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Table 3 Characterization of predicted Physcomitrella miRNA targets. Sequences of predicted Physcomitrella targets can be found at Physcomitrella patens resource cosmoss [77].

From: Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution

miRNA Predicted Physcomitrella target Gene annotation (Best hit identified by BLASTX) Category Comment Hits significance
1–22 T_1-22 MUR3; Xyloglucan galactosyltransferase [Arabidopsis thaliana] Cell wall   1,00E-40
1–39 T_1-39 Mucin-like protein [Oryza sativa (japonica cultivar-group)] Cell wall Water-holding 5,00E-36
1–63 T1_1-63 Putative protein kinase (Dsk1) [Arabidopsis thaliana] Regulation   6,00E-70
  T2_1-63 OJ000315_02.1; similar to protein phosphatase type 2C [Oryza sativa (japonica cultivar-group)] Regulation   2,00E-16
  T3_1-63 Peptidyl-prolyl cis-trans isomerase, cyclophilin type [Medicago truncatula] Regulation/Defense Cyclophilins are predicted targets in mammals 2,00E-11
2–28 T_2-28 No significant hit found.    
2–42 T_2-42 Rhodanese like protein [Arabidopsis thaliana] Defense/S-Metabolism Detoxification; in Arabidopsis miR396b is predicted to target a rhodanese-like domain containing protein [78] 1,00E-50
2–88 T1_2-88 Phosphoglycerate dehydrogenase-like protein [Arabidopsis thaliana] N-Metabolism Serine metabolism; only needed in non-photosynthetic organs 0.0
  T2_2-88 No significant hit found.    
3–14 T1_3-14 Membrane protein-like [Oryza sativa (japonica cultivar-group)] n.a.   3,00E-19
  T2_3-14 No significant hit found.    
3–36 T_3-36 No significant hit found.    
3–79 T_3-79 Ferredoxin-nitrite reductase [Physcomitrella patens] N-Metabolism   4,00E-168
3–91 T1_3-91 Kelch repeat-containing F-box family protein, putative, expressed [Oryza sativa (japonica cultivar-group)] Regulation F-Box proteins are predicted targets of miR393 and miR394 in Arabidopsis [78] 7,00E-57
  T2_3-91 No significant hit found.    
4–67 T_4-67 ThiJ/PfpI [Mycobacterium sp. KMS] S-Metabolism Thiamin biosynthesis 5,00E-36
5–21 T_5-21 Basic 2S albumin [Helianthus annuus] Seed/Spore Seed storage protein 6,00E-22
5–33 T_5-33 Conserved hypothetical protein [Medicago truncatula] n.a.   7,00E-21
miR160-1, miR160-2 T_miR160-1/2 Aspartate aminotransferase (EC 2.6.1.1) [Pinus pinaster] N-Metabolism Several isoenzymes known from Arabidopsis, differential accumulation of mRNAS w.r.t. organ 3,00E-38
miR160-1, miR160-2, miR160-3, miR160-4 T_miR160-1/2/3/4 Auxin response factor 10 [Oryza sativa] Regulation Transcription factor 7,00E-131
miR160-2, miR160-3, miR160-4 T_miR160-2/3/4 No significant hit found.    
