Exploiting gene regulation as an approach to identify, analyze and utilize the biosynthetic pathways of the glycopeptide ristomycin A and the zincophore [S,S]-EDDS in Amycolatopsis japonicum

The microbial secondary metabolism is a rich source for valuable products that have found their way into various clinical and industrial applications. A particularly productive bacterial genus for the discovery of natural products is Amycolatopsis. The most frequently reported type of secondary metabolites produced by this genus, are glycopeptide antibiotics like balhimycin or the medically relevant vancomycin. In contrast to most other members of the Amycolatopsis genus, Amycolatopsis japonicum was never described to produce any product with antibacterial activity. This strain however is known to synthesize the chelating agent ethylenediamine-disuccinate ([S,S]-EDDS), a biodegradable EDTA isomer in response to zinc deficiency. This zinc responsive repression of [S,S]-EDDS production indicates that it contributes to zinc uptake and that it belongs to the rarely described physiological group of the zincophores. Combining excellent chelating properties with the accessibility to biodegradation, [S,S]-EDDS is considered as a sustainable chelating agent, possessing the potential to replace EDTA and other environmentally threatening chelating agents in various applications. In this study, two distinct molecular genetic strategies were developed and implemented to activate the biosynthesis of the glycopeptide antibiotic ristomycin A or to identify the [S,S]-EDDS biosynthetic genes in Amycolatopsis japonicum, respectively. Genetic evaluation of the Amycolatopsis antibiotic biosynthetic potential indicated that A. japonicum might has the capability to produce a glycopeptide antibiotic. Since the biosynthesis of the predicted glycopeptide was not inducible by variations in culture conditions, a molecular genetic approach was employed to activate its production. Heterologous expression of the characterized pathway specific activator Bbr, naturally inducing the balhimycin biosynthesis in A. balhimycina, also induced the synthesis of a bioactive substance by A. japonicum. The bioactivity could be assigned to the production of ristomycin A, a highly glycosylated peptide antibiotic which is used as compound in diagnostic kits to detect widespread hereditary coagulation disorders. Full sequencing of the A. japonicum genome and its computational analysis led to the identification of the corresponding biosynthetic gene cluster which is directing the biosynthesis of ristomycin A. Such computational genome analyses by various bioinformatic tools are nowadays standardized applied strategies to identify secondary metabolite gene clusters. These approaches however failed in the identification of the [S,S]-EDDS biosynthetic genes. This required the development of a new approach which relies on the assumption that the zinc repressed biosynthesis of [S,S]-EDDS is regulated by a zinc responsive regulatory element. Therefore, the major zinc responsive transcriptional regulator of A. japonicum (Zur) was characterized in detail. Zur regulates the expression of the high affinity zinc uptake system ZnuABC by binding to a specific DNA binding sequence. The screening of the A. japonicum genome for further Zur regulated genes by using this deduced Zur binding sequence led to the identification of the operon aesA-D. Extensive transcriptional analyses and band shift assays revealed that aesA-D is zinc responsively regulated by Zur and involved in [S,S]-EDDS biosynthesis, as shown by inactivation studies. The [S,S]-EDDS biosynthesis was uncoupled from zinc repression by deleting zur. This mutant sets the stage to establish a sustainable [S,S]-EDDS production process without limits formerly imposed by zinc repression. The strategy to awake predicted silent gene clusters by using a characterized regulator as well as the strategy to identify new biosynthetic genes by characterizing an environmental signal-sensing regulator enabled the isolation of novel biosynthetic pathways in A. japonicum. Both approaches follow the joint concept to exploit knowledge of regulatory pathways and have the prospect to be generally applicable in order to guide future detection of new natural products.Der mikrobielle Sekundärmetabolismus ist eine reichhaltige Quelle für Naturstoffe, von denen viele klinische beziehungsweise industrielle Anwendung gefunden haben. Die Gattung Amycolatopsis ist für die Synthese vieler Naturstoffe bekannt. Beispielsweise