UNLABELLED: The first phototrophic member of the bacterial phylum Gemmatimonadota, Gemmatimonas phototrophica AP64T, received all its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Here, we investigated how these acquired genes, which are tightly controlled by oxygen and light in the ancestor, are integrated into the regulatory system of its new host. G. phototrophica grew well under aerobic and semiaerobic conditions, with almost no difference in gene expression. Under aerobic conditions, the growth of G. phototrophica was optimal at 80 µmol photon m-2 s-1, while higher light intensities had an inhibitory effect. The transcriptome showed only a minimal response to the dark-light shift at optimal light intensity, while the exposure to a higher light intensity (200 µmol photon m-2 s-1) induced already stronger but still transient changes in gene expression. Interestingly, a singlet oxygen defense was not activated under any conditions tested. Our results indicate that G. phototrophica possesses neither the oxygen-dependent repression of photosynthesis genes known from purple bacteria nor the light-dependent repression described in aerobic anoxygenic phototrophs. Instead, G. phototrophica has evolved as a low-light species preferring reduced oxygen concentrations. Under these conditions, the bacterium can safely employ its photoheterotrophic metabolism without the need for complex regulatory mechanisms. IMPORTANCE: Horizontal gene transfer is one of the main mechanisms by which bacteria acquire new genes. However, it represents only the first step as the transferred genes have also to be functionally and regulatory integrated into the recipient's cellular machinery. Gemmatimonas phototrophica, a member of bacterial phylum Gemmatimonadota, acquired its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Thus, it represents a unique natural experiment, in which the entire package of photosynthesis genes was transplanted into a distant host. We show that G. phototrophica lacks the regulation of photosynthesis gene expressions in response to oxygen concentration and light intensity that are common in purple bacteria. This restricts its growth to low-light habitats with reduced oxygen. Understanding the regulation of horizontally transferred genes is important not only for microbial evolution but also for synthetic biology and the engineering of novel organisms, as these rely on the successful integration of foreign genes.

Laboratory of Anoxygenic Phototrophs Institute of Microbiology of the Czech Acad Sci Třeboň Czechia

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Canfield DE, Rosing MT, Bjerrum C. 2006. Early anaerobic metabolisms. Phil Trans R Soc B 361:1819–1836. doi:10.1098/rstb.2006.1906 PubMed DOI PMC

Hohmann-Marriott MF, Blankenship RE. 2011. Evolution of photosynthesis. Annu Rev Plant Biol 62:515–548. doi:10.1146/annurev-arplant-042110-103811 PubMed DOI

Zeng Y, Feng F, Medová H, Dean J, Koblížek M. 2014. Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes. Proc Natl Acad Sci U S A 111:7795–7800. doi:10.1073/pnas.1400295111 PubMed DOI PMC

Dachev M, Bína D, Sobotka R, Moravcová L, Gardian Z, Kaftan D, Šlouf V, Fuciman M, Polívka T, Koblížek M. 2017. Unique double concentric ring organization of light harvesting complexes in Gemmatimonas phototrophica. PLOS Biol 15:e2003943. doi:10.1371/journal.pbio.2003943 PubMed DOI PMC

Qian P, Gardiner AT, Šímová I, Naydenova K, Croll TI, Jackson PJ, Nupur N, Kloz M, Čubáková P, et al. . 2022. 2.4-Å structure of the double-ring Gemmatimonas phototrophica photosystem. Sci Adv 8:eabk3139. doi:10.1126/sciadv.abk3139 PubMed DOI PMC

Koblížek M, Dachev M, Bína D, Nupur N, Piwosz K, Kaftan D. 2020. Utilization of light energy in phototrophic Gemmatimonadetes. J Photochem Photobiol B Biol 213:112085. doi:10.1016/j.jphotobiol.2020.112085 PubMed DOI

Olson JM. 2006. Photosynthesis in the Archean era. Photosynth Res 88:109–117. doi:10.1007/s11120-006-9040-5 PubMed DOI

Elsen S, Swem LR, Swem DL, Bauer CE. 2004. RegB/RegA, a highly conserved redox-responding global two-component regulatory system. Microbiol Mol Biol Rev 68:263–279. doi:10.1128/MMBR.68.2.263-279.2004 PubMed DOI PMC

