifauna [14] . Molekulêre bewyse vir Muller's Ratchet het voortgespruit uit ontledings van skadelike tRNA-geenstrukture wat deur mitochondriale genome gekodeer is [15] en ontledings van Drosophila geslagschromosoom evolusie [16]. Direkte kennis oor die vatbaarheid van natuurlike bevolkings vir Muller se Ratchet en die molekulêre meganismes wat hierdie proses onderlê, bly egter enigmaties.

Caenorhabditis briggsae, soos Caenorhabditis elegans, is 'n selfreproduserende hermafroditiese aalwurmspesie wat ook mannetjies produseer wat met hermafrodiete kan oorkruis. Ontledings van koppelingsonewewigpatrone in C. briggsae natuurlike isolate dui op 'n baie lae uitkruisingsyfer van

3,9 × 10 -5 [17]. Dieselfde studie het bevolkingsonderverdeling tussen C. briggsae stamme versamel in gematigde plekke teenoor dié van tropiese streke en nukleotieddiversiteit van nukleotiede in die stilte van die kern (πS) vir die tropiese isolate is geskat op 2,7 × 10 -3 – 'n getal wat baie soortgelyk is aan globale skattings vir C. elegans [18]. Die C. briggsae isolate van gematigde lokaliteite het egter 'n merkwaardig laer gemiddelde π getoonS waarde van 4,0 × 10 -5 . 'n Direkte skatting van die neutrale basissubstitusie mutasietempo (9.0 × 10 -9 per perseel per generasie) is beskikbaar vanaf C. elegans mutasie-akkumulasielyne [19] wat saam met π gebruik kan wordS data om die effektiewe bevolkingsgrootte te skat (N e) [20]. Aanvaar 'n algemene mutasietempo tussen C. elegans en C. briggsae, N eword geskat

63,000 vir C. briggsae tropiese isolate. Vir die C. briggsae gematigde isolate, 'n veel kleiner N evan

1 000 word geskat. Gebaseer op hierdie en ander waarnemings, word veronderstel dat C. briggsae het eers onlangs (in die laaste paar honderd jaar) gematigde breedtegrade van klein stigtingsbevolkings gekoloniseer [17]. Verder is daar bewyse vir 'n

2-voudige verhoogde mutasietempo in C. briggsae in vergelyking met C. elegans [21] wat lei tot dienooreenkomstig laer N eskattings vir C. briggsae:

31 500 vir tropiese bevolkings en

500 vir gematigde bevolkings. Die kombinasie van baie lae uitkruiskoerse, klein N een hoë mutasietempo's word verwag om te lewer C. briggsae natuurlike mitochondriale afstammelinge wat vatbaar is vir die effekte van Muller's Ratchet-geassosieerde skadelike mutasie-akkumulasie.

Om te ondersoek vir die gevolge van Muller se Ratchet in C. briggsae natuurlike populasies, het ons byna volledige mitochondriale genome van veelvuldige geografies uiteenlopende volgorde bepaal C. briggsae natuurlike isolate en gekarakteriseerde molekulêre evolusionêre prosesse deur nukleotied diversiteitspatrone in mitochondriale DNA (mtDNA) proteïenkoderende gene tussen die gematigde en tropiese klade te vergelyk C. briggsae isolate, karakterisering van heteroplasmiese genoom delesies deur gebruik te maak van kwantitatiewe real-time PCR (qPCR) benaderings en evaluering van korrelasies van verskeie natuurlike mitochondriale genoom haplotipes met nematode vrugbaarheid en fiksheid.


Basiese konsepte in RNA-virus evolusie

Aan wie korrespondensie- en herdrukversoeke gerig moet word, by: Centro de Biología Molecular "Severo Ochoa," Universidad Autónoma de Madrid, 28049 Madrid, Spanje. Soek vir meer referate deur hierdie skrywer

Centro de Biología Molecular “Severo Ochoa,”, Universidad Autónoma, 28040 Madrid, Spanje

Centro de Biología Molecular “Severo Ochoa,”, Universidad Autónoma, 28040 Madrid, Spanje

Centro de Biología Molecular “Severo Ochoa,”, Universidad Autónoma, 28040 Madrid, Spanje

Departement de Genètica en Servei de Bioinformàtica, Facultat de Biología, 46100 Buijassot, Valencia, Spanje

Departement Biologie en Sentrum vir Molekulêre Genetika, Universiteit van Kalifornië in San Diego, La Jolla, Kalifornië, 92093-0116 VSA

Departement Biologie en Sentrum vir Molekulêre Genetika, Universiteit van Kalifornië in San Diego, La Jolla, Kalifornië, 92093-0116 VSA

Departement Biologie en Sentrum vir Molekulêre Genetika, Universiteit van Kalifornië in San Diego, La Jolla, Kalifornië, 92093-0116 VSA

Centro de Biología Molecular “Severo Ochoa,”, Universidad Autónoma, 28040 Madrid, Spanje

Aan wie korrespondensie- en herdrukversoeke gerig moet word, by: Centro de Biología Molecular "Severo Ochoa," Universidad Autónoma de Madrid, 28049 Madrid, Spanje. Soek vir meer referate deur hierdie skrywer

Centro de Biología Molecular “Severo Ochoa,”, Universidad Autónoma, 28040 Madrid, Spanje

Centro de Biología Molecular “Severo Ochoa,”, Universidad Autónoma, 28040 Madrid, Spanje

Centro de Biología Molecular “Severo Ochoa,”, Universidad Autónoma, 28040 Madrid, Spanje

Departement de Genètica en Servei de Bioinformàtica, Facultat de Biología, 46100 Buijassot, Valencia, Spanje

Departement Biologie en Sentrum vir Molekulêre Genetika, Universiteit van Kalifornië in San Diego, La Jolla, Kalifornië, 92093-0116 VSA

Departement Biologie en Sentrum vir Molekulêre Genetika, Universiteit van Kalifornië in San Diego, La Jolla, Kalifornië, 92093-0116 VSA

Departement Biologie en Sentrum vir Molekulêre Genetika, Universiteit van Kalifornië in San Diego, La Jolla, Kalifornië, 92093-0116 VSA

