6 research outputs found
Additional file 5: Table S3. of Quinones are growth factors for the human gut microbiota
Quinone-induced bacteria have a disrupted menaquinone biosynthesis pathway, while related organisms not induced by quinones have a complete pathway. The genomes of the nearest type strains of all E. coli- or quinone-induced cultured bacteria were surveyed manually for the presence of a functional menaquinone biosynthesis pathway using a published dataset [24]. All organisms induced by E. coli or quinones in earlier co-culture experiments were missing large components of the menaquinone biosynthesis pathway, while Bacteroides species not induced by E. coli or quinones were predicted to have complete menaquinone biosynthetic capabilities. No strains were found to have predicted copies of genes in the futalosine pathway, an alternative means to generate menaquinone. ubiE/menG: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase; menF = Menaquinone-specific isochorismate synthase; menD = 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase; menH = 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase; menY = 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate dehydrogenase; menC = o-succinylbenzoate synthase; menE = o-succinylbenzoic acid--CoA ligase; menB = Naphthoate synthase. menI = 1,4-dihydroxy-2-naphthoyl-CoA hydrolase; menJ = 1,4-dihydroxy-2-naphthoyl-CoA hydrolasein (putative); menA = 1,4-dihydroxy-2-naphthoate polyprenyltransferase; mqnA = Chorismate dehydratase; mqnE = Aminodeoxyfutalosine synthase; mqnC = Cyclic dehypoxanthine futalosine synthase; mqnD = 1,4-dihydroxy-6-naphthoate synthase; mqnZ = 1,4-dihydroxy-6-naphthoate synthase (alternative); mqnX = Aminodeoxyfutalosine deaminase; mqnB = Futalosine hydrolase (EC 3.2.2.26); mtnN = Aminodeoxyfutalosine nucleosidase; mqnL = 1,4-dihydroxy-6-naphthoate carboxy-lyase, UbiD-like; mqnM = 2-heptaprenyl-1,4-naphthoquinone methyltransferase; mqnP = 1,4-naphthoquinone polyprenyltransferase. Data was taken and modified from Racheev, 2016. (XLSX 10 kb
Additional file 4: Figure S2. of Quinones are growth factors for the human gut microbiota
Single deletions in the E. coli menaquinone-8 pathway, but not ubiquinone-8 pathway, prevented growth induction of KLE1255. Single deletion mutants for all genes involved in ubiquinone-8 and menaquinone-8 biosynthesis were tested for induction capabilities of KLE1255. Red boxes indicate E. coli mutants with impaired growth induction capabilities for KLE1255. (PNG 364Ă‚Â kb
Additional file 6: Table S4. of Quinones are growth factors for the human gut microbiota
Quinone-dependent and control strains have predicted anaerobic reductases. The genomes of nearest type strains of all E. coli- or quinone-induced cultured bacteria were surveyed manually for the presence of individual annotated anaerobic reductases using a published dataset [35]. All analyzed organisms have the genetic capability to utilize anaerobic reductases for anaerobic respiration. Arx = Arsenate reductase; Cyd = Cytochrome bd reductase; Dms = Dimethyl sulfoxide reductase; Dsr = Sulfite reductase; Frd = Fumarate reductase; Nap = Nitrate reductase; Nar = Nitrate reductase; Nrf = Nitrite reductase; Phs = Thiosulfate reductase; Psr = Polysulfite reductase; Tor = Trimethylamine N-oxide reductase; Ttr = Tetrathionate reductase; Ynf = Selenate reductase. Data was taken and modified from Racheev, 2014 [35] and Ravcheev, 2016 [24]. (XLSX 8 kb
Additional file 3: Figure S1. of Quinones are growth factors for the human gut microbiota
Single deletions in the E. coli chorismate biosynthesis pathway prevented growth induction of KLE1255. Single deletion mutants for all genes involved in chorismate biosynthesis were tested for induction capabilities of KLE1255. Red boxes indicate E. coli mutants with impaired growth induction capabilities for KLE1255. (PNG 449Ă‚Â kb
Additional file 1: Table S1. of Quinones are growth factors for the human gut microbiota
Entire chromosome E. coli deletion library reformatted. 283 strains were first compiled from E. coli small-, medium-, and large-scale deletion libraries to cover all non-essential genes of the E. coli genome. Strains were taken from the Keio collection [19] and two larger deletion libraries [20, 21]. (XLS 36Ă‚Â kb
Additional file 2: Table S2. of Quinones are growth factors for the human gut microbiota
Strains identified in the E. coli knockout screen unable to induce the growth of KLE1255. Includes information on which genes are absent for each clone. (XLSX 18Ă‚Â kb