title: The variations in the nuclear proteome reveal new transcription factors and mechanisms involved in UV stress response in Pinus radiata.
abstract: The importance of UV stress and its side-effects over the loss of plant productivity in forest species demands a deeper understanding of how pine trees respond to UV irradiation. Although the response to UV stress has been characterized at system and cellular levels, the dynamics within the nuclear proteome triggered by UV is still unknown despite that they are essential for gene expression and regulation of plant physiology. To fill this gap this work aims to characterize the variations in the nuclear proteome as a response to UV irradiation by using state-of-the-art mass spectrometry-based methods combined with novel bioinformatics workflows. The combination of SEQUEST, de novo sequencing, and novel annotation pipelines allowed cover sensing and transduction pathways, endoplasmic reticulum-related mechanisms and the regulation of chromatin dynamism and gene expression by histones, histone-like NF-Ys, and other transcription factors previously unrelated to this stress source, as well as the role of alternative splicing and other mechanisms involved in RNA translation and protein synthesis. The determination of 33 transcription factors, including NF-YB13, Pp005698_3 (NF-YB) and Pr009668_2 (WD-40), which are correlated to stress responsive mechanisms like an increased accumulation of photoprotective pigments and reduced photosynthesis, pointing them as strong candidate biomarkers for breeding programs aimed to improve UV resistance of pine trees.
  
  
  
  The description of the nuclear proteome of Pinus radiata combining a classic approach based on the use of SEQUEST and the use of a mass accuracy precursor alignment (MAPA) allowed an unprecedented protein coverage. This workflow provided the methodological basis for characterizing the changes in the nuclear proteome triggered by UV irradiation, allowing the depiction of the nuclear events involved in stress response and adaption. The relevance of some of the discovered proteins will suppose a major advance in stress biology field, also providing a set of transcription factors that can be considered as strong biomarker candidates to select trees more tolerant to UV radiation in forest upgrade programs.
authors.affiliation: Plant Physiology Lab, Department of Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain.
authors.forename: Jesús
authors.initials: J
authors.lastname: Pascual
authors.affiliation: Plant Physiology Lab, Department of Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain.
authors.forename: Sara
authors.initials: S
authors.lastname: Alegre
authors.affiliation: Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
authors.forename: Matthias
authors.initials: M
authors.lastname: Nagler
authors.affiliation: Plant Physiology Lab, Department of Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain.
authors.forename: Mónica
authors.initials: M
authors.lastname: Escandón
authors.affiliation: Plant Physiology Lab, Department of Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain.
authors.forename: María Luz
authors.initials: ML
authors.lastname: Annacondia
authors.affiliation: Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria.
authors.forename: Wolfram
authors.initials: W
authors.lastname: Weckwerth
authors.affiliation: Plant Physiology Lab, Department of Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain. Electronic address: valledorluis@uniovi.es.
authors.forename: Luis
authors.initials: L
authors.lastname: Valledor
authors.affiliation: Plant Physiology Lab, Department of Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain. Electronic address: mjcanal@uniovi.es.
authors.forename: María Jesús
authors.initials: MJ
authors.lastname: Cañal
mesh_terms: D000222:Adaptation, Physiological; D018506:Gene Expression Regulation, Plant / Q000528:radiation effects; D009687:Nuclear Proteins / Q000032:analysis* / Q000502:physiology; D028223:Pinus / Q000737:chemistry* / Q000235:genetics / Q000528:radiation effects; D020543:Proteome / Q000032:analysis*; D013312:Stress, Physiological; D014157:Transcription Factors / Q000032:analysis; D014466:Ultraviolet Rays
chemical_list: D009687:Nuclear Proteins; D020543:Proteome; D014157:Transcription Factors
keywords: MAPA; Nuclei; Pinus; SEQUEST; Transcription factor; UV stress