Abstrak

'n Kenmerk van RNA-genome is die fout-geneigde aard van hul replikasie en retro-transkripsie. Die belangrikste biochemiese basis van die beperkte replikasiegetrouheid is die afwesigheid van proeflees/herstel en postreplikatiewe foutkorreksiemeganismes wat normaalweg werk tydens replikasie van sellulêre DNA. Ten spyte van hierdie unieke kenmerk van RNA-replikone, blyk dit dat die dinamika van virale populasies dieselfde basiese beginsels volg wat klassieke populasiegenetika vir hoër organismes daargestel het. Hier hersien ons onlangse bewyse van die diepgaande uitwerking wat genetiese knelpunte het om die nadelige uitwerking van Muller se ratel tydens RNA-virus-evolusie te versterk. Die geldigheid van die Red Queen-hipotese en van die mededingende uitsluitingsbeginsel vir RNA-virusse word beskou as die verwagte resultaat van die hoogs veranderlike en aanpasbare aard van virale kwasispesies. Virale fiksheid, of die vermoë om aansteeklike nageslag te repliseer, kan 'n miljoen keer varieer binne kort tydintervalle. Paradoksaal genoeg dui funksionele en strukturele studies uiterste beperkings op virusvariasie aan. Aanpasbaarheid van RNA-virusse blyk gebaseer te wees op die besetting van baie nou gedeeltes van volgorderuimte op enige gegewe tydstip.—Domingo, E., Escarmís, E., Sevilla, N., Moya, A., Elena, SF, Quer, J., Novella, IS, en Holland, JJ Basiese konsepte in RNA-virus-evolusie. FASEB J. 10, 859-864 (1996)


Biologiese effek van Muller's Ratchet: Veraf kapsiedplek kan Picornavirus-proteïenverwerking beïnvloed

