title: A high-resolution tissue-specific proteome and phosphoproteome atlas of maize primary roots reveals functional gradients along the root axes.
abstract: A high-resolution proteome and phosphoproteome atlas of four maize (Zea mays) primary root tissues, the cortex, stele, meristematic zone, and elongation zone, was generated. High-performance liquid chromatography coupled with tandem mass spectrometry identified 11,552 distinct nonmodified and 2,852 phosphorylated proteins across the four root tissues. Two gradients reflecting the abundance of functional protein classes along the longitudinal root axis were observed. While the classes RNA, DNA, and protein peaked in the meristematic zone, cell wall, lipid metabolism, stress, transport, and secondary metabolism culminated in the differentiation zone. Functional specialization of tissues is underscored by six of 10 cortex-specific proteins involved in flavonoid biosynthesis. Comparison of this data set with high-resolution seed and leaf proteome studies revealed 13% (1,504/11,552) root-specific proteins. While only 23% of the 1,504 root-specific proteins accumulated in all four root tissues, 61% of all 11,552 identified proteins accumulated in all four root tissues. This suggests a much higher degree of tissue-specific functionalization of root-specific proteins. In summary, these data illustrate the remarkable plasticity of the proteomic landscape of maize primary roots and thus provide a starting point for gaining a better understanding of their tissue-specific functions.
authors.affiliation: Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany (C.M., A.P., F.H.);Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.); andSection of Cell and Developmental Biology, University of California-San Diego, La Jolla, California 92093 (J.W.W., Z.S., L.G.S., S.P.B.).
authors.forename: Caroline
authors.identifier: http://orcid.org/0000-0001-6699-9441
authors.initials: C
authors.lastname: Marcon
authors.affiliation: Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany (C.M., A.P., F.H.);Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.); andSection of Cell and Developmental Biology, University of California-San Diego, La Jolla, California 92093 (J.W.W., Z.S., L.G.S., S.P.B.).
authors.forename: Waqas Ahmed
authors.initials: WA
authors.lastname: Malik
authors.affiliation: Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany (C.M., A.P., F.H.);Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.); andSection of Cell and Developmental Biology, University of California-San Diego, La Jolla, California 92093 (J.W.W., Z.S., L.G.S., S.P.B.).
authors.forename: Justin W
authors.identifier: http://orcid.org/0000-0001-7553-2237
authors.initials: JW
authors.lastname: Walley
authors.affiliation: Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany (C.M., A.P., F.H.);Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.); andSection of Cell and Developmental Biology, University of California-San Diego, La Jolla, California 92093 (J.W.W., Z.S., L.G.S., S.P.B.).
authors.forename: Zhouxin
authors.initials: Z
authors.lastname: Shen
authors.affiliation: Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany (C.M., A.P., F.H.);Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.); andSection of Cell and Developmental Biology, University of California-San Diego, La Jolla, California 92093 (J.W.W., Z.S., L.G.S., S.P.B.).
authors.forename: Anja
authors.initials: A
authors.lastname: Paschold
authors.affiliation: Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany (C.M., A.P., F.H.);Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.); andSection of Cell and Developmental Biology, University of California-San Diego, La Jolla, California 92093 (J.W.W., Z.S., L.G.S., S.P.B.).
authors.forename: Laurie G
authors.identifier: http://orcid.org/0000-0002-8294-1589
authors.initials: LG
authors.lastname: Smith
authors.affiliation: Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany (C.M., A.P., F.H.);Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.); andSection of Cell and Developmental Biology, University of California-San Diego, La Jolla, California 92093 (J.W.W., Z.S., L.G.S., S.P.B.).
authors.forename: Hans-Peter
authors.identifier: http://orcid.org/0000-0001-7813-2992
authors.initials: HP
authors.lastname: Piepho
authors.affiliation: Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany (C.M., A.P., F.H.);Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.); andSection of Cell and Developmental Biology, University of California-San Diego, La Jolla, California 92093 (J.W.W., Z.S., L.G.S., S.P.B.) sbriggs@ucsd.edu hochholdinger@uni-bonn.de.
authors.forename: Steven P
authors.identifier: http://orcid.org/0000-0002-7226-8618
authors.initials: SP
authors.lastname: Briggs
authors.affiliation: Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113 Bonn, Germany (C.M., A.P., F.H.);Institute of Crop Science, Biostatistics Unit, University of Hohenheim, 70599 Stuttgart, Germany (W.A.M., H.-P.P.); andSection of Cell and Developmental Biology, University of California-San Diego, La Jolla, California 92093 (J.W.W., Z.S., L.G.S., S.P.B.) sbriggs@ucsd.edu hochholdinger@uni-bonn.de.
authors.forename: Frank
authors.identifier: http://orcid.org/0000-0002-5155-0884
authors.initials: F
authors.lastname: Hochholdinger
mesh_terms: D015536:Down-Regulation; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018519:Meristem / Q000378:metabolism; D058977:Molecular Sequence Annotation; D009928:Organ Specificity; D010750:Phosphoproteins / Q000378:metabolism*; D010766:Phosphorylation; D018515:Plant Leaves / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D018517:Plant Roots / Q000378:metabolism*; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012639:Seeds / Q000378:metabolism; D015854:Up-Regulation; D003313:Zea mays / Q000235:genetics / Q000378:metabolism*
chemical_list: D010750:Phosphoproteins; D010940:Plant Proteins; D020543:Proteome; D012333:RNA, Messenger