werden viele Glykopeptid-Antibiotika, wie das klinisch relevante Vancomycin oder das Balhimycin, von Stämmen dieser Gattung produziert. Im Gegensatz dazu wurde der Stamm Amycolatopsis japonicum nie als Produzent einer biologisch aktiven Substanz beschrieben. Dieser Stamm produziert jedoch unter Zinkmangelbedingungen das EDTA-Isomer Ethylendiamindisuccinat ([S,S]-EDDS). Diese zinkabhängige [S,S]-EDDS Produktion lässt darauf schließen, dass [S,S]-EDDS ein Zinkophor ist, das an der Zinkaufnahme beteiligt ist. [S,S]-EDDS weist Komplexbildungseigenschaften auf, die mit denen von EDTA vergleichbar sind. Im Gegensatz zu EDTA ist [S,S]-EDDS jedoch biologisch abbaubar. Die weite industrielle Anwendung von EDTA in Kombination mit dessen Unzugänglichkeit für biologische Abbauprozesse führt zu einer umweltgefährdenden EDTA-Persistenz in aquatischen Lebensräumen. Der Naturstoff [S,S]-EDDS ist deshalb ein nachhaltiger EDTA Ersatz mit einem verbesserten ökologischen Fingerabdruck. In dieser Arbeit wurden zwei molekulargenetische Strategien entwickelt, um die Biosynthese des Glykopeptid-Antibiotikums Ristomycin A zu aktivieren und um die [S,S]-EDDS-Biosynthese-Gene in A. japonicum zu identifizieren. Untersuchungen des genetischen Potenzials der Gattung Amycolatopsis ließen vermuten, dass auch A. japonicum die Fähigkeit besitzt, ein Glykopeptid-Antibiotikum zu synthetisieren. Um dieses nicht exprimierte, sogenannte „stille Gencluster“ zu aktivieren, wurde ein molekulargenetischer Ansatz verwendet, bei dem der Biosynthese-spezifische Aktivator Bbr heterolog in A. japonicum exprimiert wurde. Bbr reguliert die Balhimycin-Biosynthese in Amycolatopsis balhimycina. In A. japonicum induzierte dessen Expression die Produktion von Ristomycin A, was durch HPLC-DAD, MS, MS/MS, HR-MS, und NMR-Analysen bestätigt werden konnte. Ristomycn A ist ein vielfach glykosyliertes Heptapeptid, das als Hauptwirkstoff in Diagnoseverfahren zur Bestimmung von angeborenen und weitverbreiteten Blutgerinnungsstörungen verwendet wird. Die Sequenzierung des A. japonicum Genoms und dessen computergestützte Auswertung führten zur Identifizierung des Biosynthese-Genclusters, das für die Synthese von Ristomycin A verantwortlich ist. Solche computergestützten Genomanalysen mittels verschiedenster bioinformatischen Plattformen werden heutzutage standardmäßig zur Identifizierung von Sekundärmetabolit-Gencluster angewandt, die bekannten Synthesemechanismen zugeordnet werden können. Allerdings konnten die [S,S]-EDDS-Biosynthese-Gene mit diesen Tools nicht entdeckt werden, was auf einen bislang nicht bekannten Biosynthesemechanismus hindeutet. Um diesen zu identifizieren, wurde ein neuer Ansatz entwickelt, der auf der Annahme beruht, dass die Zink-reprimierte [S,S]-EDDS-Biosynthese durch einen Zink-sensitiven Regulator gewährleistet wird. Die bakterielle Zink-Homöostase wird meistens durch den globalen Zink-spezifische Transkriptionsregulator Zur reguliert. Das Zur Protein von A. japonicum wurde identifiziert und detailliert charakterisiert. Es konnten gezeigt werden, dass ZurAj die Transkription des hoch affinen Zinkaufnahmesystems ZnuABCAj durch seine Zink-abhängige Bindung an spezifische DNA Bindesequenzen reguliert. Diese Zur-Bindesequenzen wurden verwendet, um das A. japonicum Genom nach weiteren, ZurAj regulierten, Genen zu durchsuchen. Dies führte zur Auffindung des aesA-D Operons. Umfangreiche Transkriptions-Untersuchungen ergaben, dass aesA-D Zink-abhängig von ZurAj reguliert wird. Die Beteiligung von aesA-D an der [S,S]-EDDS konnte durch Inaktivierungsversuche nachgewiesen werden. Zusätzlich führte die Deletion des Zinkregulators ZurAj (A. japonicum Δzur) dazu, dass auch in Gegenwart von hohen Zink-Konzentrationen [S,S]-EDDS in hohen Mengen produziert wird. A. japonicum Δzur ist eine erfolgversprechende Ausgangsbasis, um einen nachhaltigen und wirtschaftlich verwertbaren [S,S]-EDDS Produktionsprozess zu entwickeln, der keiner Limitierung durch negative Einflüsse von Zink unterliegt. Die Strategie, ein vorhergesagtes, stilles Gencluster durch die Expression eines spezifischen Regulators zu aktivieren, sowie auch die Strategie, neue Biosynthese-Gene durch die Charakterisierung eines globalen Regulators, der spezifische Umweltsignale wahrnimmt, zu identifizieren, ermöglichte die Charakterisierung neuer Naturstoffsynthesewege in A. japonicum. Beide Ansätze nutzen Erkenntnisse über regulatorische Mechanismen und besitzen das Potenzial zukünftig angewendet zu werden, um neue Naturstoffe und neue Synthesewege zu identifizieren

