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1.
Nat Commun ; 12(1): 4979, 2021 08 17.
Artigo em Inglês | MEDLINE | ID: mdl-34404804

RESUMO

Relative contributions of pre-existing vs de novo genomic variation to adaptation are poorly understood, especially in polyploid organisms. We assess this in high resolution using autotetraploid Arabidopsis arenosa, which repeatedly adapted to toxic serpentine soils that exhibit skewed elemental profiles. Leveraging a fivefold replicated serpentine invasion, we assess selection on SNPs and structural variants (TEs) in 78 resequenced individuals and discover significant parallelism in candidate genes involved in ion homeostasis. We further model parallel selection and infer repeated sweeps on a shared pool of variants in nearly all these loci, supporting theoretical expectations. A single striking exception is represented by TWO PORE CHANNEL 1, which exhibits convergent evolution from independent de novo mutations at an identical, otherwise conserved site at the calcium channel selectivity gate. Taken together, this suggests that polyploid populations can rapidly adapt to environmental extremes, calling on both pre-existing variation and novel polymorphisms.


Assuntos
Adaptação Fisiológica/efeitos dos fármacos , Adaptação Fisiológica/genética , Alelos , Arabidopsis/efeitos dos fármacos , Arabidopsis/genética , Genoma de Planta , Poliploidia , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Canais de Cálcio/metabolismo , Mutação , Polimorfismo de Nucleotídeo Único , Alcaloides de Triptamina e Secologanina/metabolismo , Solo/química
2.
Mol Biol Evol ; 38(9): 3910-3924, 2021 Aug 23.
Artigo em Inglês | MEDLINE | ID: mdl-33783509

RESUMO

Whole genome duplication (WGD) can promote adaptation but is disruptive to conserved processes, especially meiosis. Studies in Arabidopsis arenosa revealed a coordinated evolutionary response to WGD involving interacting proteins controlling meiotic crossovers, which are minimized in an autotetraploid (within-species polyploid) to avoid missegregation. Here, we test whether this surprising flexibility of a conserved essential process, meiosis, is recapitulated in an independent WGD system, Cardamine amara, 17 My diverged from A. arenosa. We assess meiotic stability and perform population-based scans for positive selection, contrasting the genomic response to WGD in C. amara with that of A. arenosa. We found in C. amara the strongest selection signals at genes with predicted functions thought important to adaptation to WGD: meiosis, chromosome remodeling, cell cycle, and ion transport. However, genomic responses to WGD in the two species differ: minimal ortholog-level convergence emerged, with none of the meiosis genes found in A. arenosa exhibiting strong signal in C. amara. This is consistent with our observations of lower meiotic stability and occasional clonal spreading in diploid C. amara, suggesting that nascent C. amara autotetraploid lineages were preadapted by their diploid lifestyle to survive while enduring reduced meiotic fidelity. However, in contrast to a lack of ortholog convergence, we see process-level and network convergence in DNA management, chromosome organization, stress signaling, and ion homeostasis processes. This gives the first insight into the salient adaptations required to meet the challenges of a WGD state and shows that autopolyploids can utilize multiple evolutionary trajectories to adapt to WGD.

3.
Science ; 369(6504)2020 08 07.
Artigo em Inglês | MEDLINE | ID: mdl-32764038

RESUMO

Sulfolobus acidocaldarius is the closest experimentally tractable archaeal relative of eukaryotes and, despite lacking obvious cyclin-dependent kinase and cyclin homologs, has an ordered eukaryote-like cell cycle with distinct phases of DNA replication and division. Here, in exploring the mechanism of cell division in S. acidocaldarius, we identify a role for the archaeal proteasome in regulating the transition from the end of one cell cycle to the beginning of the next. Further, we identify the archaeal ESCRT-III homolog, CdvB, as a key target of the proteasome and show that its degradation triggers division by allowing constriction of the CdvB1:CdvB2 ESCRT-III division ring. These findings offer a minimal mechanism for ESCRT-III-mediated membrane remodeling and point to a conserved role for the proteasome in eukaryotic and archaeal cell cycle control.


