Table 1.
Some key regulatory factors (transcription factors, epigenetic regulators and others involved in auxin homeostasis) involved in plant regeneration.
| Genes | Abbreviations | Function in Plant Regeneration | Molecular Function |
|---|---|---|---|
| ABA INSENSITIVE 3 | ABI3 | Quantitatively regulates BBM-mediated somatic embryogenesis. Acts as a positive regulator |
Dof-type transcription factor |
| ABERRANT LATERAL ROOT FORMATION 4 | ALF4 | Formative divisions of XPP cells during LR formation. Callus formation upon CIM induction |
SCFTIR1 regulation |
| AGAMOUS LIKE 15 | AGL15 | Activates auxin biosynthesis, leading to totipotency acquisition and SE initiation | MADS domain transcription factor |
| ANTHRANILATE SYNTHASE α1 | ASA1 | Tryptophan biosynthesis | Oxo-acid-lyase enzyme |
| ARABIDOPSIS RESPONSE REGULATOR 1 and 12 | ARR1 and 12 | Involved in CK-mediated ESR1 induction in order to promote shoot regeneration | Type-B Arabidopsis response regulator transcription factors |
| ARABIDOPSIS TRITHORAX-RELATED 2 | ATXR2 | Positively regulates LBD16 and LBD29 expression upon CIM induction | Histone lysine methyltransferase |
| AUXIN RESISTANT 3 | AXR3, IAA17 | Transcriptional repressor upon low auxin levels. Controls stem cell maintenance |
Aux/IAA corepressor |
| AUXIN RESPONSE FACTOR 7 and 19 | ARF7 and 19 | LR formation / Positively regulates LBD16 and LBD29 expression upon CIM induction | Auxin-responsive transcription factor |
| BABY BOOM | BBM, PLT4, AIL5 | Its ectopic expression can also directly reprogram somatic cells and induce SE in the absence of exogenous stimuli | AP2/ERF transcription factor |
| BASIC REGION/LEUCINE ZIPPER MOTIF 59 | bZIP59 | Interacts with LBD16 upon CIM induction | bZIP transcription factor |
| E2 PROMOTER BINDING FACTOR a | E2Fa | DNA replication | E2F transcription factor |
| ENHANCER OF SHOOT REGENERATION 1 | ESR1 | Induces the expression of key shoot regulators (CUC1, RAP2.6L, ESR2, WUS, and STM) to promote shoot regeneration | AP2/ERF transcription factor |
| ETHYLENE RESPONSE FACTOR 109 | ERF109 | Up-regulates ERF115 expression. Up-regulates ASA1 expression, probably involved in the auxin biosynthetic pathway | AP2/ERF transcription factor |
| ETHYLENE RESPONSE FACTOR 115 | ERF115 | Acts as as a rate-limiting factor for quiescent center (QC) cell division after DNA damaging stress. Involved in WIND1 up-regulation upon wound signaling |
AP2/ERF transcription factor |
| FUSCA 3 | FUS3 | Involved in embryo development. Essential for successful SE |
B3 domain-containing transcription factor |
| GENERAL CONTROL NONREPRESSED 5 | GCN5, HAG1 | Root stem cell niche maintenance. Callus pluripotency and shoot induction upon SIM |
Histone acetyltransferase |
| JASMONATE-ZIM DOMAIN PROTEINS | JAZ PROTEINS | Represses de novo root formation in Arabidopsis leaf explants. Their destabilization allows the action of positive regulators |
Jasmonate zinc-finger inflorescence meristem domain transcription factor |
| JUMONJI C DOMAIN-CONTAINING 30 | JMJ30, JMJD5 | Positively regulates LBD16 and LBD29 expression upon CIM induction | Histone lysine demethylase |
| LATERAL ORGAN BOUNDARIES DOMAIN 16, 17, 18 and 29 | LBD16, 17, 18 and 29 | Callus formation upon CIM induction | LOB-domain transcription factor |
| LEAFY COTYLEDON 1 | LEC1 | Its ectopic expression can also directly reprogram somatic cells and induce SE in the absence of exogenous stimuli | B3 domain-containing transcription factor |
| LEAFY COTYLEDON 2 | LEC2 | Its ectopic expression can also directly reprogram somatic cells and induce SE in the absence of exogenous stimuli | B3 domain-containing transcription factor |
| LYSINE-SPECIFIC DEMETHYLASE 1-LIKE 3 | LDL3 | Presumably removes H3K4me2 during callus formation. It may allow the genes for shoot initiation to be expressed after SIM treatment | Histone lysine demethylase |
| microRNA156 | miRNA156 | Reduces SPL2, 10 and 11 expression, promoting AR formation | microRNA molecule |
| MONOPTEROS | MP, ARF5 | Hypophysis specification during embryogenesis | Auxin-responsive transcription factor |
| MYB94 and 96 | MYB94 and 96 | Regulates LBD29 expression upon CIM induction | MYB transcription factors |
| MYC2 | MYC2 | Acts upstream of ERF109 as a positive regulator | bHLH transcription factor |
| PHYTOCHROME A SIGNAL TRANSDUCTION 1 | PAT1 | Acts as a partner of ERF115 and induces WIND1 expression | GRAS transcription factor |
| PIN-FORMED 1 | PIN1 | Auxin transport | Auxin efflux facilitator |
| PLETHORA 3, 5 and 7 | PLT3, 5 and 7 | Induce the expression of genes involved in regeneration competence acquisition (PLT2) and differentiation factors (i.e., CUC2) | AP2/ERF transcription factor |
| POLYCOMB REPRESSIVE COMPLEX 2 | PRC2 | Di- and tri-methylation of Lys27 on histone H3. PRC2 activity blocks hormone-mediated SE | Histone lysine methyltransferase |
| RWP-RK DOMAIN-CONTAINING 4 | RKD4, GRD | Induces early embryo-specific genes when overexpressed in seedlings. Its ectopic expression can also directly reprogram somatic cells and induce SE in the absence of exogenous stimuli |
RWP-RK-type transcription factor |
| SOLITARY ROOT 1 | SLR1, IAA14 | Formative divisions of XPP cells during LR formation | Aux/IAA corepressor |
| SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 2, 10 and 11 | SPL2, 10 and 11 | Their up-regulation is linked to a decrease in wound-induced ARs, presumably due to the repression of ABR1, ERF109, ERF115 and RAP2.6L, among others | SPL transcription factor |
| TAA-RELATED 2 | TAR2 | Auxin biosynthesis | Tryptophan aminotransferase enzyme |
| TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 | TAA1 | Auxin biosynthesis | Tryptophan aminotransferase enzyme |
| WOUND INDUCED DEDIFFERENTIATION 1 | WIND1, RAP2.4 | Establishes and maintains dedifferentiated cell status | AP2/ERF transcription factor |
| WUSCHEL | WUS | Shoot induction upon SIM | Homeobox transcription factor |
| WUSCHEL RELATED HOMEOBOX 11 and 12 | WOX11 and 12 | Positively regulates LBD16 and LBD29 expression upon CIM induction | Homeobox transcription factor |
| YUCCA 1 and 4 | YUC1 and 4 | Auxin biosynthesis | Flavin-containing monooxygenase enzymes |