FIG. 1 . Skema van die oorsprong van FMDV klone C 10 1, C 10 130, en sublyne a, b, c en d onderworpe aan 180 of 230 plaak-tot-plaat oordragte, en van populasie C-S8c1p50. Vierkante, biologiese klone sirkels, ongekloonde populasies dik pyle, groot populasie gange (2 × 10 6 selle geïnfekteer met 2 × 10 6 tot 5 × 10 6 PFU van C-S8c1) dun pyle, isolasie van virus vanaf 'n enkele plaak. Vir sublyn c het klone nie-sitopaties geword na oordrag 180 (20). Die oorsprong van FMDV C-S8c1 en prosedures vir infeksies en plaak-tot-gedenkplaat oordragte word in Materiale en Metodes uiteengesit. FIG. 2 . Termosensitiwiteit en opeenhoping van mutasies by onderwerping van FMDV kloon C 10 1 tot plaak-tot-plaat oordragte. Die oorsprong van C 10 1 en die eksperimentele ontwerp word in Fig. 1 beskryf. (A) Nageslagproduksie by 37°C en 42°C in parallelle infeksies van 2 × 10 6 BHK-21-selle, met die klone in die abskis aangedui, by MOI's van 0.1 tot 0,01 PFU/sel. Na 1 uur se adsorpsie by 37°C, is die monolae by 37°C of by 42°C vir 22 uur tot 44 uur geïnkubeer totdat sitopatologie by 37°C voltooi is. Titers in die selkultuursupernatante is by 37°C bepaal in drievoud standaardafwykings word gegee. (B) Nageslagproduksie by 37°C en 42°C van virus vanaf C 10 180 en C 10 230 vir sublyne b, c en d (vergelyk Fig. 1). Virus van sublyn c by oordrag 180 het 'n onopspoorbare aantal gedenkplate by 42°C (onder die waarnemingsgrens, soos aangedui deur die pyl) gelewer, virus van hierdie sublyn het nie-sitofaties geword by plaakoordrag 190 (20), en dus termosensitiwiteit by oordrag 230 kon nie gemeet word nie. Titrasies vir die drie lyne is in afsonderlike eksperimente uitgevoer, maar vir elke afstamming is die titrasies van plate in C 10 180 en C 10 230 is parallel uitgevoer, en C 10 130 (die ouerkloon van sublyne a, b, c en d) (Fig. 1) is as 'n kontrole ingesluit. Die prosedure is soos beskryf vir paneel A. (C) Nageslagproduksie by 37°C en 43°C van C-S8c1 en C-S8c1 onderworpe aan 50 reeksgange in BHK-21-selle (MOI van 1 tot 2 PFU/sel) by 37°C. Let daarop dat in hierdie kontrole die beperkende temperatuur 43°C was en dat die termosensitiwiteit van C-S8c1 nie identies hoef te wees aan dié van C 10 1 as gevolg van deurgangsgeskiedenis (Fig. 1) en aan MKZ-bevolking heterogeniteit. (D) Akkumulasie van mutasies, relatief tot die genomiese volgorde van C 10 1, as 'n funksie van die plaakoordragnommer. Waardes is gebaseer op die nukleotiedvolgorde van die hele FMDV-genoom, soos voorheen beskryf (23). Prosedures word beskryf in Materiale en Metodes. FIG. 3 . Virale opbrengs van FMDV-mutante by 37°C en 43°C. (A) Die mutasies wat C 10 onderskei 30 van C 10 1 is afsonderlik in pMT28 ingebring, die plasmiede is gelineariseer en getranskribeer, en die aansteeklike transkripsies is in selle getransfekteer om virus nageslag te produseer. Die mutasies of aminosuursubstitusies teenwoordig in elke mutant word in die abskis aangedui. C 10 1, C 10 30, en die pMT28 mutant afgeleides is gebruik om BHK-21 selle te infekteer by 'n MOI van 0.1 PFU/sel. Die 1-uur adsorpsie tydperk was by 37°C. Daarna is die infeksie voortgesit by óf 37°C óf 43°C totdat sitopatologie voltooi is in die infeksies wat by 37°C (21 uur na infeksie) uitgevoer is. Titrasies is in drievoud uitgevoer, en standaardafwykings word aangedui. (B) Groeikromme van virale nageslag van pMT28-WT (WT) en pMT28-M1054I (M1054I) by 37°C en 43°C. BHK-21 sel monolae is geïnfekteer teen 'n MOI van ongeveer 0.1 PFU/sel onder die toestande aangedui vir paneel A. Op die aangeduide tye na infeksie is aliquots van die selkultuur supernatante onttrek, en virale titers is by 37°C bepaal. Titrasies is in drievoud uitgevoer, en standaardafwykings word gegee. Sterretjies dui statisties beduidende verskille aan tussen die titers geproduseer deur pMT28-WT en pMT28-M1054I óf by 37°C óf 43°C op elke tydpunt (P < 0,025 analise van variansie toets). Prosedures word in Materiale en Metodes uiteengesit. FIG. 4 . Aansteeklike nageslagproduksie en stabiliteit van pMT28-WT (WT) en pMT28-M1054I (M1054I) by 37°C en 43°C. (A) pMT28-WT of pMT28-M1054I is geadsorbeer op BHK-21 selle vir 1 uur by 37°C teen 'n MOI van 0.1 PFU/sel. Infeksies is voortgesit vir óf 3 uur by 37°C of 1 uur by 37°C, gevolg deur 2 uur by 43°C of 2 uur by 43°C en dan deur 1 uur by 37°C of 3 uur by 43°C , soos aangedui in die abskis. Na die 3-uur periode is die virus by 37°C getitreer. Titrasies is uitgevoer in drievoud standaardafwykings word gegee. (B) Porties wat onderskeidelik 100 tot 200 PFU van virus pMT28-WT of pMT28-M1054I bevat, is by 43°C geïnkubeer vir die tye wat in die abskis aangedui word en by 37°C getitreer. Titrasies is in drievoud uitgevoer, en standaardafwykings word gegee. Die standaardafwykings vir tye 0, 15, 30, 60 en 120 min was onderskeidelik 5.3, 1.2, 6.5, 1.5 en 0 vir pMT28-WT en 39.8, 20.8, 10.4, 7 en 2, onderskeidelik vir pMT2. -M1054I. Die halfleeftyd van infektiwiteit is bereken op grond van die regressielyne vir pMT28-WT (y = 109.84 e −0.0384x r 2 = 0,9937) en pMT28-M1054I (y = 282.24 e −0.0395x r 2 = 0,9772). Prosedures word beskryf in Materiale en Metodes. FIG. 5 . Proteïenuitdrukking deur wilde tipe RNA en mutante M54I RNA. (A) Patroon van proteïenuitdrukking in BHK-21-selle wat geëlektroporeer is met transkripsies wat vir pMT28-WT (WT) en pMT28-M1054I (MI) by 37°C en 43°C kodeer. BHK-21-selle is óf gek-elektroporeer (C-bane) óf geëlektroporeer met ongeveer 20 μg RNA-transkripsies van die aangeduide plasmiede. Getransfekteerde selle is gemerk met [35S]Met-Cys by 2 tot 3, 3 tot 4, of 4 tot 5 uur na-elektroporasie (HPE). Selekstrakte is deur SDS-PAGE geanaliseer, gevolg deur fluorografie en outoradiografie. Die mate van afsluiting van gasheerselproteïensintese is bepaal deur die hoeveelheid 35S-etiket in die aktienband (as 'n persentasie van die C-baan, geneem as 100%-waardes word in die blokkies onder elke baan gegee). Die totale hoeveelheid proteïen is bepaal deur Western klad met behulp van 'n monoklonale teenliggaam spesifiek vir β-aktien (onderste paneel). Die posisies van virale proteïene 3CD, 3D, VP3 en VP1 word aan die regterkant aangedui. Mr waardes is in duisende. (B) Western klad analise van die jel getoon in paneel A met behulp van monoklonale teenliggaam SD6, spesifiek vir VP1 van FMDV. Die posisies van P1, VP3-VP1 en VP1 word aangedui. P1 en VP3-VP1 was ook positief met monoklonale teenliggaam 6C2, wat spesifiek vir VP3 is (38). Die tweede klad is 'n langer blootstelling van die jelgebied rondom VP1. Die persentasie pMT28-M1054I VP1 relatief tot pMT28-WT VP1, gegee aan die onderkant, is bepaal deur densitometrie van die VP1-bande deur die toepaslike blootstelling vir elke temperatuur (-, geen digtheid bo die agtergrond is opgespoor nie). Aanduiding van FMDV proteïene en molekulêre massa merkers is soos in paneel A. (Ons analise het nie bepaal of die bande wat aan P1 en VP3-VP1 toegeken is, 2A [50, 51, 56] insluit nie). (C) 'n Driedimensionele voorstelling van die data wat in paneel B getoon word by 3 tot 4 (4 HPE) en 4 tot 5 (5 HPE) h na-elektroporasie. Die persentasies voorloperproteïene vir die wilde tipe (WT) en mutant M54I (MI) virusse by 37°C en 43°C is bepaal deur densitometrie van 'n Western klad met die toepaslike blootstelling (regs gewys) die resultate is relatief t.o.v. die VP1-vlak, geneem as 100%. (D) Western klad analise met behulp van teenliggaampies spesifiek vir VP3, 2C en 3D van FMDV en β-aktien by 4 uur postelektroporasie. Die persentasies aan die onderkant van die vlekke is bepaal deur densitometrie van die spesifieke bande met die toepaslike blootstelling vir elke temperatuur (-, geen digtheid bo die agtergrond is opgespoor nie). Prosedures word beskryf in Materiale en Metodes. FIG. 6 . Stabiliteit in BHK-21-selle van VP1 uitgedruk vanaf pMT28-WT of pMT28-M1054I. (A) BHK-21-selle is óf gek-elektroporeer (C-bane) óf geëlektroporeer met ongeveer 20 μg RNA-transkripsies van pMT28-WT of pMT28-M1054I by 37°C of 43°C. Getransfekteerde selle is gemerk met [35S]Met-Cys teen 3 uur na-elektroporasie vir 60 min, en dan is hulle gejaag met ongemerkte Met-Cys op die aangeduide tye (min). Selekstrakte is deur SDS-PAGE ontleed, gevolg deur fluorografie en outoradiografie, soos uiteengesit in die legende vir Fig. 5 en in Materiale en Metodes. Mr waardes is in duisende. Die posisie van VP1 word aangedui. (B) Die persentasie etiket in die band wat ooreenstem met kapsied VP1, relatief tot die etiket op tyd nul geneem as 100%, word aangedui. VP1 is geïdentifiseer deur sy reaktiwiteit met monoklonale teenliggaampies SD6 (37). Prosedures word beskryf in Materiale en Metodes.