Assuntos
Proteínas Arqueais/fisiologia , Divisão Celular , Complexos Endossomais de Distribuição Requeridos para Transporte/fisiologia , Complexo de Endopeptidases do Proteassoma/fisiologia , Sulfolobus acidocaldarius/citologia , Proteínas Arqueais/química , Bortezomib/química , Bortezomib/farmacologia , Complexos Endossomais de Distribuição Requeridos para Transporte/química , Modelos Moleculares , Complexo de Endopeptidases do Proteassoma/química , Inibidores de Proteassoma/química , Inibidores de Proteassoma/farmacologia , Proteólise , Sulfolobus acidocaldarius/efeitos dos fármacos , Sulfolobus acidocaldarius/enzimologia
4.
Proc Natl Acad Sci U S A ; 117(26): 14936-14947, 2020 06 30.
Artigo em Inglês | MEDLINE | ID: mdl-32541055

RESUMO

Mre11 and Rad50 (M/R) proteins are part of an evolutionarily conserved macromolecular apparatus that maintains genomic integrity through repair pathways. Prior structural studies have revealed that this apparatus is extremely dynamic, displaying flexibility in the long coiled-coil regions of Rad50, a member of the structural maintenance of chromosome (SMC) superfamily of ATPases. However, many details of the mechanics of M/R chromosomal manipulation during DNA-repair events remain unclear. Here, we investigate the properties of the thermostable M/R complex from the archaeon Sulfolobus acidocaldarius using atomic force microscopy (AFM) to understand how this macromolecular machinery orchestrates DNA repair. While previous studies have observed canonical interactions between the globular domains of M/R and DNA, we observe transient interactions between DNA substrates and the Rad50 coiled coils. Fast-scan AFM videos (at 1-2 frames per second) of M/R complexes reveal that these interactions result in manipulation and translocation of the DNA substrates. Our study also shows dramatic and unprecedented ATP-dependent DNA unwinding events by the M/R complex, which extend hundreds of base pairs in length. Supported by molecular dynamic simulations, we propose a model for M/R recognition at DNA breaks in which the Rad50 coiled coils aid movement along DNA substrates until a DNA end is encountered, after which the DNA unwinding activity potentiates the downstream homologous recombination (HR)-mediated DNA repair.


Assuntos
Proteínas Arqueais/metabolismo , Endodesoxirribonucleases/metabolismo , Exodesoxirribonucleases/metabolismo , Proteína Homóloga a MRE11/metabolismo , Sulfolobus acidocaldarius/genética , Proteínas Arqueais/química , Proteínas Arqueais/genética , DNA Arqueal/química , DNA Arqueal/genética , DNA Arqueal/metabolismo , Endodesoxirribonucleases/química , Endodesoxirribonucleases/genética , Exodesoxirribonucleases/química , Exodesoxirribonucleases/genética , Proteína Homóloga a MRE11/química , Proteína Homóloga a MRE11/genética , Microscopia de Força Atômica , Ligação Proteica , Sulfolobus acidocaldarius/química , Sulfolobus acidocaldarius/enzimologia , Sulfolobus acidocaldarius/metabolismo
5.
Philos Trans R Soc Lond B Biol Sci ; 374(1777): 20180243, 2019 07 22.
Artigo em Inglês | MEDLINE | ID: mdl-31154972