High-Throughput Cultivation for the Selective Isolation of Acidobacteria From Termite Nests

Microbial communities in the immediate environment of socialized invertebrates can help to suppress pathogens, in part by synthesizing bioactive natural products. Here we characterized the core microbiomes of three termite species (genus Coptotermes) and their nest material to gain more insight into the diversity of termite-associated bacteria. Sampling a healthy termite colony over time implicated a consolidated and highly stable microbiome, pointing toward the fact that beneficial bacterial phyla play a major role in termite fitness. In contrast, there was a significant shift in the composition of the core microbiome in one nest during a fungal infection, affecting the abundance of well-characterized Streptomyces species (phylum Actinobacteria) as well as less-studied bacterial phyla such as Acidobacteria. High-throughput cultivation in microplates was implemented to isolate and identify these less-studied bacterial phylogenetic group. Amplicon sequencing confirmed that our method maintained the bacterial diversity of the environmental samples, enabling the isolation of novel Acidobacteriaceae and expanding the list of cultivated species to include two strains that may define new species within the genera Terracidiphilus and Acidobacterium

Draft genome sequences of 21 <i>Pedobacter</i> strains isolated from amphibian specimens

The genomes of 21 Pedobacter strains isolated from the European salamander Salamandra salamandra and different Madagascan frog species were sequenced using Illumina sequencing. Here, we report their draft genome sequences (∼4.7-7.2 Mbp in size) to allow comparative genomics and taxonomic assignment of these strains.</p

Phosphorus speciation in the organic layer of two Swedish forest soils 13-24 years after wood ash and nitrogen application

Application of wood ash to forests can restore pools of phosphorus (P) and other nutrients, which are removed following whole tree harvesting. Yet, the mechanisms that affect the fate of ash-P in the organic layer are less well known. Previous research into the extent to which ash application leads to increased P solubility in the soil is contradictory. We combined synchrotron P K-edge XANES spectroscopy, mu-XRF microscopy, and chemical ex-tractions to examine the speciation and solubility of P. We studied organic horizons of two long-term field ex-periments, Riddarhyttan (central Sweden), which had received 3, 6, and 9 Mg ash ha -1, and Ro center dot dalund (northern Sweden), where 3 Mg ash ha- 1 had been applied alone or combined with N every-three years since 2003. At the latter site, we also determined P in aboveground tree biomass. Overall, the ash application increased P in the organic layer by between 6 and 28 kg P ha -1, equivalent to 17-39 % of the initial P content in the applied ash. At Ro center dot dalund, there was 4.6 kg Ca-bound P ha- 1 (9.5 %) in the ash treatment compared to 1.6 kg ha- 1 in the ash + N treatment and < 0.4 kg ha- 1 in the N treatment and the control. At Riddarhyttan, only the treatment with the highest ash dose had residual Ca-bound P (3.8 kg ha -1). In contrast, the ash application increased Al-bound P (p < 0.001) with up to 15.6 kg P ha -1. Moreover, the ash increased Olsen-P by up to two times. There was a strong relationship between the concentrations of Olsen-P and Al-bound P (R2 = 0.83, p < 0.001) as well as Fe-bound P (R2 = 0.74, p = 0.003), suggesting that the ash application resulted in an increased amount of relatively soluble P associated with hydroxy-Al and hydroxy-Fe compounds. Further, there was an 18 % increase in P uptake by trees in the ash treatment. By contrast, repeated N fertilization, with or without ash, reduced Olsen-P. The lower P extractability was concomitant with a 39 % increase in plant P uptake in the N treatment, which indicates elevated P uptake in response to higher N availability. Hence, the application of wood ash increased Al-bound P, easily available P, and P uptake. N fertilization, while also increasing tree P uptake, instead decreased easily available P and did not cause a shift in soil P speciation

Phosphorus speciation in the organic layer of two Swedish forest soils 13–24 years after wood ash and nitrogen application