Bespreking

Mutasie-akkumulasie en indringing deur selfsugtige elemente is twee kragte wat optree teen genoomoptimalisering en vaartbelyning in eindige-grootte populasies. In ongeslagtelike organismes is eDNA-inname gevolg deur rekombinasie die enigste manier om die mutasielas wat deur Muller se ratel opgelê word, teë te werk (Takeuchi et al. 2014). eDNA-inname kan egter ook deur selfsugtige elemente uitgebuit word om oor die bevolking te versprei, wat eDNA-inname (en horisontale geenoordrag in die algemeen) in 'n tweesnydende swaard vir selle verander. Deur eenvoudige wiskundige modelle met genomiese data te kombineer, wys ons dat die tempo van HGT wat nodig is vir selle om Muller se ratel te ontsnap, tipies hoog genoeg is om ligte skadelike parasiete in die meeste bevolkings te laat voortduur. As selle dus genoomdegenerasie deur mutasie-akkumulasie wil vermy, word die volharding van parasiete (feitlik) onvermydelik. Alhoewel ons ons argument gesentreer het op die vereiste vir selle om Muller se ratel te ontsnap, beperk ander voordele wat met HGT geassosieer word, soos die verkryging van determinante van antibiotika- of virusweerstand, of biochemiese weë wat voordelig is in 'n spesifieke omgewing, die moontlikheid om die HGT pryse onder die drempel van parasiet eliminasie, versterk hierdie algemene gevolgtrekking.

Die toestande wat nodig is vir die kort- en langtermyn volharding van genetiese parasiete was 'n herhalende onderwerp in teoretiese bevolkingsbiologie na die ontdekking van selfsugtige elemente (Charlesworth en Charlesworth 1983 Langley et al. 1983 Kaplan et al. 1985 Moody 1988). Ons het 'n algemene model wat die uitwerking van HGT, duplisering, verliese en seleksie in ag neem om die lot van 'n selfsugtige element in 'n gasheerbevolking te beskryf (Moody 1988 Basten en Moody 1991 Bichsel et al. 2013 Iranzo et al. 2014) herbesoek. Ten spyte van sy eenvoud, is getoon dat hierdie model goed pas by die oorvloed verspreidings van invoegvolgorde in bakteriese genome (Iranzo et al. 2014), en sy neutrale weergawe is gebruik om die evolusionêre dinamika van geeninhoud af te lei (Csuros en Miklos 2006 Csuros 2010). In ooreenstemming met vorige bevindinge, is volharding van parasiete slegs moontlik indien horisontale oordrag kompenseer vir die effektiewe verlies van parasitiese elemente deur delesie en suiwerende seleksie. In die geval van neutrale of kwasi-neutrale elemente, soos transposons, is die sleutelfaktor wat die kritieke oordragtempo beïnvloed die intrinsieke verliesvooroordeel, dit wil sê die verskil tussen die verspreiding en verlieskoerse vir die gegewe element, laasgenoemde bepaal tot 'n groot mate deur die genoomwye uitwiskoers (Kuo en Ochman 2009, 2010). Aan die ander kant van die replikator-selfsugtigheidspektrum vereis langtermyn-oorlewing van hoogs skadelike parasiete, soos litiese virusse, dat virusse gemiddeld minstens soveel gasheerselle infekteer as wat hulle per tydseenheid doodmaak (wat gelykstaande is aan die toestand R0 > 1 vir die basiese voortplantingsverhouding wat in epidemiologie gebruik word (Heffernan et al. 2005).

Soos voorspel deur die model, toon ons rekonstruksie van die evolusionêre gebeure in die ATGC's dat die beraamde oordragtempo's vir verskillende mobiele genetiese elemente (transposons, plasmiede en profeë) hul effektiewe verlieskoerse oortref, wat aandui dat ten spyte van af en toe verliese in spesifieke afstammelinge, hierdie elemente kan stabiel bly in die biosfeer vir lang evolusionêre tye. Verder het ons gevind dat die kritieke oordragtempo vir volharding, bereken uit die beraamde effektiewe verlieskoerse, naby aan of kleiner is as die teoretiese skatting vir die minimum HGT-tempo wat nodig is om Muller se ratel teen te werk, wat parasietvolharding verbind met die voorkoming van mutasie-insmelting ( derde scenario in fig. 3).

Die resultate van hierdie werk berus in 'n mindere of meerdere mate op sekere modelaannames wat ons vir duidelikheid hier saamvat. Eerstens het ons aangeneem dat die dinamika van genetiese parasiete beskryf kan word deur 'n algemene geboorte-dood-oordragmodel (sien Aanvullende Materiaal aanlyn vir besonderhede). In die mees algemene weergawe van so 'n model, prolifereer parasiete binne 'n genoom, word verlore van 'n genoom, en besmet nuwe genome teen tempo's wat afhang van hul genomiese en bevolkingsoorvloede, terwyl gasheergenome verskille in fiksheid ervaar wat afhang van hul parasietlading. Vir eenvoud het ons alle koerse direk eweredig aan die parasietkopiegetal gemaak wat gelykstaande is aan die aanname dat elke kopie van die parasiet onafhanklik van die res optree. Hierdie aanname word empiries ondersteun deur die waarneming dat die lineêre geboorte-dood-oordrag model 'n goeie passing bied vir die kopiegetal verspreidings van 'n groot aantal MGE in bakteriese genome (Iranzo et al. 2014). Waarskynlik kan groot parasietkopiegetalle nie-lineariteite in die fiksheidsfunksie produseer (bv. as gevolg van verhoogde genomiese onstabiliteit wat verband hou met veelvuldige herhalings) of lei tot 'n versadiging van die infeksiekoers. Omdat ons doel was om die oorgang tussen die regimes van parasietuitwissing en parasietoorlewing te verken, eerder as gevalle van intense parasietverspreiding, is sulke groot kopiegetal effekte irrelevant vir die huidige studie.

Tweedens, die Muller se ratelmodel wat ons gebruik het om h P P * te bereken, aanvaar in sy oorspronklike formulering (Takeuchi et al. 2014), 'n vermenigvuldigende effek van effens nadelige mutasies op fiksheid. However, because the approximations applied in the derivation of equations (3)–(6) only consider the classes of genomes with one and zero mutations, equivalent expressions would be obtained in the case of additive fitness. Furthermore, using equation (7) instead of ( 6), we worked with a simplified expression that is independent of the particular value of the fitness cost. An additional limitation of the original Muller’s ratchet model is that it is formulated for a constant size population. The inclusion of bottlenecks or size fluctuations would reinforce the impact of Muller’s ratchet, which implies that a higher HGT rate would be necessary to prevent genome degeneration, thus facilitating the persistence of parasites. In practice, because the model is implemented for a Wright–Fisher population, size fluctuations can be captured using the effective population size Ne as we did in the expressions above.

