title: Genome-Wide Analysis of the Lysine Biosynthesis Pathway Network during Maize Seed Development.
abstract: Lysine is one of the most limiting essential amino acids for humans and livestock. The nutritional value of maize (Zea mays L.) is reduced by its poor lysine content. To better understand the lysine biosynthesis pathway in maize seed, we conducted a genome-wide analysis of the genes involved in lysine biosynthesis. We identified lysine biosynthesis pathway genes (LBPGs) and investigated whether a diaminopimelate pathway variant exists in maize. We analyzed two genes encoding the key enzyme dihydrodipicolinate synthase, and determined that they contribute differently to lysine synthesis during maize seed development. A coexpression network of LBPGs was constructed using RNA-sequencing data from 21 developmental stages of B73 maize seed. We found a large set of genes encoding ribosomal proteins, elongation factors and zein proteins that were coexpressed with LBPGs. The coexpressed genes were enriched in cellular metabolism terms and protein related terms. A phylogenetic analysis of the LBPGs from different plant species revealed different relationships. Additionally, six transcription factor (TF) families containing 13 TFs were identified as the Hub TFs of the LBPGs modules. Several expression quantitative trait loci of LBPGs were also identified. Our results should help to elucidate the lysine biosynthesis pathway network in maize seed.
authors.affiliation: State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
authors.forename: Yuwei
authors.initials: Y
authors.lastname: Liu
authors.affiliation: State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
authors.forename: Shaojun
authors.initials: S
authors.lastname: Xie
authors.affiliation: State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, China.
authors.forename: Jingjuan
authors.initials: J
authors.lastname: Yu
mesh_terms: D053898:Biosynthetic Pathways; D019295:Computational Biology / Q000379:methods; D015971:Gene Expression Regulation, Enzymologic; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D055106:Genome-Wide Association Study; D008239:Lysine / Q000096:biosynthesis*; D058977:Molecular Sequence Annotation; D059372:Nucleotide Motifs; D010802:Phylogeny; D056510:Position-Specific Scoring Matrices; D040641:Quantitative Trait Loci; D012045:Regulatory Sequences, Nucleic Acid; D012639:Seeds / Q000235:genetics* / Q000378:metabolism*; D003313:Zea mays / Q000235:genetics* / Q000378:metabolism*
chemical_list: D008239:Lysine
references.citation: PLoS Genet. 2011 Jun;7(6):e1001393
references.pmid: 21695224
references.citation: Nat Genet. 2012 Jun 17;44(7):821-4
references.pmid: 22706312
references.citation: J Mol Evol. 2002 Oct;55(4):445-59
references.pmid: 12355264
references.citation: Plant Mol Biol. 1996 Nov;32(4):611-20
references.pmid: 8980513
references.citation: Genome Res. 2008 Sep;18(9):1509-17
references.pmid: 18550803
references.citation: Proc Natl Acad Sci U S A. 1995 Sep 12;92(19):8640-4
references.pmid: 7567989
references.citation: Bioinformatics. 2012 Sep 15;28(18):2397-9
references.pmid: 22796960
references.citation: Genomics. 2006 Mar;87(3):315-28
references.pmid: 16386875
references.citation: Funct Plant Biol. 2012 Dec;39(12):1058-1067
references.pmid: 32480855
references.citation: Development. 2003 Dec;130(24):6065-73
references.pmid: 14597573
references.citation: Nucleic Acids Res. 2014 Jan;42(Database issue):D142-7
references.pmid: 24194598
references.citation: Science. 2002 Apr 26;296(5568):752-5
references.pmid: 11923494
references.citation: Plant Physiol. 2013 Apr;161(4):1783-94
references.pmid: 23447525
references.citation: Nature. 1998 Mar 12;392(6672):139
references.pmid: 9515958
references.citation: Science. 2009 Nov 20;326(5956):1112-5
references.pmid: 19965430
references.citation: Nat Genet. 2013 Jan;45(1):43-50
references.pmid: 23242369
references.citation: FEBS Lett. 2000 Dec 29;487(2):234-8
references.pmid: 11150516
references.citation: Genetics. 2007 Mar;175(3):1441-50
references.pmid: 17179097
references.citation: Nature. 2004 Aug 12;430(7001):743-7
references.pmid: 15269782
references.citation: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W293-7
references.pmid: 16845012
references.citation: Plant Biotechnol J. 2005 Nov;3(6):555-69
references.pmid: 17147627
