An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy

Abstract

Single cell sequencing has recently allowed the generation of exhaustive root cell atlases. However, some cell types are elusive and remain underrepresented. Here, we use a second-generation single cell approach, where we zoom in on the root transcriptome sorting with specific markers to profile the phloem poles at an unprecedented resolution. Our data highlight the similarities among the developmental trajectories and gene regulatory networks communal to protophloem sieve element (PSE) adjacent lineages in relation to PSE enucleation, a key event in phloem biology. As a signature for early PSE-adjacent lineages, we have identified a set of DNA-binding with one finger (DOF) transcription factors, the PINEAPPLEs (PAPL), that act downstream of PHLOEM EARLY DOF (PEAR) genes, and are important to guarantee a proper root nutrition in the transition to autotrophy. Our data provide a holistic view of the phloem poles that act as a functional unit in root development.

Pectin cell wall remodeling through PLL12 and callose deposition through polar CALS7 are necessary for long-distance phloem transport

“…S2A-D) could fully complement the pll12 phenotype. In particularly since whole phloem pole single-cell RNA sequencing conducted after our initial transcriptome mining (21), perfectly recapitulated our pPLL12::erVenus reporter analysis (Fig S1C). To determine whether PLL12 protein was SE-specific or across the entire phloem pole, we generated fluorescent protein fusions of Gamillus-GFP with the genomic PLL12 (Gam-PLL12) region expressed under its own promoter.…”

“…Of the 26 PLLs in Arabidopsis, PLL26, PLL25 and PLL12 were present in both enriched datasets. Details about generation and data curation of the mined Transcriptomic are in the respective publications (20)(21)(22).…”

“…B) Forced-direction trajectories show that PLL12 is most enriched in very late PSE (20). C) UMAP of whole phloem poles scRNAseq shows abundance of PLL12 in PSE-surrounding tissues (21). D) PLL26, PLL25 and PLL12 loci and investigated alleles; light grey refers to UTRs, dark grey to exons, triangles indicate location of insertions in mutants.…”

“…The PSE cells are therefore unique among differentiated tissues in their accessibility to high-resolution transcriptomics to describe their entire differentiation process. (20,21). To understand details of SE cell wall modifications during differentiation, we mined such root transcriptomes first for genes enriched or exclusive to sieve elements (22).…”

An environmentally responsive transcriptional state modulates cell identities during root development

“…While transcriptional characterisation of root cell populations has previously focused on the analysis of bulk sorted lineages, the recent development of single-cell technologies is enabling more precise investigation of the spatio-temporal diversity of cellular states ( 2–6 ). Single-cell RNA-sequencing (scRNA-seq) has recently been used to better define the gene expression signatures of the known cell types of the Arabidopsis root and, by arranging cells of each lineage in developmental trajectories, more finely define the dynamics of gene expression during cell differentiation ( 7–14 ). While this has been crucial for identifying transient cellular states in some cell lineages, these studies have treated each lineage independently, overlooking potential layers of gene regulation that do not depend on the developmental origin of the cell.…”