One potential amendment to the approach implemented here would involve explicit modeling of the dynamics of the genes that facilitate HGT (such as, for instance genes involved in conjugation). However, the great majority of prokaryotic genomes show clear signs of substantial HGT, suggesting that such an addition, although interesting in itself, is not essential.

Although parasite transmission implies the transfer of non-homologous genetic material, whereas prevention of Muller’s ratchet requires homologous recombination, both phenomena can result from the same basic processes, especially in the case of transposons and other parasites that do not encode an autonomous transfer machinery ( Darmon and Leach 2014 Hanage 2016). This notion is empirically supported, for example, by the association between the uptake of MGE and homologous material from core loci observed in antibiotic resistant strains of S. pneumoniae ( Hanage et al. 2009). In a similar vein, sub-lineages within the S. aureus major lineage ST239 show unusually high variation in recombination in both core loci and MGE, suggesting that the lineage-specific levels of eDNA acquisition and recombination simultaneously affect MGE and core genes ( Castillo-Ramirez et al. 2012). Although we have not explicitly invoked mobilization by MGE as a source of HGT for the cell, a significant correlation between the transfer rates of MGE and other genes was observed. Such correlation suggests the intriguing possibility that, apart from their persistence underpinned by the minimal essential HGT rate, the spread of MGE might be an important factor of microbial evolution that helps prokaryotes regain core genes that are occasionally lost during evolution.

Our results imply that prevention of Muller’s ratchet and maintenance of selfish elements are coupled through HGT. Accordingly, any prokaryotic genome that is free of genetic parasites is also expected to show signs of genome degeneration. This trend is indeed strikingly apparent in microbes whose life style leads to curtailment of HGT, such as obligate endosymbiotic bacteria ( Moran 1996 Mamirova et al. 2007 Moran et al. 2008). Die genus Wolbachia, a group of anciently host-restricted intracellular bacteria with reduced genomes (∼1 Mbp) and very small effective population sizes, seems particularly suitable to test the hypothesis. Arthropod-associated strains of Wolbachia (e.g., those from Culex aculeatus en Drosophila melanogaster) are known to coinfect hosts and undergo HGT ( Bordenstein and Wernegreen 2004 Baldo et al. 2006). These strains also host numerous prophages and functional copies of insertion sequences, suggestive of an ongoing activity of genetic parasites ( Wu et al. 2004 Cerveau et al. 2011 Duron 2013). In contrast, the strains from filarial nematodes (Brugia malayi en Onchocerca ochengi) are transmitted in a strict vertical manner that (virtually) excludes HGT ( Bandi et al. 1998), and their genomes are characterized by the lack of prophages and functional insertion sequences ( Foster et al. 2005 Cordaux 2009). Based on the coupling between parasite maintenance and Muller’s ratchet prevention, we predict that this second group of Wolbachia should exhibit signs of the effects of Muller’s ratchet, such as accumulation of mildly deleterious mutations. The other side of the coin is exemplified by Mycoplasma-related endobacteria: an association between parasite maintenance and avoidance of genome degeneration has been invoked to explain their evolutionary longevity as endosymbionts of mycorrhizal fungi ( Naito and Pawlowska 2016).

The estimates of the HGT/loss ratio indicate that not only genetic parasites but also most of the non-parasitic genes lie above the critical threshold ( fig. 2B and C) and hence typically persist in the population even in the absence of purifying selection. This observation suggests a fresh outlook on the “selfish gene” concept ( Doolittle and Sapienza 1980 Orgel and Crick 1980 Dawkins 2006). The ability of genes to evolve along trajectories distinct from those of the respective vehicles (hosts), is often viewed as a trait that evolved via gene-level selection (hence the perceived selfishness of the genes). The present results imply that the apparent ability of genes to persist via HGT even when they are neutral or slightly deleterious to the host is a by-product of the organism-level selection which maintains the level of eDNA intake sufficient to escape Muller’s ratchet. Then, extensive gene loss and genome streamlining that are most typical of parasitic and symbiotic bacteria but appear to also occur in some free-living microbes ( Lynch 2006b Wolf et al. 2012 Wolf and Koonin 2013) could be either signs of genome degeneration along the path to extinction driven by Muller’s ratchet or a manifestation of strong selection whereby certain categories of genes become deleterious to the organism. The present estimates also imply that the path to becoming a parasite is, in principle, open to any gene that is not strongly deleterious, without a need to evolve efficient propagation mechanisms from the start.

Blurring the lines between a genuine genomic parasite and a non-functional sequence, such as a pseudogene, implied by the present results, raises the question whether there exists a qualitative difference between these two types of entities. The major distinction appears to be that, upon entering a new cell, a parasite adds an intact, replication-competent copy of its genome to the host genome, whereas non-parasitic, non-functional elements are likely to lose their integrity by either integrating with the genome via homologous (or in rare cases, illegitimate) recombination or degrading. From this perspective, the critical barrier that limits the conversion of non-functional DNA into genuine selfish elements is the acquisition of mechanisms that allow them to maintain their integrity in the cells they enter. In agreement with this view, there is a broad spectrum of such mechanisms which include devices that facilitate the mobility of the elements (as in transposons), those that contribute to replication (as in self-synthesizing transposons and viruses) or those that make the host cell addicted to the element as in the case of toxin-antitoxin or restriction–modification (R–M) systems ( Kobayashi 2001 Van Melderen and Saavedra De Bast 2009 Koonin and Starokadomskyy 2016).

