Additional file 1: Figure S1. of Genome and catabolic subproteomes of the marine, nutritionally versatile, sulfate-reducing bacterium Desulfococcus multivorans DSM 2059

Distribution of the 1,307 detected proteins by 2D DIGE, whole cell shotgun analysis and preparation of the membrane protein-enriched fraction of D. multivorans grown with 17 different substrates. Figure S2 Phylogenetic relationship of the class II benzoyl-CoA reductase catalytic subunit BamB and other uncharacterized aldehyde: ferredoxin oxidoreductases (AFOR) of selected Deltaproteobacteria. Figure S3 Scale model and chromosomal localization of transmembrane redox complex containing genes of D. multivorans. Table S1 Listing of locus tags of genes manually assigned to metabolic pathways and energy conservation as displayed in Figs. 2 and 3. (PDF 433 kb

Additional file 1: Figure S1. of The predicted σ54-dependent regulator EtpR is essential for expression of genes for anaerobic p-ethylphenol and p-hydroxyacetophenone degradation in “Aromatoleum aromaticum” EbN1

Sequence verification of the ∆etpR mutant. Figure S2. Anaerobic growth with p-ethylphenol. Figure S3. Anaerobic growth with a mixture of benzoate and p-ethylphenol. Figure S4. Phylogenetic relationship of the regulatory domains of σ54-dependent NtrC-type regulators. Figure S5. Amino acid sequence comparison of σ54-dependent regulators involved in aromatic compound catabolism. (PDF 1242 kb

Data_Sheet_1_The blue light-dependent LOV-protein LdaP of Dinoroseobacter shibae acts as antirepressor of the PpsR repressor, regulating photosynthetic gene cluster expression.docx

In the marine α-proteobacterium Dinoroseobacter shibae more than 40 genes of the aerobic anoxygenic photosynthesis are regulated in a light-dependent manner. A genome-wide screen of 5,605 clones from a D. shibae transposon library for loss of pigmentation and changes in bacteriochlorophyll absorbance identified 179 mutant clones. The gene encoding the LOV-domain containing protein Dshi_1135 was identified by its colorless phenotype. The mutant phenotype was complemented by the expression of a Dshi_1135-strep fusion protein in trans. The recombinantly produced and chromatographically purified Dshi_1135 protein was able to undergo a blue light-induced photocycle mediated by bound FMN. Transcriptome analyses revealed an essential role for Dshi_1135 in the light-dependent expression of the photosynthetic gene cluster. Interactomic studies identified the repressor protein PpsR as an interaction partner of Dshi_1135. The physical contact between PpsR and the Dshi_1135 protein was verified in vivo using the bacterial adenylate cyclase-based two-hybrid system. In addition, the antirepressor function of the Dshi_1135 protein was demonstrated in vivo testing of a bchF-lacZ reporter gene fusion in a heterologous Escherichia coli-based host system. We therefore propose to rename the Dshi_1135 protein to LdaP (light-dependent antirepressor of PpsR). Using the bacterial two-hybrid system, it was also shown that cobalamin (B12) is essential for the interaction of the antirepressor PpaA with PpsR. A regulatory model for the photosynthetic gene cluster in D. shibae was derived, including the repressor PpsR, the light-dependent antirepressor LdaP and the B12-dependent antirepressor PpaA.</p

Additional file 8: Figure S5. of More than 2500Â years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis

Rarefaction curves of the functional analysis in Keri Lake metagenomic samples (A) for the detected KEGG Orthology numbers of the 10 most abundant phyla and (B) for the 68 genes of interest. The deep sequenced samples are presented after normalization by subsampling to ~2.12 million reads. (PDF 46 kb

Additional file 7: Figure S4. of More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis

Distribution and abundance of prokaryotic taxa at different depths of the NE and HE sites. The ten most abundant phyla are depicted as distinct colors. Individual data points represent different orders; the size indicates the order’s abundance while the position on the plot shows the proportion in the three depths. (PDF 42 kb

In the pigeon retina, Cry1b was expressed in ganglion cells, putative displaced ganglion cells and photoreceptor inner segments.