Zeilstra-Ryalls JH, Kaplan S. 2004. Oxygen intervention in the regulation of gene expression: the photosynthetic bacterial paradigm. Cell Mol Life Sci 61:417–436. doi:10.1007/s00018-003-3242-1 PubMed DOI PMC

Koblízek M, Shih JD, Breitbart SI, Ratcliffe EC, Kolber ZS, Hunter CN, Niederman RA. 2005. Sequential assembly of photosynthetic units in Rhodobacter sphaeroides as revealed by fast repetition rate analysis of variable bacteriochlorophyll a fluorescence. Biochim Biophys Acta 1706:220–231. doi:10.1016/j.bbabio.2004.11.004 PubMed DOI

Androga DD, Özgür E, Eroglu I, Yücel M, Gündüz U. 2012. Photofermentative hydrogen production in outdoor conditions. INTECH Open Access Publisher.

Borland CF, Cogdell RJ, Land EJ, Truscott TG. 1989. Bacteriochlorophyll a triplet state and its interactions with bacterial carotenoids and oxygen. J Photochem Photobiol B Biol 3:237–245. doi:10.1016/1011-1344(89)80065-X DOI

Halliwell B. 2006. Reactive species and antioxidants. redox biology is a fundamental theme of aerobic life. Plant Physiol 141:312–322. doi:10.1104/pp.106.077073 PubMed DOI PMC

Wright A, Bubb WA, Hawkins CL, Davies MJ. 2002. Singlet oxygen-mediated protein oxidation: evidence for the formation of reactive side chain peroxides on tyrosine residues. Photochem Photobiol 76:35–46. doi:10.1562/0031-8655(2002)076<0035:sompoe>2.0.co;2 PubMed DOI

Tomasch J, Gohl R, Bunk B, Diez MS, Wagner-Döbler I. 2011. Transcriptional response of the photoheterotrophic marine bacterium Dinoroseobacter shibae to changing light regimes. ISME J 5:1957–1968. doi:10.1038/ismej.2011.68 PubMed DOI PMC

Kopejtka K, Tomasch J, Kaftan D, Gardiner AT, Bína D, Gardian Z, Bellas C, Dröge A, Geffers R, Sommaruga R, Koblížek M. 2022. A bacterium from a mountain lake harvests light using both proton-pumping xanthorhodopsins and bacteriochlorophyll-based photosystems. Proc Natl Acad Sci U S A 119:e2211018119. doi:10.1073/pnas.2211018119 PubMed DOI PMC

Tinguely C, Paulméry M, Terrettaz C, Gonzalez D. 2023. Diurnal cycles drive rhythmic physiology and promote survival in facultative phototrophic bacteria. ISME Commun 3:125. doi:10.1038/s43705-023-00334-5 PubMed DOI PMC

Iba K, Takamiya K. 1989. Action spectra for inhibition by light of accumulation of bacteriochlorophyll and carotenoid during aerobic growth of photosynthetic bacteria. Plant Cell Physiol 30:471–477. doi:10.1093/oxfordjournals.pcp.a077765 DOI

Koblízek M, Masín M, Ras J, Poulton AJ, Prásil O. 2007. Rapid growth rates of aerobic anoxygenic phototrophs in the ocean. Environ Microbiol 9:2401–2406. doi:10.1111/j.1462-2920.2007.01354.x PubMed DOI

Spring S, Lünsdorf H, Fuchs BM, Tindall BJ. 2009. The photosynthetic apparatus and its regulation in the aerobic gammaproteobacterium Congregibacter litoralis gen. nov., sp. nov. PLoS One 4:e4866. doi:10.1371/journal.pone.0004866 PubMed DOI PMC

Berghoff BA, Glaeser J, Nuss AM, Zobawa M, Lottspeich F, Klug G. 2011. Anoxygenic photosynthesis and photooxidative stress: a particular challenge for Roseobacter. Environ Microbiol 13:775–791. doi:10.1111/j.1462-2920.2010.02381.x PubMed DOI

Fecskeová LK, Piwosz K, Hanusová M, Nedoma J, Znachor P, Koblížek M. 2019. Diel changes and diversity of pufM expression in freshwater communities of anoxygenic phototrophic bacteria. Sci Rep 9:18766. doi:10.1038/s41598-019-55210-x PubMed DOI PMC

Koblížek M. 2015. Ecology of aerobic anoxygenic phototrophs in aquatic environments. FEMS Microbiol Rev 39:854–870. doi:10.1093/femsre/fuv032 PubMed DOI

Yurkov V, Hughes E. 2017. Aerobic anoxygenic phototrophs: four decades of mystery, p 193–214. In Hallenbeck P (ed), Modern topics in the phototrophic prokaryotes. Springer, Cham.