The trade-off between genome degeneration and parasite persistence constrains the strategies available to hosts and parasites in their everlasting race. Provided that the HGT rate cannot be reduced below a critical value without affecting the genome integrity, the remaining options for the host are (i) increasing the mutational bias towards deletions, thus pushing up the critical HGT rate for parasite persistence above the minimum needed to escape Muller’s ratchet ( fig. 3), (ii) decreasing the mutation rate u, thus lowering the minimal HGT rate required for Muller’s ratchet avoidance ( fig. 3), and (iii) evolving defense systems that discriminate between benign and parasitic elements upon DNA intake. The first strategy is consistent with the general observation that, in prokaryotes, deletions are more frequent than insertions and the rate of gene loss exceeds the rates of gene acquisition and gene duplication ( Andersson and Andersson 1999, 2001 Mira et al. 2001 Kuo and Ochman 2009). Accordingly, it has been proposed that such a strong deletion bias could even be an adaptive trait that is selected for the beneficial effect of parasite elimination ( Lawrence et al. 2001). However, our present analysis of effective loss rates in prokaryotic genomes shows that, despite the generalized loss bias, HGT rates are still high enough for parasites (and more generally, neutral sequences) to survive. Actually, because high deletion rates represent a burden for the maintenance of transitorily non-essential genes, an upper bound to the loss bias should exist that a cell can attain without compromising its long-term survival. The utility of the second choice, lowering the mutation rate, is limited by the power of genetic drift ( Lynch 2011 Sung et al. 2012). Finally, the third possibility for hosts is to achieve discrimination between harmless and deleterious DNA when it enters the cell, thus decoupling the parasite onslaught from the “benign” HGT that could result in acquisition of beneficial genes. Such self-non-self discrimination is a stiff challenge but can be partially achieved by R–M systems that target unmodified virus DNA but not DNA modified similarly to the host genome ( Pleska et al. 2016) and CRISPR-Cas systems at least some of which appear to specifically target actively replicating DNA ( Amitai and Sorek 2016). In a less specific manner, the bias of transformation toward the intake of shorter DNA molecules also has been proposed as a means to combat the spread of parasites ( Croucher et al. 2016).

Parasites can advance their long-term survival through three fundamentally distinct but not mutually exclusive strategies: (i) lowering the critical transfer rate that the parasites need to survive, which can be achieved by reducing the cost they inflict onto the host, (ii) increasing proliferation rate of the parasitic element inasmuch as this does not result in significant extra cost to the host, and (iii) raising the parasite transfer rate and making it independent of the host by evolving autonomous transmission mechanisms (this is the only alternative for highly deleterious elements). The two extreme strategies employed by MGE are represented by transposons (low cost, non-autonomous transmission) and lytic viruses (high cost, autonomous transmission), respectively. Temperate viruses employ bet-hedging by taking advantage of the first strategy, while keeping the ability to autonomously transmit under conditions where the survival of the host is compromised ( Maslov and Sneppen 2015). Indeed, some prophages provide benefits to their host, and superinfection inhibition can be interpreted as a means to avoid further reduction of the host fitness. Eventually, the “reduced costs” strategy is bounded by the energy cost associated to the replication of the additional genetic material ( Lynch and Marinov 2015) which likely sets a limit to the size of non-beneficial elements that do not encode autonomous transfer mechanisms.

An intriguing conclusion from the present analysis is that cell–parasite systems seem to exist near the edge of parasite inevitability. This phenomenon could be a co-evolutionary by-product of the long-term competition between cells and parasites: to avoid the spread of parasites, cells would tend to lower their HGT rates as much as possible without falling below the Muller’s ratchet threshold, which would keep the actual HGT rate not far above that threshold. Parasites then would evolve such that the minimum HGT rate needed for persistence drops below the HGT rate realized by cells. This race would lead to a situation with both critical HGT rates close to each other and hence to life on the edge of parasite inevitability.

The “inevitability of parasites” can be interpreted as a null model, a starting point underlying the arms race between cells and selfish elements. This starting condition highlights the necessity for cells to evolve defense mechanisms that allow them to maintain HGT rates compatible with the preservation of the genome integrity while limiting the intake of genetic parasites. Parasites, conversely, face the challenge of counteracting such self vs. non-self discrimination mechanisms or evolving their own means for autonomous transfer. Remarkably, this co-evolutionary race centered on controlling HGT, on the host side, and escaping the HGT control, on the parasite side, is a major source of evolutionary innovation and exaptation, as HGT mechanisms originally evolved by selfish elements as means of their spread end up being used by cells for their own benefit, in particular, anti-parasite defense ( Koonin and Krupovic 2015a, 2015b).


Abstrak

The molecular basis of Muller's ratchet has been investigated using the important animal pathogen foot-and-mouth disease virus (FMDV). Clones from two FMDV populations were subjected to serial plaque transfers (repeated bottleneck events) on host BHK-21 cells. Relative fitness losses were documented in 11 out of 19 clones tested. Small fitness gains were observed in three clones. One viral clone attained an extremely low plating efficiency, suggesting that accumulation of deleterious mutations had driven the virus near extinction. Nucleotide sequence analysis revealed unique genetic lesions in multiply transferred clones that had never been seen in FMDVs isolated in nature or subjected to massive infections in cell culture. In particular, a frequent internal polyadenylate extension has identified a mutational hot spot on the FMDV genome. Furthermore, amino acid residue substitutions in internal capsid sites which are severely restricted during FMDV evolution, amounted to half of capsid replace- ments in the transferred clones. In addition, a striking dominance of non-synonymous replacements fixed upon large population infections of FMDV was not observed upon serial plaque transfers. The nucleotide sequence of the entire genome of a severely debilitated clone suggests that very few mutations may be sufficient to drive FMDV near extinction. The results provide an account of the molecular basis of Muller's ratchet for an RNA virus, and insight into the types of genetic variants which populate the mutant spectra of FMDV quasispecies.


Muller’s Ratchet Hypothesis

The term Muller’s Ratchet, was not actually termed by Muller himself, but actually by Joe Felsenstein in 1974, based on Muller’s idea. It is the process in which the genomes of an asexual population accumulate deleterious mutations in an irreversible manner (Muller, 1932) . Roth (2016) termed this idea to rank close to natural selection as a major contribution to explaining evolution, genetic adaptation and life itself. He also termed it to provide an explanation as to how natural selection limits genome size and may explain why genetic recombination became more prominent as biological complexity as well as the size of genomes increased.

In asexual populations, the loss is irreversible and the load of deleterious mutations increases, similar to the manner in which a ratchet performs, with the successive loss of the least-mutated individuals (Chao, 1990). Furthermore, asexual reproductive populations will carry at least one deleterious mutation of a gene, there will be no future genomes that will have no fewer mutations, resulting in accumulating mutations termed: genetiese ladingeventually causing extinction (Freeman and Herron, 2007). Sexual reproduction overcomes this problem through genetic recombination.

