*Article* **A Core Module of Nuclear Genes Regulated by Biogenic Retrograde Signals from Plastids**

**Björn Grübler, Carolina Cozzi and Thomas Pfannschmidt \***

Pflanzenphysiologie, Institut für Botanik, Naturwissenschaftliche Fakultät, Leibniz-Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; BjoernGruebler@gmx.de (B.G.); c.cozzi@botanik.uni-hannover.de (C.C.)

**\*** Correspondence: t.pfannschmidt@botanik.uni-hannover.de

**Abstract:** Chloroplast biogenesis during seedling development of angiosperms is a rapid and highly dynamic process that parallels the light-dependent photomorphogenic programme. Pre-treatments of dark-grown seedlings with lincomyin or norflurazon prevent chloroplast biogenesis upon illumination yielding albino seedlings. A comparable phenotype was found for the *Arabidopsis* mutant *plastid-encoded polymerase associated protein 7* (*pap7*) being defective in the prokaryotic-type plastid RNA polymerase. In all three cases the defect in plastid function has a severe impact on the expression of nuclear genes representing the influence of retrograde signaling pathway(s) from the plastid. We performed a meta-analysis of recently published genome-wide expression studies that investigated the impact of the aforementioned chemical and genetic blocking of chloroplast biogenesis on nuclear gene expression profiles. We identified a core module of 152 genes being affected in all three conditions. These genes were classified according to their function and analyzed with respect to their implication in retrograde signaling and chloroplast biogenesis. Our study uncovers novel genes regulated by retrograde biogenic signals and suggests the action of a common signaling pathway that is used by signals originating from plastid transcription, translation and oxidative stress.

**Citation:** Grübler, B.; Cozzi, C.; Pfannschmidt, T. A Core Module of Nuclear Genes Regulated by Biogenic Retrograde Signals from Plastids. *Plants* **2021**, *10*, 296. https://doi.org/ 10.3390/plants10020296

Academic Editor: Nunzia Scotti Received: 18 January 2021 Accepted: 29 January 2021 Published: 4 February 2021

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**Keywords:** plastids; photomorphogenesis; retrograde control; biogenic signals; lincomycin; norflurazon; *pap7-1* mutant