Piwosz K, Villena-Alemany C, Mujakić I. 2022. Photoheterotrophy by aerobic anoxygenic bacteria modulates carbon fluxes in a freshwater lake. ISME J 16:1046–1054. doi:10.1038/s41396-021-01142-2 PubMed DOI PMC

Zeng Y, Selyanin V, Lukeš M, Dean J, Kaftan D, Feng F, Koblížek M. 2015. Characterization of the microaerophilic, bacteriochlorophyll a-containing bacterium Gemmatimonas phototrophica sp. nov., and emended descriptions of the genus Gemmatimonas and Gemmatimonas aurantiaca. Int J Syst Evol Microbiol 65:2410–2419. doi:10.1099/ijs.0.000272 PubMed DOI

Shivaramu S, Tomasch J, Kopejtka K, Nupur N, Saini MK, Bokhari SNH, Küpper H, Koblížek M. 2023. The influence of calcium on the growth, morphology and gene regulation in Gemmatimonas phototrophica. Microorganisms 11:27. doi: 10.3390/microorganisms11010027 PubMed DOI PMC

Mujakić I, Cabello-Yeves PJ, Villena-Alemany C, Piwosz K, Rodriguez-Valera F, Picazo A, Camacho A, Koblížek M. 2023. Multi-environment ecogenomics analysis of the cosmopolitan phylum Gemmatimonadota. Microbiol Spectr 11:e0111223. doi:10.1128/spectrum.01112-23 PubMed DOI PMC

Winkler A, Heintz U, Lindner R, Reinstein J, Shoeman RL, Schlichting I. 2013. A ternary AppA-PpsR-DNA complex mediates light regulation of photosynthesis-related gene expression. Nat Struct Mol Biol 20:859–867. doi:10.1038/nsmb.2597 PubMed DOI PMC

Imam S, Noguera DR, Donohue TJ. 2014. Global analysis of photosynthesis transcriptional regulatory networks. PLoS Genet 10:e1004837. doi:10.1371/journal.pgen.1004837 PubMed DOI PMC

Dragnea V, Gonzalez-Gutierrez G, Bauer CE. 2022. Structural analyses of CrtJ and Its B12-binding co-regulators SAerR and LAerR from the purple photosynthetic bacterium Rhodobacter capsulatus. Microorganisms 10:912. doi:10.3390/microorganisms10050912 PubMed DOI PMC

Piwosz K, Kaftan D, Dean J, Šetlík J, Koblížek M. 2018. Nonlinear effect of irradiance on photoheterotrophic activity and growth of the aerobic anoxygenic phototrophic bacterium Dinoroseobacter shibae. Environ Microbiol 20:724–733. doi:10.1111/1462-2920.14003 PubMed DOI

Haft DH, Paulsen IT, Ward N, Selengut JD. 2006. Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic. BMC Biol 4:1–16. doi:10.1186/1741-7007-4-29 PubMed DOI PMC

Helmann JD. 2011. Bacillithiol, a new player in bacterial redox homeostasis. Antioxid Redox Signal 15:123–133. doi:10.1089/ars.2010.3562 PubMed DOI PMC

Arnold BJ, Huang IT, Hanage WP. 2022. Horizontal gene transfer and adaptive evolution in bacteria. Nat Rev Microbiol 20:206–218. doi:10.1038/s41579-021-00650-4 PubMed DOI

Zeng Y, Nupur N, Wu N, Madsen AM, Chen X, Gardiner AT, Koblížek M. 2021. Gemmatimonas groenlandica sp. nov. is an aerobic anoxygenic phototroph in the phylum Gemmatimonadetes. Front Microbiol 11:606612. doi:10.3389/fmicb.2020.606612 PubMed DOI PMC

Arai H, Roh JH, Kaplan S. 2008. Transcriptome dynamics during the transition from anaerobic photosynthesis to aerobic respiration in Rhodobacter sphaeroides 2.4.1. J Bacteriol 190:286–299. doi:10.1128/JB.01375-07 PubMed DOI PMC

Degli Esposti M, Mentel M, Martin W, Sousa FL. 2019. Oxygen reductases in alphaproteobacterial genomes: physiological evolution from low to high oxygen environments. Front Microbiol 10:499. doi:10.3389/fmicb.2019.00499 PubMed DOI PMC

