SummaryExogenous melatonin application confers abiotic stress resistance in bermudagrass through modulation of antioxidants and metabolic homeostasis, and extensive transcriptional reprogramming such as the reorientation of photorespiratory, carbohydrate, and nitrogen metabolism.

Active DNA demethylation is an important part of epigenetic regulation in plants and animals. How active DNA demethylation is regulated and its relationship with histone modification patterns are unclear. Here, we report the discovery of IDM1, a regulator of DNA demethylation in Arabidopsis. IDM1 is required for preventing DNA hypermethylation of highly homologous multicopy genes and other repetitive sequences that are normally targeted for active DNA demethylation by Repressor of Silencing 1 and related 5-methylcytosine DNA glycosylases. IDM1 binds methylated DNA at chromatin sites lacking histone H3K4 di- or trimethylation and acetylates H3 to create a chromatin environment permissible for 5-methylcytosine DNA glycosylases to function. Our study reveals how some genes are indicated by multiple epigenetic marks for active DNA demethylation and protection from silencing.

Elucidating the origins of complex biological structures has been one of the major challenges of evolutionary studies. The bacterial flagellum is a primary example of a complex apparatus whose origins and evolutionary history have proven difficult to reconstruct. The gene clusters encoding the components of the flagellum can include >50 genes, but these clusters vary greatly in their numbers and contents among bacterial phyla. To investigate how this diversity arose, we identified all homologs of all flagellar proteins encoded in the complete genome sequences of 41 flagellated species from 11 bacterial phyla. Based on the phylogenetic occurrence and histories of each of these proteins, we could distinguish an ancient core set of 24 structural genes that were present in the common ancestor to all Bacteria. Within a genome, many of these core genes show sequence similarity only to other flagellar core genes, indicating that they were derived from one another, and the relationships among these genes suggest the probable order in which the structural components of the bacterial flagellum arose. These results show that core components of the bacterial flagellum originated through the successive duplication and modification of a few, or perhaps even a single, precursor gene.

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DNA methylation is an important epigenetic mark in many eukaryotic organisms. De novo DNA methylation in plants can be achieved by the RNA-directed DNA methylation (RdDM) pathway, where the plant-specific DNA-dependent RNA polymerase IV (Pol IV) transcribes target sequences to initiate 24-nt siRNA production and action. The putative DNA binding protein DTF1/SHH1 of Arabidopsis has been shown to associate with Pol IV and is required for 24-nt siRNA accumulation and transcriptional silencing at several RdDM target loci. However, the extent and mechanism of DTF1 function in RdDM is unclear. We show here that DTF1 is necessary for the accumulation of the majority of Pol IV-dependent 24-nt siRNAs. It is also required for a large proportion of Pol IV-dependent de novo DNA methylation. Interestingly, there is a group of RdDM target loci where 24-nt siRNA accumulation but not DNA methylation is dependent on DTF1. DTF1 interacts directly with the chromatin remodeling protein CLASSY 1 (CLSY1), and both DTF1 and CLSY1 are associated in vivo with Pol IV but not Pol V, which functions downstream in the RdDM effector complex. DTF1 and DTF2 (a DTF1-like protein) contain a SAWADEE domain, which was found to bind specifically to histone H3 containing H3K9 methylation. Taken together, our results show that DTF1 is a core component of the RdDM pathway, and suggest that DTF1 interacts with CLSY1 to assist in the recruitment of Pol IV to RdDM target loci where H3K9 methylation may be an important feature. Our results also suggest the involvement of DTF1 in an important negative feedback mechanism for DNA methylation at some RdDM target loci.histone modifications | small RNA | gene silencing | transposon D NA cytosine methylation is a conserved epigenetic mark that plays important roles in maintaining genome stability, transcriptional gene silencing, and developmental regulation (1, 2). In plants, DNA methylation occurs in three sequence contexts: CG, CHG, and CHH (H = A, C, T). CG and CHG methylation are symmetric in sequence and are maintained through a semiconservative mechanism that requires the DNA methyltransferases (METHYLTRANSFERASE 1) (MET1) and CHROMOMETHYLASE 3 (CMT3), respectively. In contrast, the asymmetric CHH methylation needs to be established during each cell cycle (1, 2). In plants a 24-nt small interfering RNA (siRNA)-dependent DNA methylation pathway is involved in recruiting the de novo DNA methyltransferase DOMAINS REARRANGED METHYLASE 2 (DRM2) and is responsible for DNA methylation at many transposable elements and repetitive sequences (3, 4).Two plant-specific homologs of RNA polymerase II play important roles in the RNA-directed DNA methylation (RdDM) pathway (5). RNA polymerase IV presumably initiates 24-nt siRNA biogenesis by specifically transcribing RdDM target loci to produce single-stranded RNA (ssRNA) transcripts, which serve as templates for RNA-dependent RNA polymerase 2 (RDR2) to generate double-stranded RNAs (dsRNAs). CLASSY 1 (CLSY1), a putative ATP-dependent chromatin remodeling protein, is prop...

Members of the genus Xenorhabdus are entomopathogenic bacteria that associate with nematodes. The nematode-bacteria pair infects and kills insects, with both partners contributing to insect pathogenesis and the bacteria providing nutrition to the nematode from available insect-derived nutrients. The nematode provides the bacteria with protection from predators, access to nutrients, and a mechanism of dispersal. Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological and metabolic mechanisms. We posited that these differences would be reflected in their respective genomes. To test this, we sequenced to completion the genomes of Xenorhabdus nematophila ATCC 19061 and Xenorhabdus bovienii SS-2004. As expected, both Xenorhabdus genomes encode many anti-insecticidal compounds, commensurate with their entomopathogenic lifestyle. Despite the similarities in lifestyle between Xenorhabdus and Photorhabdus bacteria, a comparative analysis of the Xenorhabdus, Photorhabdus luminescens, and P. asymbiotica genomes suggests genomic divergence. These findings indicate that evolutionary changes shaped by symbiotic interactions can follow different routes to achieve similar end points.

SignificanceUsing strawberry fruit as a model system, we uncover the mechanistic interactions between auxin, gibberellic acid (GA), and abscisic acid (ABA) that regulate the entire process of fruit development. Interlinked regulatory loops control ABA levels during fruit development. During the early stages, auxin/GA turns on a feedback loop to activate the removal of ABA via FveCYP707A4a-dependent catabolism needed for fruit growth. Down-regulation of auxin/GA results in the suppression of the feedback loop and the activation of the ABA biosynthesis-dependent feedforward loop, leading to a steep ABA accumulation for fruit ripening. The interlinked regulatory loops provide a conceptual framework that underlies the connection between the regulation of fruit growth and that of ripening as well as a molecular basis for manipulation of fruit sizes and ripening times.

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