Pathways and substrate-specific regulation of amino acid degradation in Phaeobacter inhibens DSM 17395 (archetype of the marine Roseobacter clade)

Summary Combining omics and enzymatic approaches, catabolic routes of nine selected amino acids (tryptophan, phenylalanine, methionine, leucine, isoleucine, valine, histidine, lysine and threonine) were elucidated in substrate‐adapted cells of Phaeobacter inhibens DSM 17395 (displaying conspicuous m...

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Published inEnvironmental microbiology Vol. 16; no. 1; pp. 218 - 238
Main Authors Drüppel, Katharina, Hensler, Michael, Trautwein, Kathleen, Koßmehl, Sebastian, Wöhlbrand, Lars, Schmidt-Hohagen, Kerstin, Ulbrich, Marcus, Bergen, Nils, Meier-Kolthoff, Jan P., Göker, Markus, Klenk, Hans-Peter, Schomburg, Dietmar, Rabus, Ralf
Format Journal Article
LanguageEnglish
Published Oxford Blackwell Publishing Ltd 01.01.2014
Blackwell
Subjects
Amino Acids - metabolism
Animal and plant ecology
Animal, plant and microbial ecology
Bacterial Proteins - genetics
Bacterial Proteins - metabolism
Biological and medical sciences
Fundamental and applied biological sciences. Psychology
General aspects
Metabolic Networks and Pathways
Microbial ecology
Roseobacter - genetics
Roseobacter - metabolism
Sea water ecosystems
Species Specificity
Synecology
Degradation
Marine environment
Substrate
Bacteria
Aminoacid
Roseobacter
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Summary:Summary Combining omics and enzymatic approaches, catabolic routes of nine selected amino acids (tryptophan, phenylalanine, methionine, leucine, isoleucine, valine, histidine, lysine and threonine) were elucidated in substrate‐adapted cells of Phaeobacter inhibens DSM 17395 (displaying conspicuous morphotypes). The catabolic network [excluding tricarboxylic acid (TCA) cycle] was reconstructed from 71 genes (scattered across the chromosome; one‐third newly assigned), with 69 encoded proteins and 20 specific metabolites identified, and activities of 10 different enzymes determined. For example, Ph. inhibens DSM 17395 does not degrade lysine via the widespread saccharopine pathway but might rather employ two parallel pathways via 5‐aminopentanoate or 2‐aminoadipate. Tryptophan degradation proceeds via kynurenine and 2‐aminobenzoate; the latter is metabolized as known from Azoarcus evansii. Histidine degradation is analogous to the Pseudomonas‐type Hut pathway via N‐formyl‐l‐glutamate. For threonine, only one of the three genome‐predicted degradation pathways (employing threonine 3‐dehydrogenase) is used. Proteins of the individual peripheral degradation sequences in Ph. inhibens DSM 17395 were apparently substrate‐specifically formed contrasting the non‐modulated TCA cycle enzymes. Comparison of genes for the reconstructed amino acid degradation network in Ph. inhibens DSM 17395 across 27 other complete genomes of Roseobacter clade members revealed most of them to be widespread among roseobacters.
Bibliography:Deutsche Forschungsgemeinschaft - No. SFB TRR 51
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ArticleID:EMI12276
Fig. S1. Growth curves of P. inhibens DSM 17395 with the nine selected amino acids and succinate.Fig. S2. Proteomic data, RT-PCR data and genomic predictions for tryptophan degradation in P. inhibens DSM 17395.Fig. S3. Proteomic data and genomic predictions for phenylalanine degradation in P. inhibens DSM 17395.Fig. S4. Proteomic data and genomic predictions for methionine degradation in P. inhibens DSM 17395.Fig. S5. Proteomic data and genomic predictions for leucine degradation in P. inhibens DSM 17395.Fig. S6. Proteomic data and genomic predictions for isoleucine degradation in P. inhibens DSM 17395.Fig. S7. Proteomic data and genomic predictions for valine degradation in P. inhibens DSM 17395.Fig. S8. Proteomic data and genomic predictions for histidine degradation in P. inhibens DSM 17395.Fig. S9. Proteomic data and genomic predictions for lysine degradation in P. inhibens DSM 17395.Fig. S10. Proteomic data and genomic predictions for threonine degradation in P. inhibens DSM 17395.Fig. S11. Separation of membrane protein-enriched and soluble fractions of P. inhibens DSM 17395 by SDS-PAGE.Fig. S12. Proteomic data and genomic predictions for the TCA cycle of P. inhibens DSM 17395.Fig. S13. Proteomic data and genomic predictions for the gluconeogenesis of P. inhibens DSM 17395.Fig. S14. Proteomic data and genomic predictions for the ethylmalonyl-CoA pathway of P. inhibens DSM 17395.Fig. S15. Phylogenetic 16S, 23S, 5S rRNA gene-based tree of 28 Roseobacter clade members and 4 non-roseobacter Rhodobacterales. Branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from maximum-likelihood (left) and maximum-parsimony (right) bootstrapping, if larger than 60%.Table S1. Growth of P. inhibens DSM 17395 with the 20 proteinogenic amino acids.Table S2. Number of proteins assigned to the degradation of the nine selected amino acids in P. inhibens DSM 17395 based on the original genome annotation and their proteogenomics-based refinement in this study.Table S3. Compilation of genes of P. inhibens DSM 17395 with reannotated or refined functional prediction.Table S4. Intracellular metabolites of P. inhibens DSM 17395 identified in this study.Table S5. Extracellular metabolites of P. inhibens DSM 17395 identified in this study.Table S6. Specific activities (in U mg−1) of key enzymes for the degradation of the nine selected amino acids and of selected TCA cycle enzymes determined in crude extracts of substrate-adapted cells of P. inhibens DSM 17395.Table S7. Genes for sensory/regulatory proteins of P. inhibens DSM 17395 affiliating with the degradation of the nine studied amino acids.Table S8. Genes of P. inhibens DSM 17395 used for comparative genomics are compiled together with their locus tags, EC numbers and corresponding enzyme names.
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ISSN:1462-2912
1462-2920
DOI:10.1111/1462-2920.12276