title: Maize Cytolines Unmask Key Nuclear Genes That Are under the Control of Retrograde Signaling Pathways in Plants.
abstract: The genomes of the two plant organelles encode for a relatively small number of proteins. Thus, nuclear genes encode the vast majority of their proteome. Organelle-to-nucleus communication takes place through retrograde signaling (RS) pathways. Signals relayed through RS pathways have an impact on nuclear gene expression but their target-genes remain elusive in a normal state of the cell (considering that only mutants and stress have been used so far). Here, we use maize cytolines as an alternative. The nucleus of a donor line was transferred into two other cytoplasmic environments through at least nine back-crosses, in a time-span of > 10 years. The transcriptomes of the resulting cytolines were sequenced and compared. There are 96 differentially regulated nuclear genes in two cytoplasm-donor lines when compared with their nucleus-donor. They are expressed throughout plant development, in various tissues and organs. One-third of the 96 proteins have a human homolog, stressing their potential role in mitochondrial RS. We also identified syntenic orthologous genes in four other grasses and homologous genes in Arabidopsis thaliana These findings contribute to the paradigm we use to describe the RS in plants. The 96 nuclear genes identified here are not differentially regulated as a result of mutation, or any kind of stress. They are rather key players of the organelle-to-nucleus communication in a normal state of the cell.
authors.affiliation: National Institute of Research and Development for Biological Sciences, Cluj-Napoca, Romania mihai.miclaus@icbcluj.ro remy.bruggmann@bioinformatics.unibe.ch.|Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland.
authors.forename: Mihai
authors.initials: M
authors.lastname: Miclaus
authors.affiliation: The Oncology Institute "Prof Dr Ion Chiricuta", Cluj-Napoca, Romania.|Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.
authors.forename: Ovidiu
authors.initials: O
authors.lastname: Balacescu
authors.affiliation: Agricultural Research and Development Station, Turda, Romania.
authors.forename: Ioan
authors.initials: I
authors.lastname: Has
authors.affiliation: The Oncology Institute "Prof Dr Ion Chiricuta", Cluj-Napoca, Romania.|Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.
authors.forename: Loredana
authors.initials: L
authors.lastname: Balacescu
authors.affiliation: Agricultural Research and Development Station, Turda, Romania.
authors.forename: Voichita
authors.initials: V
authors.lastname: Has
authors.affiliation: National Institute of Research and Development for Biological Sciences, Cluj-Napoca, Romania.
authors.forename: Dana
authors.initials: D
authors.lastname: Suteu
authors.affiliation: Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland.|Vital-IT, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland.
authors.forename: Samuel
authors.initials: S
authors.lastname: Neuenschwander
authors.affiliation: Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland.|Department of Clinical Research, University of Bern, Bern, Switzerland.
authors.forename: Irene
authors.initials: I
authors.lastname: Keller
authors.affiliation: Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland mihai.miclaus@icbcluj.ro remy.bruggmann@bioinformatics.unibe.ch.
authors.forename: Rémy
authors.initials: R
authors.lastname: Bruggmann
mesh_terms: D002467:Cell Nucleus / Q000235:genetics* / Q000378:metabolism; D017343:Genes, Plant; D006824:Hybridization, Genetic; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics*; D059467:Transcriptome; D003313:Zea mays / Q000235:genetics* / Q000378:metabolism
chemical_list: D010940:Plant Proteins
keywords: bioinformatics; cytolines; maize transcriptome; nuclear gene expression; retrograde signaling