title: Phylogeny-Based Systematization of Arabidopsis Proteins with Histone H1 Globular Domain.
abstract: H1 (or linker) histones are basic nuclear proteins that possess an evolutionarily conserved nucleosome-binding globular domain, GH1. They perform critical functions in determining the accessibility of chromatin DNA to trans-acting factors. In most metazoan species studied so far, linker histones are highly heterogenous, with numerous nonallelic variants cooccurring in the same cells. The phylogenetic relationships among these variants as well as their structural and functional properties have been relatively well established. This contrasts markedly with the rather limited knowledge concerning the phylogeny and structural and functional roles of an unusually diverse group of GH1-containing proteins in plants. The dearth of information and the lack of a coherent phylogeny-based nomenclature of these proteins can lead to misunderstandings regarding their identity and possible relationships, thereby hampering plant chromatin research. Based on published data and our in silico and high-throughput analyses, we propose a systematization and coherent nomenclature of GH1-containing proteins of Arabidopsis (Arabidopsis thaliana[L.] Heynh) that will be useful for both the identification and structural and functional characterization of homologous proteins from other plant species.
authors.affiliation: Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland (M.K., A.J.).|Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland (L.K., K.G.).|Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.M., K.R., M.L., A.J.).|Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland (K.R., C.B.); and.|Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany (A.S.).
authors.forename: Maciej
authors.identifier: http://orcid.org/0000-0002-0821-077X
authors.initials: M
authors.lastname: Kotliński
authors.affiliation: Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland (M.K., A.J.).|Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland (L.K., K.G.).|Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.M., K.R., M.L., A.J.).|Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland (K.R., C.B.); and.|Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany (A.S.).
authors.forename: Lukasz
authors.initials: L
authors.lastname: Knizewski
authors.affiliation: Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland (M.K., A.J.).|Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland (L.K., K.G.).|Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.M., K.R., M.L., A.J.).|Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland (K.R., C.B.); and.|Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany (A.S.).
authors.forename: Anna
authors.identifier: http://orcid.org/0000-0002-4578-844X
authors.initials: A
authors.lastname: Muszewska
authors.affiliation: Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland (M.K., A.J.).|Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland (L.K., K.G.).|Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.M., K.R., M.L., A.J.).|Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland (K.R., C.B.); and.|Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany (A.S.).
authors.forename: Kinga
authors.identifier: http://orcid.org/0000-0003-4035-675X
authors.initials: K
authors.lastname: Rutowicz
authors.affiliation: Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland (M.K., A.J.).|Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland (L.K., K.G.).|Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.M., K.R., M.L., A.J.).|Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland (K.R., C.B.); and.|Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany (A.S.).
authors.forename: Maciej
authors.identifier: http://orcid.org/0000-0001-7831-7495
authors.initials: M
authors.lastname: Lirski
authors.affiliation: Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland (M.K., A.J.).|Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland (L.K., K.G.).|Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.M., K.R., M.L., A.J.).|Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland (K.R., C.B.); and.|Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany (A.S.).
authors.forename: Anja
authors.initials: A
authors.lastname: Schmidt
authors.affiliation: Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland (M.K., A.J.); cbaroux@botinst.uzh.ch andyj@ibb.waw.pl.|Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland (L.K., K.G.); cbaroux@botinst.uzh.ch andyj@ibb.waw.pl.|Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.M., K.R., M.L., A.J.); cbaroux@botinst.uzh.ch andyj@ibb.waw.pl.|Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland (K.R., C.B.); and cbaroux@botinst.uzh.ch andyj@ibb.waw.pl.|Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany (A.S.) cbaroux@botinst.uzh.ch andyj@ibb.waw.pl.
authors.forename: Célia
authors.identifier: http://orcid.org/0000-0001-6307-2229
authors.initials: C
authors.lastname: Baroux
authors.affiliation: Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland (M.K., A.J.).|Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland (L.K., K.G.).|Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.M., K.R., M.L., A.J.).|Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland (K.R., C.B.); and.|Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany (A.S.).
authors.forename: Krzysztof
authors.initials: K
authors.lastname: Ginalski
authors.affiliation: Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland (M.K., A.J.); cbaroux@botinst.uzh.ch andyj@ibb.waw.pl.|Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, 02-089 Warsaw, Poland (L.K., K.G.); cbaroux@botinst.uzh.ch andyj@ibb.waw.pl.|Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (A.M., K.R., M.L., A.J.); cbaroux@botinst.uzh.ch andyj@ibb.waw.pl.|Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, 8008 Zurich, Switzerland (K.R., C.B.); and cbaroux@botinst.uzh.ch andyj@ibb.waw.pl.|Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany (A.S.) cbaroux@botinst.uzh.ch andyj@ibb.waw.pl.
authors.forename: Andrzej
authors.identifier: http://orcid.org/0000-0002-4684-4503
authors.initials: A
authors.lastname: Jerzmanowski
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics; D030541:Databases, Genetic; D030562:Databases, Protein; D006657:Histones / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D010944:Plants / Q000145:classification / Q000235:genetics / Q000378:metabolism; D013045:Species Specificity
chemical_list: D029681:Arabidopsis Proteins; D006657:Histones; D010940:Plant Proteins