title: Six Medicago truncatula Dicer-like protein genes are expressed in plant cells and upregulated in nodules.
abstract: Here we report the existence of six putative Dicer-like genes in the Medicago truncatula genome. They are ubiquitously expressed throughout the plant and significantly induced in root nodules. Over the past decade, small noncoding RNAs (sncRNA) have emerged as widespread and important regulatory molecules influencing both the structure and expression of plant genomes. One of the key factors involved in sncRNA biogenesis in plants is a group of RNase III-type nucleases known as Dicer-like (DCL) proteins. Based on functional analysis of DCL proteins identified in Arabidopsis thaliana, four types of DCLs were distinguished (DCL1-4). DCL1 mainly produces 21 nt miRNAs. The products generated by DCL2, DCL3, and DCL4 belong to various classes of siRNAs that are 22, 24 and 21 nt in length, respectively. M. truncatula is a model legume plant closely related to many economically important cultivable species. By screening the recent M. truncatula genome assembly, we were able to identify three new DCL genes in addition to the MtDCL1-3 genes that had been earlier characterized. The newly found genes include MtDCL4 and two MtDCL2 homologs. We showed that all six M. truncatula DCL genes are expressed in plant cells. The first of the identified MtDCL2 paralogs encodes a truncated version of the DCL2 protein, while the second undergoes substantial and specific upregulation in the root nodules. Additionally, we identified an alternative splicing variant of MtDCL1 mRNA, similar to the one found in Arabidopsis. Our results indicate that DCL genes are differently activated during Medicago symbiosis with nitrogen fixing bacteria and upon pathogen infection. In addition, we hypothesize that the alternative splicing variant of MtDCL1 mRNA may be involved in tissue-specific regulation of the DCL1 level.
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
authors.forename: Aleksander
authors.initials: A
authors.lastname: Tworak
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
authors.forename: Anna
authors.initials: A
authors.lastname: Urbanowicz
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
authors.forename: Jan
authors.initials: J
authors.lastname: Podkowinski
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
authors.forename: Anna
authors.initials: A
authors.lastname: Kurzynska-Kokorniak
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
authors.forename: Natalia
authors.initials: N
authors.lastname: Koralewska
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. marekf@ibch.poznan.pl.|Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland. marekf@ibch.poznan.pl.
authors.forename: Marek
authors.initials: M
authors.lastname: Figlerowicz
mesh_terms: D017398:Alternative Splicing; D018076:DNA, Complementary / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D046913:Medicago truncatula / Q000235:genetics* / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics*; D009928:Organ Specificity; D010940:Plant Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics; D043244:Ribonuclease III / Q000235:genetics*; D053204:Root Nodules, Plant / Q000235:genetics / Q000378:metabolism; D015533:Transcriptional Activation; D015854:Up-Regulation
chemical_list: D018076:DNA, Complementary; D035683:MicroRNAs; D010940:Plant Proteins; D012333:RNA, Messenger; D018749:RNA, Plant; D034741:RNA, Small Interfering; D043244:Ribonuclease III
keywords: Dicer-like (DCL); Legume; Medicago truncatula; MicroRNA (miRNA); Nodule; Small interfering RNA (siRNA)
references.citation: Plant Cell Rep. 2011 Jul;30(7):1347-63
references.pmid: 21404010
references.citation: Genome Biol. 2014;15(9):457
references.pmid: 25248950
references.citation: Science. 2006 Jan 13;311(5758):195-8
references.pmid: 16410517
references.citation: Mol Cell. 2011 Apr 22;42(2):172-84
references.pmid: 21419681
references.citation: Nat Methods. 2013 Oct;10(10):1003-5
references.pmid: 23995387
references.citation: RNA. 2010 Mar;16(3):474-81
