Transcriptome analysis of Rhodobacter capsulatus grown on different nitrogen sources
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ORIGINAL PAPER
Transcriptome analysis of Rhodobacter capsulatus grown on different nitrogen sources Nilüfer Afsar Erkal1,2 · Muazzez Gürgan Eser3 · Ebru Özgür2,4 · Ufuk Gündüz1 · Inci Eroglu4 · Meral Yücel1 Received: 21 July 2018 / Revised: 10 October 2018 / Accepted: 18 February 2019 © Springer-Verlag GmbH Germany, part of Springer Nature 2019
Abstract This study investigated the effect of different nitrogen sources, namely, ammonium chloride and glutamate, on photoheterotrophic metabolism of Rhodobacter capsulatus grown on acetate as the carbon source. Genes that were significantly differentially expressed according to Affymetrix microarray data were categorized into Clusters of Orthologous Groups functional categories and those in acetate assimilation, hydrogen production, and photosynthetic electron transport pathways were analyzed in detail. Genes related to hydrogen production metabolism were significantly downregulated in cultures grown on ammonium chloride when compared to those grown on glutamate. In contrast, photosynthetic electron transport and acetate assimilation pathway genes were upregulated. In detail, aceA encoding isocitrate lyase, a unique enzyme of the glyoxylate cycle and ccrA encoding the rate limiting crotonyl-CoA carboxylase/reductase enzyme of ethylmalonyl-coA pathway were significantly upregulated. Our findings indicate for the first time that R. capsulatus can operate both glyoxylate and ethylmalonyl-coA cycles for acetate assimilation. Keywords Photoheterotrophic growth · Rhodobacter capsulatus · Purple non-sulfur bacteria · Microarray · Hydrogen metabolism · Acetate metabolism
Introduction Biological hydrogen production processes offer sustainable and renewable energy without polluting the environment. Photofermentation using purple non-sulfur bacteria (PNS) is an advantageous way of biological hydrogen production, since a wide variety of organic substrates such as organic acids, agricultural, or industrial wastes can be utilized with Communicated by Shuang-Jiang Liu. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00203-019-01635-x) contains supplementary material, which is available to authorized users. * Meral Yücel [email protected] 1
Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
2
Mikro Biyositemler Inc, 06530 Ankara, Turkey
3
Department of Biology, Namık Kemal University, 59030 Tekirdağ, Turkey
4
Department of Chemical Engineering, Middle East Technical University, 06800 Ankara, Turkey
high substrate conversion efficiencies (Basak and Das 2007; Redwood et al. 2009; Eroglu and Melis 2011). Rhodobacter capsulatus is a Gram-negative PNS bacterium. Growth mode of this bacterium can be photoheterothrophy, photoautotrophy, aerobic/anaerobic respiration, or fermentation according to environmental conditions (Imhoff 2006; Madigan and Jung 2009). In the photoheterotrophic growth mode, R. capsulatus can convert small organic acids into biohydrogen by the activity
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