Gene loss and compensatory evolution promotes the emergence of morphological novelties in budding yeast

Nature Ecology & Evolution, Год журнала: 2022, Номер 6(6), С. 763 - 773

Опубликована: Апрель 28, 2022

Язык: Английский

---

Adaptive Evolution Is Common in Rapid Evolutionary Radiations

Current Biology, Год журнала: 2019, Номер 29(18), С. 3081 - 3086.e5

Опубликована: Сен. 1, 2019

One of the most long-standing and important mysteries in evolutionary biology is why biological diversity so unevenly distributed across space taxonomic lineages. Nowhere this disparity more evident than multitude rapid radiations found on oceanic islands mountain ranges globe [1Schluter D. The Ecology Adaptive Radiation. Oxford University Press, 2000Google Scholar, 2Stroud J.T. Losos J.B. Ecological opportunity adaptive radiation.Annu. Rev. Ecol. Evol. Syst. 2016; 47: 507-532Crossref Scopus (252) Google 3Simpson G.G. Major Features Evolution. Columbia 1953Crossref 4Linder H.P. Plant species radiations: where, when, why?.Philos. Trans. R. Soc. Lond. B Biol. Sci. 2008; 363: 3097-3105Crossref PubMed (200) 5Hughes C.E. Atchison G.W. ubiquity alpine plant from Andes to Hengduan Mountains.New Phytol. 2015; 207: 275-282Crossref (209) Scholar]. processes driving these diversification events remain unclear [6Simões M. Breitkreuz L. Alvarado Baca S. Cooper J.C. Heins Herzog K. Lieberman B.S. evolving theory radiations.Trends 31: 27-34Abstract Full Text PDF (118) 7Rundell R.J. Price T.D. radiation, nonadaptive ecological speciation nonecological speciation.Trends 2009; 24: 394-399Abstract (395) 8Givnish T.J. radiation versus 'radiation' 'explosive diversification': conceptual distinctions are fundamental understanding evolution.New 297-303Crossref (126) Recent genome-wide studies suggest that natural selection may be frequent during radiations, as inferred work cichlid fish [9Brawand Wagner Li Y.I. Malinsky Keller I. Fan Simakov O. Ng A.Y. Lim Z.W. Bezault E. et al.The genomic substrate for African fish.Nature. 2014; 513: 375-381Crossref (639) Scholar], white-eye birds [10Cornetti Valente L.M. Dunning L.T. Quan X. Black R.A. Hébert Savolainen V. genome "Great Speciator" provides insights into bird diversification.Genome 7: 2680-2691Crossref (32) new world lupins [11Nevado B. Hughes Filatov D.A. Widespread evolution repeated New World lupins.Nat. Commun. 12384Crossref (56) wild tomatoes [12Pease Haak D.C. Hahn M.W. Moyle L.C. Phylogenomics reveals three sources variation a radiation.PLoS 14: e1002379Crossref (212) However, whether general feature remains untested. Here we show significantly compared background levels slowly diversifying This result consistent wide range angiosperm lineages analyzed: 12 which together comprise 1,377 described species, originating some biologically diverse systems Earth. In addition, find significant negative correlation between population size frequency radiations. A possible explanation pattern at least partly driven by positive advantageous mutations compensate fixation slightly deleterious smaller populations.

Язык: Английский

---

The evolutionary plasticity of chromosome metabolism allows adaptation to constitutive DNA replication stress

eLife, Год журнала: 2020, Номер 9

Опубликована: Фев. 11, 2020

Many biological features are conserved and thus considered to be resistant evolutionary change. While rapid genetic adaptation following the removal of genes has been observed, we often lack a mechanistic understanding how happens. We used budding yeast, Saccharomyces cerevisiae, investigate plasticity chromosome metabolism, network modules. experimentally evolved cells constitutively experiencing DNA replication stress caused by absence Ctf4, protein that coordinates enzymatic activities at forks. Parallel populations adapted stress, over 1000 generations, acquiring multiple, concerted mutations. These mutations altered two metabolism modules, sister chromatid cohesion, inactivated third, damage checkpoint. The selected define functionally reproducible trajectory. suggest implications for genome evolution in natural cancer.All plants, animals fungi share common ancestor, though they have become very distinct billions years, all essential machinery needed grow divide. At heart this is complex interaction proteins involved replication, process duplicating material every time cell divides. needs done with great care, error rates as small one mistake billion. Otherwise, can accumulate genome, causing problems long-term survival. Despite overall principles remaining same, underlying mechanisms vary across different organisms. Given precision complexity replicating DNA, it was not clear had differences. Fumasoni Murray set out answer forcing strain yeast evolve removing gene an important, but essential, component replication. were still able reproduce, hampered mutation. studied after reproduced thousand giving enough acquire new would allow compensate initial defects. In eight separate samples, made many same changes order overcome original segregation third feature normally protect against accumulation damaged DNA. findings show pathways controlled, laboratory environment quickly processes damaged. behavior mutated mimicked cancer cells, which struggling adapt their machinery. Studying follows perturbations could help researchers better deal challenges treatment development antibiotic resistance bacteria, well leading deeper both biology.

Язык: Английский

---

Identifying Targets of Selection in Laboratory Evolution Experiments

Journal of Molecular Evolution, Год журнала: 2023, Номер 91(3), С. 345 - 355

Опубликована: Фев. 21, 2023

Язык: Английский

---

Can gene-inactivating mutations lead to evolutionary novelty?

