title: Rye B chromosomes encode a functional Argonaute-like protein with in vitro slicer activities similar to its A chromosome paralog.
abstract: B chromosomes (Bs) are supernumerary, dispensable parts of the nuclear genome, which appear in many different species of eukaryote. So far, Bs have been considered to be genetically inert elements without any functional genes. Our comparative transcriptome analysis and the detection of active RNA polymerase II (RNAPII) in the proximity of B chromatin demonstrate that the Bs of rye (Secale cereale) contribute to the transcriptome. In total, 1954 and 1218 B-derived transcripts with an open reading frame were expressed in generative and vegetative tissues, respectively. In addition to B-derived transposable element transcripts, a high percentage of short transcripts without detectable similarity to known proteins and gene fragments from A chromosomes (As) were found, suggesting an ongoing gene erosion process. In vitro analysis of the A- and B-encoded AGO4B protein variants demonstrated that both possess RNA slicer activity. These data demonstrate unambiguously the presence of a functional AGO4B gene on Bs and that these Bs carry both functional protein coding genes and pseudogene copies. Thus, B-encoded genes may provide an additional level of gene control and complexity in combination with their related A-located genes. Hence, physiological effects, associated with the presence of Bs, may partly be explained by the activity of B-located (pseudo)genes.
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany.
authors.forename: Wei
authors.initials: W
authors.lastname: Ma
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany.
authors.forename: Tobias Sebastian
authors.initials: TS
authors.lastname: Gabriel
authors.affiliation: Institute of Bioinformatics and Systems Biology/Munich Information Center for Protein Sequences, Helmholtz Center Munich, German Research Center for Environmental Health, 85764, Neuherberg, Germany.|National Bioinformatics Infrastructure Sweden, Department of Clinical and Experimental Medicine, Linköping University, SE-558185, Linköping, Sweden.
authors.forename: Mihaela Maria
authors.initials: MM
authors.lastname: Martis
authors.affiliation: Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Faculty of Life Sciences, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany.
authors.forename: Torsten
authors.initials: T
authors.lastname: Gursinsky
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany.
authors.forename: Veit
authors.initials: V
authors.lastname: Schubert
authors.affiliation: Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic.
authors.forename: Jan
authors.initials: J
authors.lastname: Vrána
authors.affiliation: Institute of Experimental Botany, Center of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371, Olomouc, Czech Republic.
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Doležel
authors.affiliation: Institute of Bioinformatics and Systems Biology/Munich Information Center for Protein Sequences, Helmholtz Center Munich, German Research Center for Environmental Health, 85764, Neuherberg, Germany.
authors.forename: Heidrun
authors.initials: H
authors.lastname: Grundlach
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany.
authors.forename: Lothar
authors.initials: L
authors.lastname: Altschmied
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany.
authors.forename: Uwe
authors.initials: U
authors.lastname: Scholz
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany.
authors.forename: Axel
authors.initials: A
authors.lastname: Himmelbach
authors.affiliation: Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Faculty of Life Sciences, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany.
authors.forename: Sven-Erik
authors.initials: SE
authors.lastname: Behrens
authors.affiliation: Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, PO Box 13145-1384, Tehran, Iran.
authors.forename: Ali Mohammad
authors.initials: AM
authors.lastname: Banaei-Moghaddam
authors.affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Houben
mesh_terms: D060565:Argonaute Proteins / Q000378:metabolism*; D001483:Base Sequence; D002467:Cell Nucleus / Q000378:metabolism; D002843:Chromatin / Q000378:metabolism; D032461:Chromosomes, Plant / Q000235:genetics*; D003198:Computer Simulation; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D005784:Gene Amplification; D018628:Gene Dosage; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant; D010940:Plant Proteins / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012434:Secale / Q000201:enzymology / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D060565:Argonaute Proteins; D002843:Chromatin; D010940:Plant Proteins; D012333:RNA, Messenger; D012321:DNA-Directed RNA Polymerases
keywords: Argonaute; B chromosomes; B-located genes; Secale cereale; gene erosion; gene expression; pseudogenization