Transcriptome analysis highlights nuclear control of chloroplast development in the shoot apex

Abstract

In dicots, the key developmental process by which immature plastids differentiate into photosynthetically competent chloroplasts commences in the shoot apical meristem (SAM), within the shoot apex. Using laser-capture microdissection and single-cell RNA sequencing methodology, we studied the changes in the transcriptome along the chloroplast developmental pathway in the shoot apex of tomato seedlings. The analysis revealed the presence of transcripts for different chloroplast functions already in the stem cell-containing region of the SAM. Thereafter, an en masse up-regulation of genes encoding for various proteins occurs, including chloroplast ribosomal proteins and proteins involved in photosynthesis, photoprotection and detoxification of reactive oxygen species. The results highlight transcriptional events that operate during chloroplast biogenesis, leading to the rapid establishment of photosynthetic competence.

A king and vassals' tale: Molecular signatures of clonal integration in Posidonia oceanica under chronic light shortage

“…This was not an obvious observation, as for instance in maize very few photosynthetic‐related genes are found to be expressed in the SAM and leaf primordia (Brooks III et al, 2009). On the contrary, our results are quite similar to those found for the shoot apex of tomato, where the presence of transcripts for different chloroplast functions was already detected in the stem cell‐containing region of the SAM, revealing an early acquisition of photosynthetic capacity (Dalal et al., 2018). Another important consideration is that LL exposure seems to significantly impair the SAM transcriptional machinery responsible for chloroplast biogenesis and later for the establishment of photosynthetic competence, and these gene‐expression changes likely anticipated leaf‐related responses.…”

Deconvoluting apocarotenoid‐mediated retrograde signaling networks regulating plastid translation and leaf development

“…Likewise, our study demonstrates that the essential role of plastid translation in leaf morphology is restricted to an early developmental window, as has been previously observed for the expression of nuclear photosynthetic genes in mustard ( Sinapis alba ) (Oelmüller et al ., 1986). This result correlates with the massive increases in transcript abundance of nuclear‐encoded plastid‐specific ribosomal subunits observed during chloroplast biogenesis very early in the leaf differentiation process within the CZ of the SAM and progressing towards the leaf primordia in eudicots (Dalal et al ., 2018). Interestingly, three of the nuclear‐encoded plastid‐specific ribosomal genes accumulating during leaf differentiation, PRSP3, RPL6, and RPL27, are among the strongest repressed in an ACS1‐dependent manner in clb5 .…”

“…Transcriptomic analysis comparing the CZ and leaf primordia within the tomato ( Solanum lycopersicum ) SAM region demonstrated that not only chloroplast differentiation is under strong nuclear control, but also confirms that chloroplast biogenesis and leaf development occur in parallel, raising the possibility of the two processes being connected (Dalal et al ., 2018). In fact, diverse evidence supports proper plastid biogenesis as being essential for several aspects of plant development (López‐Juez and Pyke, 2005; Van Dingenen et al ., 2016).…”

New insights into tomato CLE peptide repertoire and perception mechanisms

“…To investigate the gene structure diversity of tomato CLE s, the exon-intron composition was predicted based on sequence homologies (Figure 1A). In addition, we used publicly available RNAseq datasets [32-34, 45, 46], from root, shoot and fruit samples, to support these gene structure predictions. Reads were mapped on the anticipated coding region of 28 CLE genes out of the 37 newly uncovered loci (Figure 1A).…”