Current Biology, Год журнала: 2020, Номер 30(10), С. R465 - R471

Опубликована: Май 1, 2020

Язык: Английский

---

Evolutionary rescue of phosphomannomutase deficiency in yeast models of human disease

eLife, Год журнала: 2022, Номер 11

Опубликована: Окт. 10, 2022

The most common cause of human congenital disorders glycosylation (CDG) are mutations in the phosphomannomutase gene PMM2, which affect protein N -linked glycosylation. yeast SEC53 encodes a homolog PMM2 . We evolved 384 populations harboring one two human-disease-associated alleles, sec53- V238M and sec53 -F126L, or wild-type find that after 1000 generations, compensate for slow-growth phenotype associated with alleles. Through whole-genome sequencing we identify compensatory mutations, including known genetic interactors. observe an enrichment other genes whose homologs Type 1 CDG, PGM1 , minor isoform phosphoglucomutase yeast. By reconstruction, show pgm1 dominant allele-specific interactors restore both growth -V238M allele. Finally, characterize enzymatic activity purified Pgm1 mutant proteins. reduction, but not elimination, best compensates deleterious phenotypes Broadly, our results demonstrate power experimental evolution as tool identifying pathways

Язык: Английский

---

Evolutionary adaptation to hyperstable microtubules selectively targets tubulins and is empowered by the spindle assembly checkpoint

Cell Reports, Год журнала: 2025, Номер 44(2), С. 115323 - 115323

Опубликована: Фев. 1, 2025

Microtubules are polymers required for chromosome segregation. Their drug-induced hyperstabilization impairs segregation and is an established anti-cancer therapy. How cells respond to microtubule hyperstabilization, however, incompletely understood. To study this, we evolved budding yeast expressing a microtubule-hyperstabilizing tubulin mutant isolated adapted strains. Aneuploidy of specific chromosomes carrying the regulators STU2 VIK1/KAR3 was first observable adaptation. In longer run, aneuploidies were outcompeted by mutations in α- or β-tubulin, partially overlapping with cancer patients. Thus, compensation follows restrained reproducible path where new combine original offending mutation on same carrier. While partly compensatory, several failed re-establish fully normal dynamics. Sustained growth relied mitotic checkpoint, indicating that extended timing limits genomic instability caused reduced Our results predict potential vulnerability resistant agents.

Язык: Английский

---

Evolutionary rescue of spherical mreB deletion mutants of the rod-shape bacterium Pseudomonas fluorescens SBW25

Опубликована: Фев. 18, 2025

Maintenance of rod-shape in bacterial cells depends on the actin-like protein MreB. Deletion mreB from Pseudomonas fluorescens SBW25 results viable spherical variable volume and reduced fitness. Using a combination time-resolved microscopy biochemical assay peptidoglycan synthesis, we show that fitness is consequence perturbed cell size homeostasis arises primarily differential growth daughter cells. A 1,000-generation selection experiment resulted rapid restoration with derived retaining shape. Mutations synthesis Pbp1A were identified as main route for evolutionary rescue genetic reconstructions demonstrating causality. Compensatory pbp1A mutations targeted transpeptidase activity enhanced homogeneity wall lateral surfaces restored homeostasis. Mechanistic explanations require understanding why deletion causes heterogeneity synthesis. We conclude by presenting two testable hypotheses, one which posits stems non-functional machinery, while second machinery functional, albeit stalled. Overall, our data provide support hypothesis draw attention to importance balance between glycosyltransferase functions building enzymes shape determination.

Язык: Английский

---

Evolutionary rescue of spherical mreB deletion mutants of the rod-shape bacterium Pseudomonas fluorescens SBW25

eLife, Год журнала: 2025, Номер 13

Опубликована: Март 31, 2025

Maintenance of rod-shape in bacterial cells depends on the actin-like protein MreB. Deletion mreB from Pseudomonas fluorescens SBW25 results viable spherical variable volume and reduced fitness. Using a combination time-resolved microscopy biochemical assay peptidoglycan synthesis, we show that fitness is consequence perturbed cell size homeostasis arises primarily differential growth daughter cells. A 1000-generation selection experiment resulted rapid restoration with derived retaining shape. Mutations synthesis Pbp1A were identified as main route for evolutionary rescue genetic reconstructions demonstrating causality. Compensatory pbp1A mutations targeted transpeptidase activity enhanced homogeneity wall lateral surfaces restored homeostasis. Mechanistic explanations require understanding why deletion causes heterogeneity synthesis. We conclude by presenting two testable hypotheses, one which posits stems non-functional machinery, while second machinery functional, albeit stalled. Overall, our data provide support hypothesis draw attention to importance balance between glycosyltransferase functions building enzymes shape determination.

Язык: Английский

---

Evolutionary repair: Changes in multiple functional modules allow meiotic cohesin to support mitosis

PLoS Biology, Год журнала: 2020, Номер 18(3), С. e3000635 - e3000635

Опубликована: Март 10, 2020

The role of proteins often changes during evolution, but we do not know how cells adapt when a protein is asked to participate in different biological function. We forced the budding yeast, Saccharomyces cerevisiae, use meiosis-specific kleisin, recombination 8 (Rec8), mitotic cell cycle, instead its paralog, Scc1. This perturbation impairs sister chromosome linkage, advances timing genome replication, and reduces reproductive fitness by 45%. evolved 15 parallel populations for 1,750 generations, substantially increasing their fitness, analyzed genotypes phenotypes cells. Only one population contained mutation Rec8, many had mutations transcriptional mediator complex, cohesin-related genes, cycle regulators that induce S phase. These improve cohesion delay replication Rec8-expressing conclude known novel partners allow an existing new functions.

Язык: Английский

---