RESUMO
Helitrons are the only group of rolling-circle transposons that encode a transposase with a helicase domain (Hel), which belongs to the Pif1 family. Because Pif1 helicases are important components of eukaryotic genomes, it has been suggested that Hel domains probably originated after a host eukaryotic Pif1 gene was captured by a Helitron ancestor. However, the few analyses exploring the evolution of Helitron transposases (RepHel) have focused on its Rep domain, which is also present in other mobile genetic elements. Here, we used phylogenetic and nonmetric multidimensional scaling analyses to investigate the relationship between Hel domains and Pif1-like helicases from a variety of organisms. Our results reveal that Hel domains are only distantly related to genomic helicases from eukaryotes and prokaryotes, and thus are unlikely to have originated from a captured Pif1 gene. Based on this evidence, and on recent studies indicating that Rep domains are more closely related to rolling-circle plasmids and phages, we suggest that Helitrons are descendants of a RepHel-encoding prokaryotic plasmid element that invaded eukaryotic genomes before the radiation of its major groups. We discuss how a Pif1-like helicase domain might have favored the transposition of Helitrons in eukaryotes beyond simply unwinding DNA intermediates. Finally, we demonstrate that some examples in the literature describing genomic helicases from eukaryotes actually consist of Hel domains from Helitrons, a finding that underscores how transposons can hamper the analysis of eukaryotic genes. This investigation also revealed that two groups of land plants appear to have lost genomic Pif1 helicases independently.
Assuntos
Elementos de DNA Transponíveis , Células Procarióticas , Células Eucarióticas , Filogenia , PlasmídeosRESUMO
Arabidopsis thaliana HomeoBox 1 (AtHB1) is a homeodomain-leucine zipper transcription factor described as a transcriptional activator with unknown function. Its role in A. thaliana development was investigated. AtHB1 expression was analyzed in transgenic plants bearing its promoter region fused to reporter genes. Knock-down mutant and overexpressor plant phenotypes were analyzed in different photoperiod regimes. AtHB1 was mainly expressed in hypocotyls and roots and up-regulated in seedlings grown under a short-day photoperiod. AtHB1 knock-down mutants and overexpressors showed shorter and longer hypocotyls, respectively, than wild type (WT). AtHB1 transcript levels were lower in PHYTOCHROME-INTERACTING FACTOR 1 (PIF1) mutants than in controls, suggesting that AtHB1 is regulated by PIF1 in hypocotyls. ß-glucuronidase (GUS) activity in Nicotiana benthamiana leaves cotransformed with PromAtHB1::GUS and 35S::PIF1 indicated that PIF1 induces AtHB1 expression. Hypocotyl lenght was measured in seedlings of athb1, pif1, or double athb1/pif1 mutants and PIF1 or AtHB1 overexpressors in WT, athb1 or pif1 backgrounds, both in short- or long-day. These analyses allowed us to determine that AtHB1 is a factor acting downstream of PIF1. Finally, a transcriptome analysis of athb1 mutant hypocotyls revealed that AtHB1 regulates genes involved in cell wall composition and elongation. The results suggest that AtHB1 acts downstream of PIF1 to promote hypocotyl elongation, especially in response to short-day photoperiods.
Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Fatores de Transcrição Hélice-Alça-Hélice Básicos/metabolismo , Hipocótilo/crescimento & desenvolvimento , Hipocótilo/metabolismo , Fatores de Transcrição/metabolismo , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Hipocótilo/genética , Modelos Biológicos , Dados de Sequência Molecular , Raízes de Plantas/metabolismo , Fatores de Transcrição/genéticaRESUMO
Phytochrome A (phyA) is crucial to initiate the early steps of the transition between skoto- and photomorphogenesis upon light exposure and to complete this process under far-red light (typical of dense vegetation canopies). However, under prolonged red or white light, phyA mutants are hyper-photomorphogenic in many respects. To investigate this issue, we analyzed the late response of the transcriptome of the phyA mutant to red light. Compared to the wild-type (WT), hyper-responsive genes outnumbered the genes showing reduced response to red light in phyA. A network analysis revealed the co-expression of PHYTOCHROME INTERACTING FACTOR 1 (PIF1) with those genes showing hyper-promotion by red light in phyA. The enhanced responses of gene expression, cotyledon unfolding, hypocotyl growth, and greening observed in the phyA mutant compared to the WT were absent in the phyA pif1 double mutant compared to pif1, indicating that the hyper-photomorphogenic phenotype of phyA requires PIF1. PIF1 directly binds to gene promoters that displayed PIF1-mediated enhanced response to red light. Expression of mutant PIF1 deficient in interactions with phyA and phyB enhanced the long-term growth response to red light but reduced the expression of selected genes in response to red light. We propose that phytochrome-mediated degradation of PIF1 prevents over-activation of photomorphogenesis during early seedling development.
Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/crescimento & desenvolvimento , Arabidopsis/metabolismo , Fatores de Transcrição Hélice-Alça-Hélice Básicos/metabolismo , Luz , Fitocromo A/metabolismo , Arabidopsis/efeitos da radiação , Proteínas de Arabidopsis/química , Fatores de Transcrição Hélice-Alça-Hélice Básicos/química , Regulação da Expressão Gênica de Plantas/efeitos da radiação , Mutação , Fitocromo A/genética , Fitocromo B/metabolismo , Estabilidade Proteica/efeitos da radiação , Estrutura Terciária de Proteína , Proteólise/efeitos da radiação , Plântula/crescimento & desenvolvimento , Plântula/efeitos da radiaçãoRESUMO
In Arabidopsis seeds, germination is promoted only by phytochromes, principally phytochrome B (phyB) and phytochrome A (phyA). Despite the abundant information concerning the molecular basis of phyB signaling downstream of PIF1/PIL5, the signaling network inducing germination by phyA is poorly known. Here, we describe the influence of phyA on the transcriptome of Arabidopsis seeds when germination is induced by a far-red (FR) pulse. The expression of 11% of the genome was significantly regulated by phyA. Most of the genes were up-regulated and the changes noted late (i.e. 5 h after a FR pulse), whereas changes in down-regulated genes were more abundant earlier (i.e. 0.5 h after a FR pulse). Auxin- and GA-associated elements were overrepresented in the genes that were modified by phyA. A significant number of genes whose expression was affected by phyA had not been previously reported to be dependent on PIL5. Among them, homozygotic mutant seeds of MYB66, a SAUR-like protein, PIN7, and GASA4 showed an impaired promotion of germination by phyA. Natural variation at the transcriptional level was found in early signaling and GA metabolic genes, but not in ABA metabolic and expansin genes between Columbia and Landsberg erecta accessions. Although phyA and phyB/PIL5 signaling pathways share some molecular components, our data suggest that phyA signaling is partially independent of PIL5 when germination is promoted by very low fluences of light.