<p>Vertical slices of pigeon retina labelled with gwCry1b antibody (A, B green) and Roti® Mount nuclear marker (A, red) showed strong expression of Cry1b protein in the cytoplasm of ganglion cells and single cells in the proximal INL (B, arrow) and weak Cry1b expression in the outer parts of photoreceptors (B, arrowheads). This labelling was absent in controls with pre-immune serum (C, D) and in controls with gwCry1b antibody blocked by the accordant gwCry1b peptides (E, F). Projection (10.1 μm) of gwCry1b labelling (G, H green) together with the Roti® Mount nuclear marker (G red) in the ganglion cell layer showed strong Cry1b expression in the cytoplasm of several ganglion cells, whereas weak or no staining was observed in other ganglion cells (G, H asterisks). With the bright field image for comparison (I), Cry1b immunoreactivity (J, K green) in the photoreceptors was located distal to the outer limiting membrane and proximal to the pigment epithelium. Double immunostaining (K) revealed that Cry1b immunoreactivity (K green) in the outer parts of photoreceptors was not present in outer segments of OPN1SW labelled cones (K red), but in the photoreceptor inner segments proximal to the outer segments. Images (A-F) are maximum projections of confocal stacks and were taken from the same experiment with identical microscope settings and without any image adjustments<b>.</b> Scale bars: A-F, 10 μm G, H, 5 μm; I, J, K 10 μm. PE, pigment epithelium; OS, photoreceptor outer segments; IS, photoreceptor inner segments; OLM, outer limiting membrane; ONL, outer nuclear layer; OPL, outer plexiform layer; INL, inner nuclear layer; IPL, inner plexiform layer; GCL, ganglion cell layer.</p

Antibodies against erCry1b confirm Cry1b expression of ganglion cells and inner segments in European robin and Northern wheatear.

<p>Immunolabelling of the erCry1b antibody in the retina of a European robin (A) revealed Cry1b expression (B) in several ganglion cells, in the photoreceptor inner segments and in few cells in the INL (B asterisks). Immunoreactive cells in the very proximal INL (C-H) were significantly bigger than surrounding bipolar cells (C, D, F, G) and showed a large cytosolic space. Immunoreactivity pattern shown in B was absent in controls with the erCry1b antibody blocked by erCry1b peptides (J) and in controls using pre-immune serum (L). In the retina of the Northern wheatear (M, N), the erCry1b antibody showed the same pattern as seen in European robins (N). Staining beneath the photoreceptor oil droplets (M arrowheads) and distal to the OLM indicated Cry1b expression in photoreceptor inner segments (M). Immunocytochemistry of N2a cells expressing erCry1b-GFP fusion protein (O green) showed that the erCry1b antibody (P red) detects erCry1b protein (Q yellow in the overlay). Immunolabelling of erCry1a-GFP expressing cells (R green) indicated that the same antibody did not detect Cry1a protein (S, T). In Western blots, the erCry1b antibody detected a band of the expected size of ~92 kDa in protein homogenates of erCry1b-GFP expressing N2a cells (U middle lane). No band at the appropriate molecular mass was seen in homogenates of erCry1a-GFP (U left lane) or GFP expressing cells (U right lane). The signal at the appropriate molecular mass was absent in negative controls after probing the blot with pre-immune serum (V). Western blots on protein homogenates from retinae of European robins incubated with the erCry1b antibody showed a band of the appropriate size ~64 kDa (W asterisk). This band was absent in controls when the blot was incubated with the pre-adsorbed antibody (Q). Molecular mass marker proteins are indicated on the left (kDa). All confocal images are maximum projections (B, J, L 12.8 μm; N, 3 μm). Images A-L were taken with identical settings. PE, pigment epithelium; IS, photoreceptor inner segments; OLM, outer limiting membrane; ONL outer nuclear layer; OPL, outer plexiform layer; INL, inner nuclear layer; IPL, inner plexiform layer; GCL, ganglion cell layer. Scale bars: A, B 50 μm; D-H, M, N 10 μm; I-L, O-T 25 μm.</p

Specificity of gwCry1b antibody.

<p>N2a cells expressing a gwCry1b-GFP fusion protein (A green) stained with gwCry1b antibody (B red) indicated that the antibody detects gwCry1b-GFP protein (C yellow). The same labelling of gwCry1a-GFP expressing cells (D-F) indicated no detection of gwCry1a protein. In Western blots, gwCry1b antibody detected a single protein of the expected size (~64 kDa) in samples of purified gwCry1b protein (G left lane) but not in samples of gwCry1a protein (G right lane). Western blots incubated with gwCry1b antibody showed a band of ~64 kDa on retinal total homogenates from pigeons (H left lane) and purified gwCry1b protein (H right lane). No bands were detected in blots incubated with pre-immune serum (I) and gwCry1b antibody blocked by gwCry1b peptides (J). In G-J, the molecular mass in kDa is indicated on the left. All images (A-E) are maximum projections of confocal stacks and were taken from the same experiment with identical microscope settings and without any image adjustments<b>. </b></p