*2.6. Quantitative RT-PCR*

For quantitative RT-PCR, total RNA was isolated after 10 min of photooxidative stress as described for RNA-seq. Samples were treated with TURBO DNA-free ™ Kit (Invitrogen, Thermo Fisher Scientific, Schwerte, Germany) to remove DNA contaminations. The Brilliant III Ultra-Fast SYBR Green QRT-PCR Master Mix (Agilent Technologies, Waldbronn, Germany) was applied using 4 ng·μL−<sup>1</sup> of total RNA per reaction. RT-PCR was performed in a CFX Connect ™ Real-Time System (Bio-Rad). Cycle threshold (Ct) values were determined using the CFX Maestro ™ Software (Bio-Rad, Feldkirchen, Germany), and relative transcript levels calculated according to Pfa ffl (2001) [52]. The *rpoZ* gene was used for normalization. Primers and their amplification e fficiencies are listed in Table S3.

#### *2.7. Protein Sample Preparation and Mass Spectrometry*

Protein sample preparation was performed as previously described [53]. For mass spectrometry (MS) analysis, peptides were eluted from STAGE tips by solvent B (80% acetonitrile, 0.1% formic acid), dried down in a SpeedVac Concentrator (Thermo Fisher Scientific, Schwerte, Germany) and dissolved in solvent a (0.1% formic acid). Peptides were separated using an UHPLC system (EASY-nLC 1000, ThermoFisher Scientific, Waltham, MA, USA) and 20 cm, in-house packed C18 silica columns

(1.9 μm C18 beads, Dr. Maisch GmbH) coupled in line to a Q-Exactive HF orbitrap mass spectrometer (ThermoFisher Scientific) using an electrospray ionization source. a gradient of 240 min was applied using a linearly increasing concentration of solvent B (80% acetonitrile, 0.1% formic acid) over solvent a (0.1% formic acid) from 5% to 30% for 215 min and from 30% to 60% for 5 min, followed by washing with 95% of solvent B for 5 min and re-equilibration with 5% of solvent B. Full MS spectra were acquired in a mass range of 300 to 1750 m/z with a resolution of 60,000 at 200 m/z. The ion injection target was set to 3 × 10<sup>6</sup> and the maximum injection time limited to 20 ms. Ions were fragmented by high-energy collision dissociation (HCD) using a normalized collision energy of 27 and an ion injection target of 5 × 10<sup>5</sup> with a maximum injection time of 20 ms. The resulting tandem mass spectra (MS/MS) were acquired with a resolution of 15,000 at 200 m/z using data dependent mode with a loop count of 15 (top 15). MS raw data were processed by MaxQuant (1.5.3.12) [54] using the Uniprot database for *R. capsulatus* containing 4290 entries (release date July 2016). The following parameters were used for data processing: maximum of two miss cleavages, mass tolerance of 4.5 ppm for main search, trypsin as digesting enzyme, carbamidomethylation of cysteines as fixed modification, oxidation of methionine, and acetylation of the protein N-terminus as variable modifications. For protein quantification, the LFQ function of MaxQuant was used. Peptides with a minimum of seven amino acids and at least one unique peptide were required for protein identification. Only proteins with at least two peptides and at least one unique peptide were considered to have been identified and were used for further data analysis. LFQ intensities for all identified proteins can be found in Table S4.

#### *2.8. Search for Orthologous Rhodobacter Genes and Synteny Analysis*

To find orthologous genes in *R. capsulatus* and *R. sphaeroides,* the Genome Gene Best Homologs tool from the IMG web resources was used [55]. The pBLAST-based search of orthologous genes used a 30% amino acid identity as a cuto ff value for homology. Phyre<sup>2</sup> was applied for a structural homology search [56]. Synteny analysis was performed using Edgar 2.3, a software platform for comparative gene content analyses [57].

#### *2.9. Gene Ontology Enrichment Analysis*

Significantly enriched functional groups were determined with the program Cytoscape version 3.6.0 [58] according to Gene Ontology (GO) terms using the BiNGO tool [59]. Overrepresented GO categories in the data sets were determined with a hypergeometric test with Benjamini-Hochberg false discovery rate correction and a significance level of 0.05. The whole *R. capsulatus* genome served as a reference. The selected ontology file was *gb.obo*, format-version 1.2, released 06/10/2017 [60,61]. The resulting networks were searched for overrepresented GO categories.
