title: Genome-wide co-expression analysis predicts protein kinases as important regulators of phosphate deficiency-induced root hair remodeling in Arabidopsis.
abstract: BACKGROUND
  Phosphorus (P) is one of the essential but often limiting elements for plants. Based on transcriptional profiling we reported previously that more than 3,000 genes are differentially expressed between phosphate (Pi)-deficient and Pi-sufficient Arabidopsis roots (MCP 11(11):1156-1166, 2012). The current study extends these findings by focusing on the analysis of genes that encode protein kinases (PK) and phosphatases (PP) by mining PK and PP genes that were differentially expressed in response to Pi deficiency.
  
  
  RESULTS
  Subsets of 1,118 and 205 annotated PK and PP genes were mined on the basis of the TAIR10 release of the Arabidopsis genome. Analysis of RNA-seq data showed that 92 PK and 19 PP genes were not detected in roots (zero reads in three biological repeats); 96 PK and 10 PP showed low abundance (≤ 10 reads). Gene ontology analysis revealed that the 188 PK genes with no or low expression level in Arabidopsis roots are mainly involved in pollen recognition, pollen tube growth or other processes not relevant for root hair formation. More than 50% of the cysteine-rich RLK (receptor-like protein kinase) subfamily genes belong to this group. Among the 29 PP genes with no or low expression level, purple acid phosphatases, haloacid dehalogenase-like hydrolases, and PP2C genes with functions in the dephosphorylation of RNA polymerase II C-terminal domain and mRNA capping were enriched. Subsets of 173 PK and 35 PP genes were differentially expressed under Pi-deficient conditions. Putative functional modules (clusters) of these PK and PP genes were constructed based on co-expression analysis using the MACCU toolbox. A co-expression network comprising 65 known or annotated PK and PP genes (60 PK and 5 PP genes, respectively) was subdivided into several highly co-expressed gene sub-clusters. The largest sub-cluster was composed of 22 genes, most of which have been assigned to the RLK superfamily and were associated with cell wall metabolism, pollen tube and/or root hair development and growth.
  
  
  CONCLUSIONS
  We here provide comprehensive 'digital' transcriptional information on PK and PP genes in Arabidopsis roots. The co-expression network derived from our data mining approach sets the stage for follow-up experimentation that helps to complete our understanding of the post-translational regulation of Pi deficiency-induced changes in root hair morphogenesis.
authors.affiliation: State Key Laboratory of Soil and Sustainable Agriculture,Institute of Soil Science, Chinese Academy Sciences, Nanjing, 210008, People's Republic of China. plan@issas.ac.cn
authors.forename: Ping
authors.initials: P
authors.lastname: Lan
authors.forename: Wenfeng
authors.initials: W
authors.lastname: Li
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Schmidt
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000254:growth & development*; D057225:Data Mining; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D017343:Genes, Plant / Q000502:physiology*; D005810:Multigene Family; D010710:Phosphates / Q000172:deficiency*; D010749:Phosphoprotein Phosphatases / Q000235:genetics* / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000254:growth & development*; D011494:Protein Kinases / Q000235:genetics* / Q000378:metabolism
chemical_list: D010710:Phosphates; D011494:Protein Kinases; D010749:Phosphoprotein Phosphatases
references.citation: Plant Physiol. 2011 Jul;156(3):1006-15
references.pmid: 21562330
references.citation: Plant Cell Physiol. 2007 Mar;48(3):381-90
references.pmid: 17251202
references.citation: BMC Plant Biol. 2010 May 25;10:95
references.pmid: 20500828
references.citation: J Integr Plant Biol. 2012 Jul;54(7):486-99
references.pmid: 22676405
references.citation: PLoS Genet. 2012 Jan;8(1):e1002446
references.pmid: 22253603
references.citation: Plant Physiol. 2007 Jan;143(1):156-71
references.pmid: 17085508
references.citation: Plant Physiol. 2007 May;144(1):232-47
references.pmid: 17369438
references.citation: Plant Physiol. 2003 Jun;132(2):530-43
references.pmid: 12805585
references.citation: Proc Natl Acad Sci U S A. 2005 Aug 16;102(33):11934-9
references.pmid: 16085708
references.citation: Plant Physiol. 2003 Jun;132(2):578-96
references.pmid: 12805589
references.citation: Philos Trans R Soc Lond B Biol Sci. 2012 Sep 19;367(1602):2619-39
references.pmid: 22889912
