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Auxin signaling is essential for organogenesis but not for cell survival in the liverwort Marchantia polymorpha.

Suzuki, H., et al. · 2023 · Plant Cell   research

doi:10.1093/plcell/koac367   PMID:36529527   PMC10015169

Linked genes (19)  6 core 13 peripheral

Gene ID	Name	Evidence / Role	Function (this paper)
Mp1g12750	MpARF1	experimental subject	MpARF1, the sole class-A ARF, was examined via knockout mutants that grew as thalli with much milder phenotypes than Mptir1 mutants, supporting its role downstream in auxin-mediated transcriptional activation.
Mp4g11820	MpARF2	experimental subject	MpARF2, the sole class-B ARF, mediates competitive repression in auxin signaling; its knockout phenotype was compared against Mptir1 mutants in this study.
Mp2g24200	MpC2HDZ	experimental subject	MpC2HDZ, an auxin-responsive transcription factor gene, was used and validated by RT-qPCR and RNA-seq as an auxin response readout, showing upregulation under all conditions and reduced expression in Mptir1 knockout cells.
Mp6g05000	MpIAA	experimental subject	MpIAA was functionally analyzed as the auxin signaling partner of MpTIR1, interacting in an auxin-dependent manner in pull-down assays. DII degron degradation and mutant DII constructs were tested in vivo across conditional knockout backgrounds.
Mp6g02750	MpTIR1	experimental subject	MpTIR1 is the central focus of this study, characterized as an evolutionarily conserved auxin receptor. Null and conditional knockout mutants were generated and shown to be viable; the protein interacted with MpIAA in auxin-dependent pull-down assays. Loss of MpTIR1 abolished organogenesis but not cell survival.
Mp1g09500	MpWIP	experimental subject	MpWIP, an auxin-responsive transcription factor gene, was quantified by RT-qPCR and RNA-seq as an auxin signaling readout; upregulated under all conditions and showing lower expression in Mptir1-1ko cells.
Mp5g14320	MpTAA	citation comparator	MpTAA, the sole TAA auxin biosynthesis gene, cited from prior work where its knockout generates cell masses lacking organogenesis; also downregulated in this study's auxin-feedback context.
—	MpEF1A missing	sequence tool	MpEF1A used as a technical tool: its promoter confers strong ubiquitous transgene expression and the gene served as the internal control for RT-qPCR normalization.
Mp1g07070	MpARF3	experimental background	MpARF3 mentioned as an ARF family member in the auxin signaling context.
Mp5g06970	MpERF20	experimental background	MpLAXR (LOW-AUXIN RESPONSIVE), which triggers cellular reprogramming to undifferentiated cells, was highly expressed in Mptir1-1ko cells.
Mp2g20695	MpLRL	experimental background	MpLRL (LOTUS JAPONICUS ROOTHAIRLESS1-LIKE homolog), a rhizoid/organ differentiation factor, showed significantly lower expression in expression analyses.
Mp2g07720	MpNAC1	experimental background	MpNAC1, orthologous to CUP-SHAPED COTYLEDONs (boundary genes), was upregulated in Mptir1-1ko cells.
Mp2g02890	MpncARF	experimental background	MpNCARF appeared in transcriptome data with lower transcript levels in sporelings versus thalli (Supplemental Figure 13C).
Mp4g21790	MpR2R3-MYB20	experimental background	MpR2R3-MYB20, paralog of GEMMA CUP-ASSOCIATED MYB1, upregulated in Mptir1-1ko cells in the mutant phenotype context.
Mp3g05910	MpR2R3-MYB21	experimental background	MpR2R3-MYB21 listed among transcription factor genes upregulated under all conditions in expression data.
Mp3g17930	MpRSL1	experimental background	MpRSL1 (ROOT HAIR DEFECTIVE SIX-LIKE1 homolog), a rhizoid/organ differentiation factor, showed significantly lower expression in expression analyses.
Mp8g10660	MpSKP2A	citation background	MpSKP2A mentioned in passing as a hypothetical alternative auxin receptor, the homolog of S-PHASE KINASE-ASSOCIATED PROTEIN 2.
Mp7g17410	MpTPL	citation background	MpTPL (MpTOPLESS) cited as the co-repressor recruited to MpARFs, causing auxin-insensitive cell-mass formation.
Mp8g08780	MpYUC2	experimental background	MpYUC2, a major vegetative YUC homolog, showed lower transcript levels in sporelings than thalli and was among auxin biosynthesis genes downregulated under all conditions.