Additional file 1: Figure S1. of Exploring the genomic traits of fungus-feeding bacterial genus Collimonas
Creators: name: Chunxu Song
name: Schmidt, Ruth
name: Jager, Victor De
name: Krzyzanowska, Dorota
name: Esmer Jongedijk
name: Cankar, Katarina
name: Beekwilder, Jules
name: Veen, Anouk Van
name: Boer, Wietse De
name: Veen, Johannes Van
name: Garbeva, Paolina
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: Plant Biology

description: Phylogenetic tree based on 16S rDNA depicting the relationships of sequenced strains of Collimonas. Underneath the genes are the module and domain organization of PKS or NRPS genes. The domains are as follows: C, condensation; A, adenylation; T, thiolation; E, Epimerization; TE, thioesterification; CAL, Co-enzyme A ligase domain; KS, Ketosynthase domain; AT, Acyltransferase domain; ER, Enoylreductase domain; KR, Ketoreductase domain; DH, Dehydratase domain; and ACP, Acyl-carrier protein domain. Underneath the domains are the amino acids that are incorporated into the peptide moiety. The number associated with the amino acid refers to the position of the amino acid in the peptide chain. Figure S2. Synteny of the six Collimonas genomes. Pairwise alignments of genomes were generated using Mauve (A) C. fungivorans (B) C. pratensis (C) C. arenae and (D) The three species together. Colored outlined blocks surround the regions of the genomic sequence that aligned to another genome. The colored bars inside the blocks are related to the level of sequence similarities. The analysis showed that the highest number of rearrangements was evident between all the three species. Figure S3. (A) Conserved gene clusters for type II (T2SSa/T2SSb), III (T3SSa/T3SSb) and VI (T6SS) secretion systems identified in Collimonas strains. Quorum sensing assays of the Collimonas strains. Quorum sensing activity of Collimonas strains Ter331, Ter6, Ter91, Ter291, Ter10 and Ter282 with indicator strain (B) C. violaceum CV026 and (C) A. tumefaciens NT1 (outer colonies). A purple (C. violaceum CV026) or blue (A. tumefaciens NT1) pigment produced by the indicator strains is indicative of quorum sensing activity of the tested strains. Figure S4. Organization of the orphan gene clusters and predicted amino acid compositions. Figure S5. Amino acid alignment of Collimonas terpene synthases CPter91_2617 and CPter291_2730 with previously characterised bacterial terpene synthases. The Collimonas terpene synthases were aligned with the Streptomyces exfoliatus pentalenene synthase (Se_pentalenene), S. coelicolor geosmin synthase (Sc_geosmin, 336 amino acids of the N-terminus), Streptosporangium roseum epi-cubenol synthase (Sr_epicubenol), S. avermitilis avermitilol synthase (Sa_avermitilol), S. clavuligerus 1,8-cineole synthase (Scl_cineole) and Pseudomonas fluorescens 2-methylenebornane synthase (Pf_methylenebornane). The characteristic terpene synthase divalent metal-binding motifs, namely the acidic amino acid-rich motif and the NSE triad, are boxed. Figure S6. GC-MS chromatograms of Ter91 terpene cyclase incubated with different substrates, and mass spectra of major products. The GC-MS chromatograms of Ter291 were identical to Ter91 (data not shown). Empty vector chromatograms shows products from a control enzyme extract (pACYC-duet-1). (A) Ter91 terpene synthase with GPP. TIC 100 % = 1.19E4. Major monoterpene product at RT 6.79, identified as Beta-pinene by authentic standard. (B) Ter91 terpene synthase with GGPP. TIC 100 % = 2.12E4. Major diterpene product at RT 20.24, identified as 13-epimanool comparison of mass spectra to the NIST8 library. (PDF 570 kb)