RESUMO

It is a plausible hypothesis that parallel adaptation events to the same environmental challenge should result in genetic changes of similar or identical effects, depending on the underlying fitness landscapes. However, systematic testing of this is scarce. Here we examine this hypothesis in two closely related plant species, Arabidopsis halleri and Arabidopsis arenosa, which co-occur at two calamine metalliferous (M) sites harbouring toxic levels of the heavy metals zinc and cadmium. We conduct individual genome resequencing alongside soil elemental analysis for 64 plants from eight populations on M and non-metalliferous (NM) soils, and identify genomic footprints of selection and local adaptation. Selective sweep and environmental association analyses indicate a modest degree of gene as well as functional network convergence, whereby the proximal molecular factors mediating this convergence mostly differ between site pairs and species. Notably, we observe repeated selection on identical single nucleotide polymorphisms in several A. halleri genes at two independently colonized M sites. Our data suggest that species-specific metal handling and other biological features could explain a low degree of convergence between species. The parallel establishment of plant populations on calamine M soils involves convergent evolution, which will probably be more pervasive across sites purposely chosen for maximal similarity in soil composition. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.


Assuntos
Arabidopsis/genética , Evolução Biológica , Adaptação Fisiológica , Arabidopsis/classificação , Arabidopsis/fisiologia , Cádmio/metabolismo , Polimorfismo de Nucleotídeo Único , Solo/química , Poluentes do Solo/análise , Poluentes do Solo/metabolismo , Zinco/metabolismo
6.
Proc Natl Acad Sci U S A ; 115(52): E12443-E12452, 2018 12 26.
Artigo em Inglês | MEDLINE | ID: mdl-30530653

RESUMO

Stressors such as soil salinity and dehydration are major constraints on plant growth, causing worldwide crop losses. Compounding these insults, increasing climate volatility requires adaptation to fluctuating conditions. Salinity stress responses are relatively well understood in Arabidopsis thaliana, making this system suited for the rapid molecular dissection of evolutionary mechanisms. In a large-scale genomic analysis of Catalonian A. thaliana, we resequenced 77 individuals from multiple salinity gradients along the coast and integrated these data with 1,135 worldwide A. thaliana genomes for a detailed understanding of the demographic and evolutionary dynamics of naturally evolved salinity tolerance. This revealed that Catalonian varieties adapted to highly fluctuating soil salinity are not Iberian relicts but instead have immigrated to this region more recently. De novo genome assembly of three allelic variants of the high-affinity K+ transporter (HKT1;1) locus resolved structural variation between functionally distinct alleles undergoing fluctuating selection in response to seasonal changes in soil salinity. Plants harboring alleles responsible for low root expression of HKT1;1 and consequently high leaf sodium (HKT1;1 HLS ) were migrants that have moved specifically into areas where soil sodium levels fluctuate widely due to geography and rainfall variation. We demonstrate that the proportion of plants harboring HKT1;1 HLS alleles correlates with soil sodium level over time, HKT1;1 HLS -harboring plants are better adapted to intermediate levels of salinity, and the HKT1;1 HLS allele clusters with high-sodium accumulator accessions worldwide. Together, our evidence suggests that HKT1;1 is under fluctuating selection in response to climate volatility and is a worldwide determinant in adaptation to saline conditions.


Assuntos
Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Proteínas de Transporte de Cátions/genética , Proteínas de Transporte de Cátions/metabolismo , Simportadores/genética , Simportadores/metabolismo , Adaptação Biológica/genética , Adaptação Fisiológica/genética , Alelos , Arabidopsis/genética , Arabidopsis/fisiologia , Proteínas de Arabidopsis/fisiologia , Proteínas de Transporte de Cátions/fisiologia , Frequência do Gene/genética , Transporte de Íons , Salinidade , Tolerância ao Sal , Sódio/metabolismo , Cloreto de Sódio , Solo , Simportadores/fisiologia
7.
J Exp Bot ; 68(20): 5453-5470, 2017 Nov 28.
Artigo em Inglês | MEDLINE | ID: mdl-29096001

RESUMO

Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.