references.pmid: 20106953
references.citation: Plant J. 2008 Jun;54(5):876-87
references.pmid: 18298674
references.citation: BMC Bioinformatics. 2014;15:4
references.pmid: 24387046
references.citation: Science. 1992 May 15;256(5059):998-1000
references.pmid: 10744524
references.citation: Mol Biol Evol. 2013 Mar;30(3):627-41
references.pmid: 23180579
references.citation: Genes Dev. 2011 Dec 1;25(23):2540-53
references.pmid: 22156213
references.citation: Science. 2010 Apr 16;328(5976):327-34
references.pmid: 20223951
references.citation: PLoS One. 2015;10(2):e0118226
references.pmid: 25723393
references.citation: Science. 2006 Jul 7;313(5783):68-71
references.pmid: 16741077
references.citation: Plant Physiol. 2010 Aug;153(4):1759-70
references.pmid: 20508137
references.citation: Mol Biol Evol. 2013 Dec;30(12):2725-9
references.pmid: 24132122
references.citation: Front Plant Sci. 2013 Jul 10;4:236
references.pmid: 23847640
references.citation: Plant J. 2012 Feb;69(3):462-74
references.pmid: 21973320
references.citation: Plant J. 1999 May;18(3):265-76
references.pmid: 10377992
references.citation: RNA. 2004 Oct;10(10):1507-17
references.pmid: 15383676
references.citation: Mol Cell. 2011 Mar 4;41(5):589-99
references.pmid: 21362554
references.citation: BMC Plant Biol. 2011;11:79
references.pmid: 21569262
references.citation: Nucleic Acids Res. 2015 May 19;43(9):4365-80
references.pmid: 25883138
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D302-5
references.pmid: 22053084
references.citation: Syst Appl Microbiol. 2011 Jul;34(5):368-75
references.pmid: 21514760
references.citation: PLoS Biol. 2004 May;2(5):E104
references.pmid: 15024409
references.citation: Plant Cell. 2009 Sep;21(9):2780-96
references.pmid: 19767456
references.citation: Curr Biol. 2003 Apr 29;13(9):784-9
references.pmid: 12725739
references.citation: Int Rev Cell Mol Biol. 2015;316:111-58
references.pmid: 25805123
references.citation: J Mol Biol. 2012 Sep 28;422(4):466-76
references.pmid: 22727743
references.citation: Philos Trans R Soc Lond B Biol Sci. 2012 Jun 5;367(1595):1570-9
references.pmid: 22527400
references.citation: Genes Dev. 2006 Nov 15;20(22):3084-8
references.pmid: 17114582
references.citation: BMC Genomics. 2014;15:312
references.pmid: 24767513
references.citation: Annu Rev Genet. 2011;45:119-44
references.pmid: 21838550
references.citation: Funct Integr Genomics. 2009 Aug;9(3):277-86
references.pmid: 19221817
references.citation: Cell. 2012 Nov 9;151(4):900-11
references.pmid: 23141545
references.citation: Annu Rev Plant Biol. 2014;65:473-503
references.pmid: 24579988
references.citation: BMC Genomics. 2008;9:451
references.pmid: 18826656
references.citation: FEBS Lett. 2006 May 1;580(10):2442-50
references.pmid: 16638569
references.citation: Plant Physiol. 2009 Nov;151(3):1002-8
references.pmid: 19789286
references.citation: Proc Natl Acad Sci U S A. 2004 Jul 6;101(27):10217-22
references.pmid: 15220482
references.citation: Curr Biol. 2005 Aug 23;15(16):1494-500
references.pmid: 16040244
references.citation: Biochim Biophys Acta. 2013 Dec;1829(12):1300-8
references.pmid: 24185199
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D225-9
references.pmid: 21109532
references.citation: Mini Rev Med Chem. 2009 Jul;9(8):927-37
references.pmid: 19601888
references.citation: Acta Biochim Pol. 2003;50(1):217-29
references.pmid: 12673363
references.citation: BMC Biol. 2015;13:32
references.pmid: 25980406
references.citation: Nat Rev Genet. 2013 Feb;14(2):100-12
references.pmid: 23329111
references.citation: Proc Natl Acad Sci U S A. 2005 Jul 19;102(29):10375-80
references.pmid: 16006515
references.citation: Genes Dev. 2006 Dec 15;20(24):3407-25
references.pmid: 17182867
references.citation: Curr Pharm Biotechnol. 2011 Nov;12(11):1774-80
references.pmid: 21902631
references.citation: Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12984-9
references.pmid: 16129836
references.citation: Funct Integr Genomics. 2012 Nov;12(4):671-82
references.pmid: 22527487
references.citation: Genes Dev. 1988 Mar;2(3):282-93
references.pmid: 3288541