
==== Front
bioRxiv
BIORXIV
bioRxiv
2692-8205
Cold Spring Harbor Laboratory

10.1101/2024.08.17.608367
preprint
1
Article
A florigen-expressing subpopulation of companion cells expresses other small proteins and reveals a nitrogen-sensitive FT repressor
Takagi Hiroshi http://orcid.org/0000-0003-0321-0284

Ito Shogo http://orcid.org/0000-0002-8434-6652

Shim Jae Sung http://orcid.org/0000-0002-7352-437X

Kubota Akane http://orcid.org/0000-0003-1347-3950

Hempton Andrew K. http://orcid.org/0000-0002-3018-6091

Lee Nayoung http://orcid.org/0000-0002-0353-6455

Suzuki Takamasa http://orcid.org/0000-0002-1977-0510

Yang Chansie http://orcid.org/0000-0002-8118-2883

Nolan Christine T. http://orcid.org/0009-0001-9257-9595

Bubb Kerry L. http://orcid.org/0000-0002-1117-2591

Alexandre Cristina M. http://orcid.org/0000-0003-0047-0312

Kurihara Daisuke http://orcid.org/0000-0003-2703-0405

Sato Yoshikatsu http://orcid.org/0000-0002-4967-2698

Tada Yasuomi http://orcid.org/0000-0001-9900-069X

Kiba Takatoshi http://orcid.org/0000-0001-8651-0404

Pruneda-Paz Jose L. http://orcid.org/0000-0002-0054-0918

Queitsch Christine http://orcid.org/0000-0002-0905-4705

Cuperus Josh T. http://orcid.org/0000-0002-8019-7733

Imaizumi Takato http://orcid.org/0000-0001-9396-4412

19 8 2024
2024.08.17.608367https://creativecommons.org/licenses/by-nc-nd/4.0/ This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
http://biorxiv.org/lookup/doi/10.1101/2024.08.17.608367
nihpp-2024.08.17.608367.pdf
Abstract

The precise onset of flowering is crucial to ensure successful plant reproduction. The gene FLOWERING LOCUS T ( FT ) encodes florigen, a mobile signal produced in leaves that initiates flowering at the shoot apical meristem. In response to seasonal changes, FT is induced in phloem companion cells located in distal leaf regions. Thus far, a detailed molecular characterization of the FT -expressing cells has been lacking. Here, we used bulk nuclei RNA-seq and single nuclei RNA (snRNA)-seq to investigate gene expression in FT -expressing cells and other phloem companion cells. Our bulk nuclei RNA-seq demonstrated that FT -expressing cells in cotyledons and in true leaves differed transcriptionally. Within the true leaves, our snRNA-seq analysis revealed that companion cells with high FT expression form a unique cluster in which many genes involved in ATP biosynthesis are highly upregulated. The cluster also expresses other genes encoding small proteins, including the flowering and stem growth inducer FPF1-LIKE PROTEIN 1 (FLP1) and the anti-florigen BROTHER OF FT AND TFL1 (BFT). In addition, we found that the promoters of FT and the genes co-expressed with FT in the cluster were enriched for the consensus binding motifs of NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1). Overexpression of the paralogous NIGT1.2 and NIGT1.4 repressed FT expression and significantly delayed flowering under nitrogen-rich conditions, consistent with NIGT1s acting as nitrogen-dependent FT repressors. Taken together, our results demonstrate that major FT -expressing cells show a distinct expression profile that suggests that these cells may produce multiple systemic signals to regulate plant growth and development.
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