Chidgey JW, Jackson PJ, Dickman MJ, Hunter CN. 2017. PufQ regulates porphyrin flux at the haem/bacteriochlorophyll branchpoint of tetrapyrrole biosynthesis via interactions with ferrochelatase. Mol Microbiol 106:961–975. doi:10.1111/mmi.13861 PubMed DOI PMC

Bill N, Tomasch J, Riemer A, Müller K, Kleist S, Schmidt-Hohagen K, Wagner-Döbler I, Schomburg D. 2017. Fixation of CO2 using the ethylmalonyl-CoA pathway in the photoheterotrophic marine bacterium Dinoroseobacter shibae. Environ Microbiol 19:2645–2660. doi:10.1111/1462-2920.13746 PubMed DOI

Kopejtka K, Tomasch J, Zeng Y, Selyanin V, Dachev M, Piwosz K, Tichý M, Bína D, Gardian Z, Bunk B, Brinkmann H, Geffers R, Sommaruga R, Koblížek M. 2020. Simultaneous presence of bacteriochlorophyll and xanthorhodopsin genes in a freshwater bacterium. mSystems 5:e01044-20. doi:10.1128/mSystems.01044-20 PubMed DOI PMC

Tomasch J, Kopejtka K, Bílý T, Gardiner AT, Gardian Z, Shivaramu S, Koblížek M, Kaftan D. 2024. A photoheterotrophic bacterium from Iceland has adapted its photosynthetic machinery to the long days of polar summer. mSystems 9:e0131123. doi:10.1128/msystems.01311-23 PubMed DOI PMC

Pucelik S, Becker M, Heyber S, Wöhlbrand L, Rabus R, Jahn D, Härtig E. 2024. The blue light-dependent LOV-protein LdaP of Dinoroseobacter shibae acts as antirepressor of the PpsR repressor, regulating photosynthetic gene cluster expression. Front Microbiol 15:1351297. doi:10.3389/fmicb.2024.1351297 PubMed DOI PMC

Mujakić I, Andrei A-Ş, Shabarova T, Fecskeová LK, Salcher MM, Piwosz K, Ghai R, Koblížek M. 2021. Common presence of phototrophic Gemmatimonadota in temperate freshwater lakes. mSystems 6:10–1128. doi:10.1128/mSystems.01241-20 PubMed DOI PMC

Huang Y, Zeng Y, Lu H, Feng H, Zeng Y, Koblížek M. 2016. Novel acsF gene primers revealed a diverse phototrophic bacterial population, including Gemmatimonadetes, in Lake Taihu (China). Appl Environ Microbiol 82:5587–5594. doi:10.1128/AEM.01063-16 PubMed DOI PMC

Pinto FL, Thapper A, Sontheim W, Lindblad P. 2009. Analysis of current and alternative phenol based RNA extraction methodologies for cyanobacteria. BMC Mol Biol 10:1–8. doi:10.1186/1471-2199-10-79 PubMed DOI PMC

Shishkin AA, Giannoukos G, Kucukural A, Ciulla D, Busby M, Surka C, Chen J, Bhattacharyya RP, Rudy RF, Patel MM, Novod N, Hung DT, Gnirke A, Garber M, Guttman M, Livny J. 2015. Simultaneous generation of many RNA-seq libraries in a single reaction. Nat Methods 12:323–325. doi:10.1038/nmeth.3313 PubMed DOI PMC

Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. doi:10.1038/nmeth.1923 PubMed DOI PMC

Liao Y, Smyth GK, Shi W. 2014. featureCounts: an efficient general-purpose read summarization program. Bioinformatics 30:923–930. doi:10.1093/bioinformatics/btt656 PubMed DOI

Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140. doi:10.1093/bioinformatics/btp616 PubMed DOI PMC

Dudek CA, Jahn D. 2022. PRODORIC: state-of-the-art database of prokaryotic gene regulation. Nucleic Acids Res 50:D295–D302. doi:10.1093/nar/gkab1110 PubMed DOI PMC

Kaftan D, Bína D, Koblížek M. 2019. Temperature dependence of photosynthetic reaction centre activity in Rhodospirillum rubrum. Photosynth Res 142:181–193. doi:10.1007/s11120-019-00652-7 PubMed DOI PMC