references.citation: Plant Cell. 2006 Nov;18(11):2958-70
references.pmid: 17098810
references.citation: Biosci Biotechnol Biochem. 2003 Dec;67(12):2533-40
references.pmid: 14730130
references.citation: Plant Physiol. 2010 Oct;154(2):927-38
references.pmid: 20713616
references.citation: Plant Physiol. 2011 Mar;155(3):1383-402
references.pmid: 21248074
references.citation: Nat Rev Mol Cell Biol. 2010 Jan;11(1):9-22
references.pmid: 20027184
references.citation: Sci STKE. 2001 Dec 18;2001(113):re22
references.pmid: 11752632
references.citation: Plant J. 2002 May;30(3):289-99
references.pmid: 12000677
references.citation: Mol Plant. 2010 Jan;3(1):212-23
references.pmid: 19969521
references.citation: Plant Physiol. 2006 Jul;141(3):1000-11
references.pmid: 16679417
references.citation: J Biol Chem. 2002 Aug 2;277(31):27772-81
references.pmid: 12021284
references.citation: Planta. 2011 Mar;233(3):523-37
references.pmid: 21110039
references.citation: Mol Cell Proteomics. 2012 Nov;11(11):1156-66
references.pmid: 22843991
references.citation: Annu Rev Plant Biol. 2011;62:185-206
references.pmid: 21370979
references.citation: Mol Syst Biol. 2005;1:2005.0016
references.pmid: 16729051
references.citation: Plant Cell Environ. 2009 Dec;32(12):1633-51
references.pmid: 19712066
references.citation: Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6478-83
references.pmid: 17420480
references.citation: Plant Mol Biol. 2010 Aug;73(6):629-41
references.pmid: 20473553
references.citation: J Exp Bot. 2008;59(1):93-109
references.pmid: 18212031
references.citation: Nat Biotechnol. 2004 Jan;22(1):86-92
references.pmid: 14647306
references.citation: Plant Cell Environ. 2007 Jan;30(1):85-112
references.pmid: 17177879
references.citation: Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10763-8
references.pmid: 11526204
references.citation: Plant Cell. 2011 Apr;23(4):1523-35
references.pmid: 21521698
references.citation: Curr Biol. 2009 Aug 11;19(15):1327-31
references.pmid: 19646876
references.citation: Plant Cell. 2002 May;14(5):969-77
references.pmid: 12034890
references.citation: Nat Genet. 2007 Jun;39(6):792-6
references.pmid: 17496893
references.citation: Plant Mol Biol. 2003 Sep;53(1-2):61-74
references.pmid: 14756307
references.citation: Plant Physiol. 2009 Jul;150(3):1459-73
references.pmid: 19448035
references.citation: Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8
references.pmid: 9843981
references.citation: Cell Mol Life Sci. 2012 Oct;69(19):3259-67
references.pmid: 22847330
references.citation: PLoS Genet. 2010 Sep 09;6(9):e1001102
references.pmid: 20838596
references.citation: Biochem J. 2008 Feb 15;410(1):19-37
references.pmid: 18215152
references.citation: Trends Plant Sci. 2003 Sep;8(9):424-31
references.pmid: 13678909
references.citation: New Phytol. 2010 Oct;188(2):615-25
references.pmid: 20618910
references.citation: Nat Rev Genet. 2011 Feb;12(2):87-98
references.pmid: 21191423
references.citation: Arabidopsis Book. 2007;5:e0106
references.pmid: 22303230
references.citation: Plant J. 2008 Mar;53(5):731-8
references.pmid: 17988220
references.citation: Genes Dev. 2001 Aug 15;15(16):2122-33
references.pmid: 11511543
references.citation: Plant Physiol. 2006 Jul;141(3):988-99
references.pmid: 16679424
references.citation: Plant Cell. 2004 May;16(5):1220-34
references.pmid: 15105442
references.citation: Plant Mol Biol. 2005 Nov;59(4):581-94
references.pmid: 16244908
references.citation: Plant J. 2012 May;70(4):599-613
references.pmid: 22225700
references.citation: Development. 2012 Sep;139(18):3402-12
references.pmid: 22912415
references.citation: Plant Physiol. 2003 Jul;132(3):1260-71
references.pmid: 12857808
references.citation: Plant Cell Environ. 2007 Dec;30(12):1499-512
references.pmid: 17927693
references.citation: Proteomics. 2009 Jan;9(1):159-70
references.pmid: 19053143
references.citation: Plant J. 2009 May;58(3):474-84
references.pmid: 19144004
references.citation: Proteomics. 2007 May;7(9):1501-12
references.pmid: 17407179
references.citation: Plant Physiol. 2009 May;150(1):12-26
references.pmid: 19321712
references.citation: Development. 2009 Oct;136(19):3279-88
references.pmid: 19736323
references.citation: Proc Natl Acad Sci U S A. 2005 May 24;102(21):7760-5
references.pmid: 15894620
references.citation: Biochem J. 2012 Oct 15;447(2):291-9
references.pmid: 22827269
references.citation: Nat Cell Biol. 2009 Jan;11(1):78-84
references.pmid: 19079245
references.citation: BMC Plant Biol. 2012 Aug 09;12:138
references.pmid: 22877077