MOESM1 of Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader ‘Candidatus Leucobacter sulfamidivorax’ strain GP
Creators: name: Reis, Ana
name: Kolvenbach, Boris
name: Chami, Mohamed
name: Gales, Luís
name: Egas, Conceição
name: Corvini, Philippe
name: Nunes, Olga
Publisher: name: figshare
Year: 2019
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Plant Biology

description: Additional file 1: Figure S1. Fluorescence microscopy composite images of DAPI-stained cells of the microbial consortium (blue) and (A) cells hybridized with the modified ActORD1 FISH probe (stains strain GP, 5′ fluorophore: FAM, green, sequence: 5’- CACCAGGAATTCCAATCTCC-3’, original probe accession number: pB-1931, reference: [147]) or with (B) cells hybridized with Alca2 FISH probe (stains strain PR1; 5’ fluorophore: Cy3, orange/red; sequence: 5’- CATCTTTCTTTCCGAACCGC-3’; probe accession number: pB-2127, reference: [148]) Figure S2: Electron micrographs of negatively stained Achromobacter denitrificans PR1 showing the absence heatmap representation of peritrichous flagella(FG) Figure S3: Cladogram of the 16S rRNA gene inferred from maximum likelihood estimation with MEGA6 with the best-fitting model: TN93+G+I [87]. Leucobacter spp. strains sequenced in this study are marked with an asterisk, and sulfonamide degraders are shown in bold. The tree was rooted at the outgroup and visualized with FigTree [125]. The scale bar represents the number of expected substitutions per site. Bootstrap values were inferred from 1000 replicates, values above 70% are shown at the corresponding nodes Figure S4: Presence/absence heatmap representation and dendrograms of the 12,998 orthologs gene clusters found in the pangenome of Leucobacter spp. and strain GP obtained with the GET_HOMOLOGUES package [54]. Each column represents a different gene cluster which can be absent (white) or present (blue) in each strain. As paralogs were included in the analysis, some clusters have more than one homolog per genome, and these are shown in darker blue Figure S5: Visualization of the reads of the strain GP’s MAG on the Interactive Genomics Viewer (IGV) [133] mapping to the reference genome and annotations of Leucobacter chironomi strain DSM 19883 T (assembly accession number GCA_000421845.1). This region from strain DSM 19883 (ATXU0100005.1:1..268438) contains the genes from the purine de novo biosynthetic pathway and the porphyrin and chlorophyll metabolism pathway (left to right): phosphoribosylformylglycinamidine synthase subunit PurQ (accession no. WP_017883592.1, locus tag H629_RS0106495); porphobilinogen synthase HemB (accession no. WP_024356487.1, locus tag H629_RS0106505); porphobilinogen deaminase HemC (accession no. WP_084705356.1, locus tag H629_RS14980); uroporphyrinogen decarboxylase HemE (accession no. WP_024356489.1, locus tag H629_RS0106525); glutamyl-tRNA reductase HemA (accession no WP_024356490.1, locus tag H629_RS0106530) Figure S6: Visualization of the reads of the strain GP’s MAG on the IGV [133] mapping to the reference genome and annotations of Leucobacter chironomi strain DSM 19883 T (assembly accession number GCA_000421845.1). This region from strain DSM 19883 (ATXU01000008.1:1..186096) contains the genes related to amino acid metabolism and from the glutathione and L-cysteine ABC transporter pathway (left to right): leucine--tRNA ligase (accession no. WP_017793981.1, locus tag H629_RS0110150); alpha/beta hydrolase (accession no. WP_010837840.1, locus tag H629_RS011055); thiol reductant ABC exporter subunit CydC (accession no. WP_024357158.1, locus tag H629_RS0110165); thiol reductant ABC exporter subunit CydD (accession no. WP_024357159.1, locus tag H629_RS0110170) Figure S7: Heatmaps representing amino acid identity (BLASTp) of the SadABC (a, b and c) complex and YceI transporter (d) among isolates from the Microbacterium genus (strains BR1, C488, SDZm4 and CJ77), Arthrobacter genus (strains D2 and D4) and strain GP Figure S8: Amino acid alignment with MUSCLE [122] of Acyl-CoA domains: Nterminal (a), middle (b) and C-terminal (c); between SadA and SadB homologs in Microbacterium sp. BR1, Arthrobacter sp. D2 and D4 and strain GP (SadB1: D3X82_00235; SadB2: D3X82_03160). Conserved regions within SadA and SadB and highlighted in green and conserved regions shared between all proteins are marked with an asterisk Figure S9: Close-up of the substrate-binding pocket of XiaF (PDB: 5LVW) bound to FADH and indole obtained by Kugel et al. [90]. FADH is the co-factor, indole the substrate and S121 and I237 are the residues that are modified in SadA of Microbacterium sp. BR1 and strain GP. The ribbon (a) and electrostatic surface potential (b) diagrams have been prepared with PyMol [149]. In b negative potential is shown in red and positive potential in blue.