Application of wood ash to forests can restore pools of phosphorus (P) and other nutrients, which are removed following whole tree harvesting. Yet, the mechanisms that affect the fate of ash-P in the organic layer are less well known. Previous research into the extent to which ash application leads to increased P solubility in the soil is contradictory. We combined synchrotron P K-edge XANES spectroscopy, µ-XRF microscopy, and chemical extractions to examine the speciation and solubility of P. We studied organic horizons of two long-term field experiments, Riddarhyttan (central Sweden), which had received 3, 6, and 9 Mg ash ha−1, and Rödålund (northern Sweden), where 3 Mg ash ha−1 had been applied alone or combined with N every-three years since 2003. At the latter site, we also determined P in aboveground tree biomass. Overall, the ash application increased P in the organic layer by between 6 and 28 kg P ha−1, equivalent to 17–39 % of the initial P content in the applied ash. At Rödålund, there was 4.6 kg Ca-bound P ha−1 (9.5 %) in the ash treatment compared to 1.6 kg ha−1 in the ash + N treatment and < 0.4 kg ha−1 in the N treatment and the control. At Riddarhyttan, only the treatment with the highest ash dose had residual Ca-bound P (3.8 kg ha−1). In contrast, the ash application increased Al-bound P (p < 0.001) with up to 15.6 kg P ha−1. Moreover, the ash increased Olsen-P by up to two times. There was a strong relationship between the concentrations of Olsen-P and Al-bound P (R2 = 0.83, p < 0.001) as well as Fe-bound P (R2 = 0.74, p = 0.003), suggesting that the ash application resulted in an increased amount of relatively soluble P associated with hydroxy-Al and hydroxy-Fe compounds. Further, there was an 18 % increase in P uptake by trees in the ash treatment. By contrast, repeated N fertilization, with or without ash, reduced Olsen-P. The lower P extractability was concomitant with a 39 % increase in plant P uptake in the N treatment, which indicates elevated P uptake in response to higher N availability. Hence, the application of wood ash increased Al-bound P, easily available P, and P uptake. N fertilization, while also increasing tree P uptake, instead decreased easily available P and did not cause a shift in soil P speciation

Bioactive natural products from Bacteroidetes

The bacterial phylum Bacteroidetes harbors promising natural product producers. This review summarizes the bioactive compounds known to date and provides an overview if biosynthesis is elucidated and/or chemical synthesis is achieved.</jats:p

Phosphorus abundance and speciation in acid forest Podzols - Effect of postglacial weathering

The molecular speciation of phosphorus (P) in forest soils is of strategic importance for sustainable forest management. However, only limited information exists about soil P speciation in boreal forests. We combined P K-edge XANES spectroscopy, wet chemical P extractions, and X-ray diffraction analysis of soil minerals to investigate the vertical distribution of P species in seven podzolised forest soils differing in soil properties and climatic conditions. The results showed that the total P stock was on average, 4.0 g m(-2) in the Oe horizon, 9.5 g m(-2) in the A and E horizons, and substantially higher (117.5 g m(-2), and 109.3 g m(-2)) in the B and C horizons down to 80 cm depth, respectively. Although the Oe horizons contain a minor total P stock, 87% of it was stored as organic P. The composition of P species in the P-depleted A/E horizons was highly variable depending on the site. However, of the P stored in B and C horizons down to 80 cm, 58% was adsorbed P, mostly to Al, while apatite accounted for 25% of P, most of which was found in the C horizons. The apatite stocks in the A/E, B, and C horizons (down to 80 cm) accounted for 2.5%, 20%, and 77.2%, respectively, of the total apatite for all the mineral soils studied. These figures can be explained, first, by the dissolution of primary mineral apatite caused mainly by acidification. Second, P uptake by plants and microorganisms, and the associated formation of the Oe horizons, led to the formation of soil organic P. Further, the formation of organo-metal complexes and podzolization led to the translocation of P to the B horizons, where P accumulated mostly as P adsorbed to imogolite-type materials (e.g. allophane) and ferrihydrite, as shown by P K-edge XANES spectroscopy. In conclusion, this study shows that despite the young age of these soils (<15,000 years), most of the primary mineral apatite in the upper 30 cm has been transformed into organic P, and Fe-, Al-bound PO 4 . Moreover, the subsoil P, mainly consisting of adsorbed P to Al, and apatite, dominates the P inventory and probably serves as a long-term buffer of P