1) Kaiser and Charlesworth (2010) have explored the reasoning behind the degeneration of the Drosophila Miranda Neo-Y Chromosome. They found that the chromosome had lost approximately half of the genes that it originally contained. They showed that selection at nonsynonymous coding sites can accelerate the process of gene loss with this varying with the number of genes still present on the chromosome. This is a simple, conspicuous example that nicely explains Muller’s ratchet hypothesis.

2) The molecular basis of Muller’s ratchet has been explored using the animal pathogen foot-and-mouth disease. Clones from two of these populations were subjected to serial plaque transfers on host BHK-21 cells (Escarmiset al., 1996). Relative fitness losses were documented in 11 out of 19 clones tested. Small fitness gains were observed in three clones. One viral clone attained an extremely low plating efficiency, suggesting that accumulation of deleterious mutations had driven the virus near extinction. The results provide an account of the molecular basis of Muller’s ratchet for an RNA virus, and an insight into the types of genetic variants which populate the foot and mouth disease virus quasispecies.

3) Muller’s ratchet has now been known to operate on a non-segmented, non-recombining pathogenic RNA virus that occurs in animals and humans (Duarte et al., 1992). What Duarte et al. (1992) looked at was a genetic bottleneck passage of vesicular stomatitis virus (VSV) and then quantified relative fitness of the bottleneck clones by allowing replication competition in cultures of mixed infections. Variable fitness drops were detected following only 20 plaque-to-plaque transfers of VSV. There were no fitness changes detected in some clones. What was surprising was that the most regular and severe fitness losses occurred during virus passages on a new host cell type. These results show how Muller’s ratchet could have significant implications for variability of disease severity during virus outbreaks (Duarte et al., 1992). This is all very important and interesting research that could be carried further and allow scientists to find out more on the development of this hypothesis as well as it being important for world health.

4) As stated above, those that reproduce asexually, are at a disadvantage when evolving, according to Muller’s ratchet hypothesis. However, there are some Amoebae (e.g. Acanthamoeba en Nageleria),that reproduce asexually and have escaped this hole through being polyploid (Maciver, 2016). By being polyploidy it reduces spontaneous mutation accumulation by gene conversion, the freshly mutated being corrected by the presence of multiple other wild-type copies. The amoebae can then reap the benefits of living in an asexually reproducing life that is both rapid and convenient. Further evidence of this mechanism comes from plants, archaea and bacteria that are polyploid (Maciver , 2016).

The Muller’s ratchet hypothesis is a well developed, well supported hypothesis across the scientific community. It is very useful in explaining how it is advantageous in sexual populations and also points out any floors it has for asexual populations, as well as providing proof that this may not be true. It provides good food for thought.


Max Planck scientist investigates the evolutionary model of Muller’s ratchet

From protozoans to mammals, evolution has created more and more complex structures and better-adapted organisms. This is all the more astonishing as most genetic mutations are deleterious. Especially in small asexual populations that do not recombine their genes, unfavourable mutations can accumulate. This process is known as Muller’s ratchet in evolutionary biology. The ratchet, proposed by the American geneticist Hermann Joseph Muller, predicts that the genome deteriorates irreversibly, leaving populations on a one-way street to extinction. In collaboration with colleagues from the US, Richard Neher from the Max Planck Institute for Developmental Biology has shown mathematically how Muller’s ratchet operates and he has investigated why populations are not inevitably doomed to extinction despite the continuous influx of deleterious mutations.

The great majority of mutations are deleterious. “Due to selection individuals with more favorable genes reproduce more successfully and deleterious mutations disappear again,” explains the population geneticist Richard Neher, leader of an independent Max Planck research group at the Max Planck Institute for Developmental Biology in Tübingen, Germany. However, in small populations such as an asexually reproducing virus early during infection, the situation is not so clear-cut. “It can then happen by chance, by stochastic processes alone, that deleterious mutations in the viruses accumulate and the mutation-free group of individuals goes extinct,” says Richard Neher. This is known as a click of Muller’s ratchet, which is irreversible – at least in Muller’s model.

Muller published his model on the evolutionary significance of deleterious mutations in 1964. Yet to date a quantitative understanding of the ratchet’s processes was lacking. Richard Neher and Boris Shraiman from the University of California in Santa Barbara have now published a new theoretical study on Muller’s ratchet. They chose a comparably simple model with only deleterious mutations all having the same effect on fitness. The scientists assumed selection against those mutations and analyzed how fluctuations in the group of the fittest individuals affected the less fit ones and the whole population. Richard Neher and Boris Shraiman discovered that the key to the understanding of Muller’s ratchet lies in a slow response: If the number of the fittest individuals is reduced, the mean fitness decreases only after a delay. “This delayed feedback accelerates Muller’s ratchet,” Richard Neher comments on the results. It clicks more and more frequently.

Equilibrium of mutation and selection processes: A population can be divided into groups of individuals that carry different numbers of deleterious mutations. Groups with few mutations are amplified by selection but loose members to other groups by mutation. Groups with many mutations don't reproduce as much, but gain members by mutation. © Richard Neher/MPI for Developmental Biology

“Our results are valid for a broad range of conditions and parameter values – for a population of viruses as well as a population of tigers.” However, he does not expect to find the model’s conditions one-to-one in nature. “Models are made to understand the essential aspects, to identify the critical processes,” he explains.

In a second study Richard Neher, Boris Shraiman and several other US-scientists from the University of California in Santa Barbara and Harvard University in Cambridge investigated how a small asexual population could escape Muller’s ratchet. “Such a population can only stay in a steady state for a long time when beneficial mutations continually compensate for the negative ones that accumulate via Muller’s ratchet,” says Richard Neher. For their model the scientists assumed a steady environment and suggest that there can be a mutation-selection balance in every population. They have calculated the rate of favorable mutations required to maintain the balance. The result was surprising: Even under unfavorable conditions, a comparably small proportion in the range of several percent of positive mutations is sufficient to sustain a population.

These findings could explain the long-term maintenance of mitochondria, the so-called power plants of the cell that have their own genome and divide asexually. By and large, evolution is driven by random events or as Richard Neher says: “Evolutionary dynamics are very stochastic.”