miR160-3 T_miR160-3 Intracellular pathogenesis-related protein-like protein [Physcomitrella patens] Defense   7,00E-68
miR166 T_miR166 Class III homeodomain-leucine zipper protein HB10 [Physcomitrella patens] Regulation Transcription factor 0.0
miR167 T1_miR167 Putative mitochondrial processing peptidase [Oryza sativa] Protein localisation Cleaves signal peptide in mitochondria 3,00E-148
  T2_miR167 Delta-COP (coatomer delta subunit) [Zea mays] Protein localisation Vesicle transport, poplar miR168 is predicted to target vesicle coat protein complex COPI [79] 2,00E-63
miR171-1 T_miR171-1 UDP-N-acetylglucosamine pyrophosphorylase-like [Oryza sativa] Cell wall   6,00E-14
miR319-1 T_miR319-1 Nucleotide binding [Arabidopsis thaliana] & WD repeat protein-like [Arabidopsis thaliana] Regulation Putative transcription factor 2,00E-109 & 4,00E-93
miR408 T1_miR408 Protein carrier [Arabidopsis thaliana] Protein localisation Predicted targets for miR408: Peptide chain release factor; plantacyanin [59] 2,00E-39
  T2_miR408 Copper ion binding/electron transporter [Arabidopsis thaliana] gb|AAB95306.1| putative phytocyanin [Arabidopsis thaliana] Defense Redox catalyst 2,00E-16
  T3_miR408 Phytocyanin homolog [Pinus taeda] Defense Redox catalyst 1,00E-14
  T4_miR408 Hypothetical protein P0592C05.16 [Oryza sativa] n.a.   9,00E-11
  T5_miR408 Putative blue copper binding protein [Oryza sativa] Defense Redox catalyst 1,00E-11
miR414 T1_miR414 TIF3H1; translation initiation factor [Arabidopsis thaliana] Regulation   4,00E-131
  T2_miR414 Hypothetical protein OSJNBb0016H12.28 [Oryza sativa] n.a.   3,00E-85
  T3_miR414 Protein disulfide isomerase-like PDI-M [Physcomitrella patens] Regulation PDI is a regulator of chloroplast translational activation [80] 4,00E-67
  T4_miR414 Putative heterotrimeric G protein beta subunit [Physcomitrella patens] Regulation Signal transduction 2,00E-66
  T5_miR414 RNA binding [Arabidopsis thaliana] & Pre-mRNA splicing factor cwc22, putative, expressed [Oryza sativa (japonica cultivar-group)] Regulation Splicing/Cell cycle 2,00E-58 & 4,00E-56
  T6_miR414 AC069474_30 nascent polypeptide associated complex (NAC) alpha chain, putative [Arabidopsis thaliana] Regulation Translation, protein targeting 3,00E-40
  T7_miR414 Hypothetical protein P0665A11.10 [Oryza sativa] n.a.   3,00E-25
  T8_miR414 ELM2; AT-rich interaction region; Homeodomain-related [Medicago truncatula] & putative MYB family transcription factor [Arabidopsis thaliana] Regulation Transcription factor (MYB) 3,00E-24 & 5,00E-23
  T9_miR414 No significant hit found.    
  T10_miR414 No significant hit found.    
  T11_miR414 No significant hit found.    
  T12_miR414 No significant hit found.    
miR418 T_miR418 Peptidyl-prolyl cis-trans isomerase, cyclophilin type [Medicago truncatula] Regulation/Defense Cyclophilins are predicted targets in mammals 1,00E-91
miR419 T_miR419 Dreg-2 like protein [Oryza sativa] & phospho-glycolate phosphatase [Arabidopsis thaliana] Regulation Signal transduction phosphatase 8,00E-82 & 2,00E-79
miR473-2 T1_miR473-2 Protein translocase/protein transporter [Arabidopsis thaliana] Protein localisation   8,00E-38
  T2_miR473-2 PSAG_ARATH Photosystem I reaction center subunit V, chloroplast precursor (PSI-G) [Arabidopsis thaliana] Photo-synthesis   2,00E-32
  T3_miR473-2 No significant hit found.    
miR477 T1_miR477 Peptidylprolyl isomerase D (cyclophilin D) [Rattus norvegicus] Regulation/Defense Cyclophilins are predicted targets in mammals 6,00E-43
  T2_miR477 Transcription factor/zinc ion binding CONSTANS-like [Arabidopsis thaliana] Regulation Transcription Factor 1,00E-22
  T3_miR477 Transcription factor/zinc ion binding CONSTANS-like [Arabidopsis thaliana] Regulation Transcription factor 2,00E-20
  T4_miR477 Putative cyclophilin-40 [Oryza sativa] Regulation/Defense Cyclophilins are predicted targets in mammals 4,00E-16
  T5_miR477 No significant hit found.    
  T6_miR477 No significant hit found.    
miR473-1, miR477 T_miR473-1/miR477 No significant hit found.    
miR533-2 T_miR533-2 Hydrolase-like protein [Oryza sativa] & chloroplast Phyllo [Arabidopsis thaliana] Metabolism/Regulation Phylloquinone biosynthesis; homology to lysophospholipase region of PHYLLO locus. 5,00E-16 & 2,00E-14
miR534-1 T1_miR534-1 Inorganic pyrophosphatase [Nitrosospira multiformis] Metabolism   4,00E-21
  T2_miR534-1 BTB/POZ domain protein (BLADE-ON-PETIOLE 2) [Arabidopsis thaliana] Regulation Leaf and floral patterning 7,00E-11
  1. Experimentally verified targets are underlined, n.a.: no category assignment.