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 |
| Â | T2_1-63 | OJ000315_02.1; similar to protein phosphatase type 2C [Oryza sativa (japonica cultivar-group)] | Regulation | Â | 2,00E-16 |
| Â | 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 |
| Â | T2_2-88 | No significant hit found. | Â | Â | Â |
3–14 | T1_3-14 | Membrane protein-like [Oryza sativa (japonica cultivar-group)] | n.a. |  | 3,00E-19 |
| Â | T2_3-14 | No significant hit found. | Â | Â | Â |
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 |
| Â | T2_3-91 | No significant hit found. | Â | Â | Â |
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. | Â | Â | Â |
miR160-3 | T_miR160-3 | Intracellular pathogenesis-related protein-like protein [Physcomitrella patens] | Defense | Â | 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 |
| Â | 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 | Â | 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 |
| Â | T2_miR408 | Copper ion binding/electron transporter [Arabidopsis thaliana] gb|AAB95306.1| putative phytocyanin [Arabidopsis thaliana] | Defense | Redox catalyst | 2,00E-16 |
| Â | T3_miR408 | Phytocyanin homolog [Pinus taeda] | Defense | Redox catalyst | 1,00E-14 |
| Â | T4_miR408 | Hypothetical protein P0592C05.16 [Oryza sativa] | n.a. | Â | 9,00E-11 |
| Â | 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 | Â | 4,00E-131 |
| Â | T2_miR414 | Hypothetical protein OSJNBb0016H12.28 [Oryza sativa] | n.a. | Â | 3,00E-85 |
| Â | T3_miR414 | Protein disulfide isomerase-like PDI-M [Physcomitrella patens] | Regulation | PDI is a regulator of chloroplast translational activation [80] | 4,00E-67 |
| Â | T4_miR414 | Putative heterotrimeric G protein beta subunit [Physcomitrella patens] | Regulation | Signal transduction | 2,00E-66 |
| Â | 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 |
| Â | T6_miR414 | AC069474_30 nascent polypeptide associated complex (NAC) alpha chain, putative [Arabidopsis thaliana] | Regulation | Translation, protein targeting | 3,00E-40 |
| Â | T7_miR414 | Hypothetical protein P0665A11.10 [Oryza sativa] | n.a. | Â | 3,00E-25 |
| Â | 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 |
| Â | T9_miR414 | No significant hit found. | Â | Â | Â |
| Â | T10_miR414 | No significant hit found. | Â | Â | Â |
| Â | T11_miR414 | No significant hit found. | Â | Â | Â |
| Â | T12_miR414 | No significant hit found. | Â | Â | Â |
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 | Â | 8,00E-38 |
| Â | T2_miR473-2 | PSAG_ARATH Photosystem I reaction center subunit V, chloroplast precursor (PSI-G) [Arabidopsis thaliana] | Photo-synthesis | Â | 2,00E-32 |
| Â | T3_miR473-2 | No significant hit found. | Â | Â | Â |
miR477 | T1_miR477 | Peptidylprolyl isomerase D (cyclophilin D) [Rattus norvegicus] | Regulation/Defense | Cyclophilins are predicted targets in mammals | 6,00E-43 |
| Â | T2_miR477 | Transcription factor/zinc ion binding CONSTANS-like [Arabidopsis thaliana] | Regulation | Transcription Factor | 1,00E-22 |
| Â | T3_miR477 | Transcription factor/zinc ion binding CONSTANS-like [Arabidopsis thaliana] | Regulation | Transcription factor | 2,00E-20 |
| Â | T4_miR477 | Putative cyclophilin-40 [Oryza sativa] | Regulation/Defense | Cyclophilins are predicted targets in mammals | 4,00E-16 |
| Â | T5_miR477 | No significant hit found. | Â | Â | Â |
| Â | T6_miR477 | No significant hit found. | Â | Â | Â |
miR473-1, miR477 | T_miR473-1/miR477 | No significant hit found. | Â | Â | Â |
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 | Â | 4,00E-21 |
| Â | T2_miR534-1 | BTB/POZ domain protein (BLADE-ON-PETIOLE 2) [Arabidopsis thaliana] | Regulation | Leaf and floral patterning | 7,00E-11 |