The Vast, Ancient World of Viruses

Viruses are no part of the modern synthesis or more generally the traditional narrative of evolutionary biology. Until very recently, viruses have been viewed primarily as pathogens of animals, plants, and bacteria. Several lines of recent discovery have radically changed this view and promoted viruses to a central position on the stage of evolution. This change in the evolutionary status of viruses and related selfish genetic elements has been discussed in detail elsewhere (Claverie, 2006 Koonin et al., 2006, 2011 Raoult and Forterre, 2008). Here we quickly recapitulate several key points, with a focus on the importance of viruses for evolutionary biology in general. Metagenomic and ecological genomics studies have shown that, astonishingly, viruses are the most common biological entities on earth (Edwards and Rohwer, 2005 Suttle, 2005, 2007). Viruses and/or virus-like mobile elements are present in all cellular life forms. Strikingly, in mammals sequences derived from mobile elements and endogenous viruses account for at least 50% of the genome whereas in plants this fraction can reach 90% (Feschotte et al., 2002 Kazazian et al., 2004 Devos et al., 2005 Hedges and Batzer, 2005). Even the genomes of some unicellular eukaryotes, such as Trichomonas vaginalis, consist mostly of inactivated transposons (Carlton et al., 2007 Pritham et al., 2007). Recruitment of mobile element sequences for transcription regulation and other cellular functions such as microRNA formation is a common phenomenon the full extent of which is not yet fully appreciated (Jordan et al., 2003 Piriyapongsa et al., 2007 Lisch and Bennetzen, 2011). Although genomes of prokaryotes are not so overwhelmed by mobile elements, due to the intense purifying selection, nearly all of them encompass multiple prophages and mobile elements. Notably, deletion of all prophages leads to a substantial drop of fitness in E coli (Wang et al., 2010).

In at least some common environments such as ocean water and soil, the number of virus particles exceeds the number of cells by factors of 10� (Edwards and Rohwer, 2005 Suttle, 2007 Srinivasiah et al., 2008 Breitbart, 2012). Similarly, the genetic diversity of viruses, measured as the number of distinct genes, substantially exceeds the genetic diversity of cellular life forms. Furthermore, viruses, in particular bacteriophages, are major biogeochemical agents. Periodical killing of microbes, in particular cyanobacteria, has been identified as a major contributor to sediment formation and major contributors to the nutrient cycles in the biosphere (Suttle, 2007 Rohwer and Thurber, 2009). The same process obviously is a key determinant of the population dynamics of the hosts that shapes the selection-drift balance throughout the course of evolution (Weinbauer and Rassoulzadegan, 2004).

The very fact that viruses greatly outnumber bacteria in the environment implies that antivirus defense systems are central to the evolution of bacteria and archaea. This is indeed the case as made evident by the remarkable proliferation of diverse antivirus systems including CRISPR-Cas discussed above as well as multiple restriction-modification, abortive infection, toxin-antitoxin and other, still poorly characterized defense systems that in different combinations and with different abundances are present in most prokaryotes (Juhas et al., 2009 Labrie et al., 2010 Makarova et al., 2011 Martinez-Borra et al., 2012). Taken together, these findings and theoretical considerations strongly support the view that the virus-host arms race is one of the principal processes in all evolution (Forterre and Prangishvili, 2009 Stern and Sorek, 2011).

With regard to the classification of life forms, the only defensible position appears to be that viruses (and related mobile elements) and cells are the two principal categories of biological organization (Figure 7) (Raoult and Forterre, 2008 Koonin, 2010 O'Malley and Koonin, 2011) this view is independent of the semantic issue of viruses being 𠇊live” or not (Koonin et al., 2009 Moreira and Lopez-Garcia, 2009 Raoult, 2009). These two categories of biological entities can be characterized as informational (genetic) parasites, i.e., viruses and other selfish elements, and genetically self-sustained organisms, i.e., cellular life forms. Mathematical modeling indicates that genetic parasites inevitably emerge in any replicator system (Szathmary and Maynard Smith, 1997 Takeuchi and Hogeweg, 2012). This conclusion is certainly intuitively plausible: one expects that cheaters will appear in any system with limited resources—in particular, in any system of replicators, such parasites will attempt to utilize the replication machinery without making it (Koonin and Martin, 2005). Also, the notion that virus-like selfish elements are an intrinsic part of life since its inception [which can be reasonably considered to coincide with the origin of replication (O'Malley and Koonin, 2011)] is compatible with the ubiquity of these elements in nature. In mathematical modeling, the outcome of the virus-host interaction depends on the specific parameters of the adapted model. In homogeneous models, virus-like parasites tend to cause collapse of the entire systems but in models with compartmentalization, which are most relevant for the actual evolution of life, stable host-parasite coexistence is possible (Takeuchi and Hogeweg, 2009). Moreover, the destructive effect of genetic parasites on the host is mitigated when a dedicated genetic information storage medium evolves, which could be one of the driving forces behind the evolution of DNA in the primordial RNA world (Takeuchi et al., 2011).

Figure 7. The viral and cellular 𠇎mpires” of life forms and domains within them. The cellular empire domains: A, Archaea B, Bacteria E, Eukaryota. The Virus empire domains: +R, positive-strand RNA viruses −R, negative-strand RNA viruses dsR, double-stranded RNA viruses dsD, double-stranded DNA viruses ssD, single-stranded DNA viruses RT, retro-transcribing elements/viruses VR, viroids.

Further support for the classification of viruses as one of the two 𠇎mpires” of life is the diversity of the replication-expression cycles that is found among viruses and related elements. Indeed, while cellular life forms all use a uniform replication-expression strategy based on double-stranded (ds)DNA replication, transcription of genes into mRNA or non-coding RNA, and translation of mRNA into protein, viral genome can be represented by all known forms of nucleic acids, and alternative replication processes such as RNA replication and reverse transcription are widely used (Figure 7) (Koonin et al., 2006). Finally, although viral genomes are generally small compared to the genomes of cellular life forms (viruses being the ultimate genetic parasites), the range of genomic complexity is remarkable, from only about 300 nucleotides and no genes in the simplest virus-like parasites, the viroids, to over a megabase and more than 1000 genes (genomes that are more complex than those of many bacterial parasites and symbionts) in the giant mimiviruses (Raoult et al., 2004 Colson et al., 2012). Overall, the conclusion is inescapable that the entire history of life is a story of perennial interplay between genetic parasites and their hosts that is a major driver of evolution for both biological empires.


In 1931, geneticist Hermann Joseph Muller gave a speech at a scientific conference in New Orleans, Louisiana. In his remarks, Dr. Muller proposed a theory to answer a long-standing and controversial question: why do so many organisms use sexual reproduction &hellip Continue reading &rarr

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