references.citation: Biochemistry. 1999 Mar 9;38(10):3019-24
references.pmid: 10074354
references.citation: BMC Bioinformatics. 2010 Apr 01;11:165
references.pmid: 20356413
references.citation: Nat Rev Genet. 2004 Feb;5(2):101-13
references.pmid: 14735121
references.citation: Proc Natl Acad Sci U S A. 1994 Mar 29;91(7):2577-81
references.pmid: 8146157
references.citation: Plant Cell. 2015 Mar;27(3):532-45
references.pmid: 25691733
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D109-14
references.pmid: 22080510
references.citation: Genome Res. 2004 Jun;14(6):1060-7
references.pmid: 15173112
references.citation: Nature. 2010 Apr 1;464(7289):773-7
references.pmid: 20220756
references.citation: Plant Mol Biol. 1999 Mar;39(4):695-708
references.pmid: 10350084
references.citation: Mol Biol Evol. 2011 Oct;28(10):2731-9
references.pmid: 21546353
references.citation: Am J Hum Genet. 2011 Jan 7;88(1):76-82
references.pmid: 21167468
references.citation: BMC Syst Biol. 2007 Nov 21;1:54
references.pmid: 18031580
references.citation: Nature. 2011 May 25;474(7351):380-4
references.pmid: 21614001
references.citation: Genome Res. 2003 Nov;13(11):2498-504
references.pmid: 14597658
references.citation: Nat Rev Genet. 2009 Jan;10(1):57-63
references.pmid: 19015660
references.citation: Plant Cell. 1998 Mar;10(3):383-98
references.pmid: 9501112
references.citation: Biotechnology (N Y). 1995 Jun;13(6):577-82
references.pmid: 9634796
references.citation: Cell Biochem Biophys. 2006;46(1):43-64
references.pmid: 16943623
references.citation: Trends Genet. 2008 Aug;24(8):408-15
references.pmid: 18597885
references.citation: Plant Physiol. 2014 Sep;166(1):252-64
references.pmid: 25037214
references.citation: Plant Physiol. 2011 Jul;156(3):1244-56
references.pmid: 21606319
references.citation: Nat Methods. 2008 Jul;5(7):621-8
references.pmid: 18516045
references.citation: Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):E4808-17
references.pmid: 24248366
references.citation: PLoS One. 2011;6(10):e26683
references.pmid: 22039529
references.citation: Microbiol Rev. 1988 Jun;52(2):248-73
references.pmid: 3045517
references.citation: Stat Appl Genet Mol Biol. 2005;4:Article17
references.pmid: 16646834
references.citation: Plant Physiol. 2015 Aug;168(4):1512-26
references.pmid: 26063505
references.citation: Nat Biotechnol. 2012 May 13;30(6):549-54
references.pmid: 22580950
references.citation: Nat Biotechnol. 2012 May 13;30(6):555-61
references.pmid: 22580951
references.citation: Am J Hum Genet. 2007 Sep;81(3):559-75
references.pmid: 17701901
references.citation: BMC Bioinformatics. 2008 Dec 29;9:559
references.pmid: 19114008
references.citation: Curr Opin Plant Biol. 2004 Apr;7(2):202-9
references.pmid: 15003222
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D1178-86
references.pmid: 22110026
references.citation: Plant J. 1998 Oct;16(1):53-62
references.pmid: 9807827
references.citation: Plant Mol Biol. 1992 Aug;19(5):815-23
references.pmid: 1643284
references.citation: PLoS One. 2012;7(6):e38318
references.pmid: 22761676
references.citation: Adv Enzymol Relat Areas Mol Biol. 1998;72:279-324
references.pmid: 9559056
references.citation: Nature. 2003 Mar 20;422(6929):297-302
references.pmid: 12646919
references.citation: PLoS One. 2012;7(7):e40318
references.pmid: 22792278
references.citation: Plant Cell. 2004 Feb;16(2):353-66
references.pmid: 14729919
references.citation: Proc Natl Acad Sci U S A. 1990 Jan;87(1):46-50
references.pmid: 2296602
references.citation: Plant Cell. 1995 Jul;7(7):899-906
references.pmid: 12242392
references.citation: J Bacteriol. 1970 Jan;101(1):323-4
references.pmid: 5411754
references.citation: Trends Plant Sci. 2002 Dec;7(12):555-60
references.pmid: 12475498
references.citation: Bioessays. 2011 Mar;33(3):189-202
references.pmid: 21319185
references.citation: Plant Mol Biol. 1985 Jul;4(4):197-204
references.pmid: 24310835
references.citation: Plant Physiol. 2009 Dec;151(4):2058-72
references.pmid: 19783646
references.citation: Plant J. 2014 May;78(3):424-40
references.pmid: 24547885
references.citation: Plant Cell Physiol. 2008 Sep;49(9):1263-71
references.pmid: 18701524
references.citation: Science. 1964 Jul 17;145(3629):279-80
references.pmid: 14171571
references.citation: Plant Physiol. 2006 Jan;140(1):292-301
references.pmid: 16361515
references.citation: Nat Commun. 2013;4:2832
references.pmid: 24343161