Assuntos
Alelos , Fluxo Gênico/genética , Hibridização Genética/genética , Plantas/genética , Adaptação Biológica , Transferência Genética Horizontal/genética
8.
Nat Commun ; 6: 8163, 2015 Sep 08.
Artigo em Inglês | MEDLINE | ID: mdl-26348592

RESUMO

In eukaryotes, the covalent attachment of ubiquitin chains directs substrates to the proteasome for degradation. Recently, ubiquitin-like modifications have also been described in the archaeal domain of life. It has subsequently been hypothesized that ubiquitin-like proteasomal degradation might also operate in these microbes, since all archaeal species utilize homologues of the eukaryotic proteasome. Here we perform a structural and biochemical analysis of a ubiquitin-like modification pathway in the archaeon Sulfolobus acidocaldarius. We reveal that this modifier is homologous to the eukaryotic ubiquitin-related modifier Urm1, considered to be a close evolutionary relative of the progenitor of all ubiquitin-like proteins. Furthermore we demonstrate that urmylated substrates are recognized and processed by the archaeal proteasome, by virtue of a direct interaction with the modifier. Thus, the regulation of protein stability by Urm1 and the proteasome in archaea is likely representative of an ancient pathway from which eukaryotic ubiquitin-mediated proteolysis has evolved.


Assuntos
Proteínas Arqueais/genética , Complexo de Endopeptidases do Proteassoma/metabolismo , Sulfolobus acidocaldarius/genética , Ubiquitinas/genética , Proteínas Arqueais/metabolismo , Cromatografia em Gel , Cromatografia Líquida , Dicroísmo Circular , Cristalografia por Raios X , Espectrometria de Massas , Microscopia Eletrônica , Complexo de Endopeptidases do Proteassoma/ultraestrutura , Proteólise , Sulfolobus acidocaldarius/metabolismo , Ubiquitinas/metabolismo
9.
Nat Commun ; 5: 5506, 2014 Nov 25.
Artigo em Inglês | MEDLINE | ID: mdl-25420454

RESUMO

The HerA ATPase cooperates with the NurA nuclease and the Mre11-Rad50 complex for the repair of double-strand DNA breaks in thermophilic archaea. Here we extend our structural knowledge of this minimal end-resection apparatus by presenting the first crystal structure of hexameric HerA. The full-length structure visualizes at atomic resolution the N-terminal HerA-ATP synthase domain and a conserved C-terminal extension, which acts as a physical brace between adjacent protomers. The brace also interacts in trans with nucleotide-binding residues of the neighbouring subunit. Our observations support a model in which the coaxial interaction of the HerA ring with the toroidal NurA dimer generates a continuous channel traversing the complex. HerA-driven translocation would propel the DNA towards the narrow annulus of NurA, leading to duplex melting and nucleolytic digestion. This system differs substantially from the bacterial end-resection paradigms. Our findings suggest a novel mode of DNA-end processing by this integrated archaeal helicase-nuclease machine.


Assuntos
Adenosina Trifosfatases/química , Adenosina Trifosfatases/metabolismo , Archaea/enzimologia , Proteínas Arqueais/metabolismo , DNA Arqueal/genética , Translocação Genética , Adenosina Trifosfatases/genética , Sequência de Aminoácidos , Archaea/química , Archaea/genética , Proteínas Arqueais/química , Proteínas Arqueais/genética , Quebras de DNA de Cadeia Dupla , DNA Arqueal/metabolismo , Desoxirribonucleases/genética , Desoxirribonucleases/metabolismo , Modelos Moleculares , Dados de Sequência Molecular , Alinhamento de Sequência
10.
Biochem Soc Trans ; 41(1): 314-20, 2013 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-23356304

RESUMO

During DNA repair by HR (homologous recombination), the ends of a DNA DSB (double-strand break) must be resected to generate single-stranded tails, which are required for strand invasion and exchange with homologous chromosomes. This 5'-3' end-resection of the DNA duplex is an essential process, conserved across all three domains of life: the bacteria, eukaryota and archaea. In the present review, we examine the numerous and redundant helicase and nuclease systems that function as the enzymatic analogues for this crucial process in the three major phylogenetic divisions.


Assuntos
Dano ao DNA , DNA Arqueal/genética , DNA Bacteriano/genética , DNA/genética , Células Eucarióticas/metabolismo , Filogenia
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