Botrytis cinerea, the causative agent of gray mold disease, is an aggressive fungal pathogen that infects more than 200 plant species. Here, we show that some B. cinerea small RNAs (Bc-sRNAs) can silence Arabidopsis and tomato genes involved in immunity. These Bc-sRNAs hijack the host RNA interference (RNAi) machinery by binding to Arabidopsis Argonaute 1 (AGO1) and selectively silencing host immunity genes. The Arabidopsis ago1 mutant exhibits reduced susceptibility to B. cinerea, and the B. cinerea dcl1 dcl2 double mutant that can no longer produce these Bc-sRNAs displays reduced pathogenicity on Arabidopsis and tomato. Thus, this fungal pathogen transfers “virulent” sRNA effectors into host plant cells to suppress host immunity and achieve infection, which demonstrates a naturally occurring cross-kingdom RNAi as an advanced virulence mechanism.

Of the 20 ribosomally coded amino acid residues, lysine is the most frequently post-translationally modified, which has important functional and regulatory consequences. Here we report the identification and verification of a previously unreported form of protein post-translational modification (PTM): lysine succinylation. The succinyllysine residue was initially identified by mass spectrometry and protein sequence alignment. The identified succinyllysine peptides derived from in vivo proteins were verified by western blot analysis, in vivo labeling with isotopic succinate, MS/MS and HPLC coelution of their synthetic counterparts. We further show that lysine succinylation is evolutionarily conserved and that this PTM responds to different physiological conditions. Our study also implies that succinyl-CoA might be a cofactor for lysine succinylation. Given the apparent high abundance of lysine succinylation and the significant structural changes induced by this PTM, it is expected that lysine succinylation has important cellular functions.Protein post-translational modifications are one of the most efficient biological mechanisms for expanding the genetic code and for regulating cellular physiology 1,2 . The remarkable complexity of PTM networks is exemplified by modifications at the side chain of lysine, one of the three basic residues critical for protein structure and function. Lysine residues in proteins can be subjected to a variety of PTMs, including methylation, acetylation, biotinylation, ubiquitination, ubiquitin-like modifications, propionylation and butyrylation, the last two of which were recently identified by us 3,4 . Extensive studies in the past few decades have revealed that most, if not all, of these lysine PTMs are important in cellular physiology and pathology 5-8 .The method of choice for mapping a PTM site uses the molecular weight of the peptide and its fragments, which can be determined by mass spectrometry. The PTM induces both a structural change and a mass shift to its substrate residue. For example, lysine acetylation and lysine dimethylation lead to mass increases of 42.0106 and 28.0313 daltons (Da), © 2011 Nature America, Inc. All rights reserved * Correspondence and requests for materials should be addressed to Y.Z. yingming.zhao@uchicago.edu. 2 These authors contributed equally to this work. Author contributions Y.Z., M.T. and Z.X. designed the experiments. Y.Z. wrote the paper with the assistance from M.T., Z.Z. and Z.X. Z.Z. contributed to antibody purification and western blots of purified E. coli proteins; M.T. to HPLC-MS and data analysis; Z.X. to western blots, in vivo succinate labeling, mutagenesis, enzymatic assay, circular dichromism experiments, sequence alignment and structural analysis; L.D. to the chemical synthesis; Y.C. to PTMap analysis. Competing financial interestsThe authors declare no competing financial interests.Additional information Supplementary information and chemical compound information is available online at http://www.nature.com/naturechemica...

The orchestrated binding of transcriptional activators and repressors to specific DNA sequences in the context of chromatin defines the regulatory program of eukaryotic genomes. We developed a digital approach to assay regulatory protein occupancy on genomic DNA in vivo by dense mapping of individual DNase I cleavages from intact nuclei using massively parallel DNA sequencing. Analysis of > 23 million cleavages across the Saccharomyces cerevisiae genome revealed thousands of protected regulatory protein footprints, enabling de novo derivation of factor binding motifs as well as the identification of hundreds of novel binding sites for major regulators. We observed striking correspondence between nucleotide-level DNase I cleavage patterns and protein-DNA interactions determined by crystallography. The data also yielded a detailed view of larger chromatin features including positioned nucleosomes flanking factor binding regions. Digital genomic footprinting provides a powerful approach to delineate the cis-regulatory framework of any organism with an available genome sequence.