ABSTRACT
Geosmin may be the most familiar volatile compound, as it lends the earthy smell to soil. The compound is a member of the largest family of natural products, the terpenoids. The broad distribution of geosmin among bacteria in both terrestrial and aquatic environments suggests that this compound has an important ecological function, for example, as a signal (attractant or repellent) or as a protective specialized metabolite against biotic and abiotic stresses. While geosmin is part of our everyday life, scientists still do not understand the exact biological function of this omnipresent natural product. This minireview summarizes the current general observations regarding geosmin in prokaryotes and introduces new insights into its biosynthesis and regulation, as well as its biological roles in terrestrial and aquatic environments.
Subject(s)
Bacteria , Odorants , Odorants/analysis , Bacteria/genetics , Bacteria/metabolism , Naphthols/chemistry , Naphthols/metabolism , SensationABSTRACT
In this announcement, we present the set of putative terpene synthase (TS) gene fragments detected in a subseafloor sediment sample collected off Shimokita Peninsula, Japan. This data set contains sequences with 72 to 100% identity to TS from actinobacteria and cyanobacteria.
ABSTRACT
Plants are intimately connected with their associated microorganisms. Chemical interactions via natural products between plants and their microbial symbionts form an important aspect in host health and development, both in aquatic and terrestrial ecosystems. These interactions range from negative to beneficial for microbial symbionts as well as their hosts. Symbiotic microbes synchronize their metabolism with their hosts, thus suggesting a possible coevolution among them. Metabolites, synthesized from plants and microbes due to their association and coaction, supplement the already present metabolites, thus promoting plant growth, maintaining physiological status, and countering various biotic and abiotic stress factors. However, environmental changes, such as pollution and temperature variations, as well as anthropogenic-induced monoculture settings, have a significant influence on plant-associated microbial community and its interaction with the host. In this review, we put the prominent microbial metabolites participating in plant-microbe interactions in the natural terrestrial and aquatic ecosystems in a single perspective and have discussed commonalities and differences in these interactions for adaptation to surrounding environment and how environmental changes can alter the same. We also present the status and further possibilities of employing chemical interactions for environment remediation. Our review thus underlines the importance of ecosystem-driven functional adaptations of plant-microbe interactions in natural and anthropogenically influenced ecosystems and their possible applications.
Subject(s)
Ecosystem , Plants , Plants/metabolism , Adaptation, Physiological , Symbiosis , Environmental PollutionABSTRACT
Actinomycetes isolated from the marine environment often require the presence of seawater for their growth and/or morphological development. Here, we report the isolation and genome sequencing of marine sponge-derived Streptomyces sp. strain G-5 with such a seawater requirement.
ABSTRACT
Covering: through June 2021Terpenoids are the largest class of natural products recognised to date. While mostly known to humans as bioactive plant metabolites and part of essential oils, structurally diverse terpenoids are increasingly reported to be produced by microorganisms. For many of the compounds biological functions are yet unknown, but during the past years significant insights have been obtained for the role of terpenoids in microbial chemical ecology. Their functions include stress alleviation, maintenance of cell membrane integrity, photoprotection, attraction or repulsion of organisms, host growth promotion and defense. In this review we discuss the current knowledge of the biosynthesis and evolution of microbial terpenoids, and their ecological and biological roles in aquatic and terrestrial environments. Perspectives on their biotechnological applications, knowledge gaps and questions for future studies are discussed.
Subject(s)
Biological Products , Terpenes , Biological Products/chemistry , Ecology , Humans , Plants/metabolism , Terpenes/chemistryABSTRACT
Salinispora spp. are obligate marine actinomycetes reported mainly from shallow tropical and subtropical marine habitats. In this announcement, we present the isolation and draft genome sequence of Salinispora sp. strain H7-4 of a new 16S rDNA phylotype from deep-sea sediments of the Shikoku Basin.
ABSTRACT
In recent years, research in the field of Microbial Ecology has revealed the tremendous diversity and complexity of microbial communities across different ecosystems. Microbes play a major role in ecosystem functioning and contribute to the health and fitness of higher organisms. Scientists are now facing many technological and methodological challenges in analyzing these complex natural microbial communities. The advances in analytical and omics techniques have shown that microbial communities are largely shaped by chemical interaction networks mediated by specialized (water-soluble and volatile) metabolites. However, studies concerning microbial chemical interactions need to consider biotic and abiotic factors on multidimensional levels, which require the development of new tools and approaches mimicking natural microbial habitats. In this review, we describe environmental factors affecting the production and transport of specialized metabolites. We evaluate their ecological functions and discuss approaches to address future challenges in microbial chemical ecology (MCE). We aim to emphasize that future developments in the field of MCE will need to include holistic studies involving organisms at all levels and to consider mechanisms underlying the interactions between viruses, micro-, and macro-organisms in their natural environments.
Subject(s)
Bacteria/chemistry , Bacteria/metabolism , Ecosystem , Microbial Interactions , Bacteria/classification , Ecology , MicrobiotaABSTRACT
The genome of streptomycetes has the ability to produce many novel and potentially useful bioactive compounds, but most of which are not produced under standard laboratory cultivation conditions and are referred to as silent/cryptic secondary metabolites. Streptomyces lavendulae FRI-5 produces several types of bioactive compounds. However, this strain may also have the potential to biosynthesize more useful secondary metabolites. Here, we activated a silent biosynthetic gene cluster of an uncharacterized compound from S. lavendulae FRI-5 using heterologous expression. The engineered strain carrying the silent gene cluster produced compound 5, which was undetectable in the culture broth of S. lavendulae FRI-5. Using various spectroscopic analyses, we elucidated the chemical structure of compound 5 (named lavendiol) as a new diol-containing polyketide. The proposed assembly line of lavendiol shows a unique biosynthetic mechanism for polyketide compounds. The results of this study suggest the possibility of discovering more silent useful compounds from streptomycetes by genome mining and heterologous expression.
Subject(s)
Polyketides/metabolism , Streptomyces/genetics , Biosynthetic Pathways/genetics , Gene Expression , Genes, Fungal , Polyketides/chemistry , Secondary Metabolism , Streptomyces/metabolismABSTRACT
Bacteria belonging to the Streptomyces genus are characterized by a complex life cycle and the production of many bioactive secondary metabolites. Trace metals play an important role in streptomycete metabolism and development, however, their mechanism of action is not fully understood. In this review, we summarize the present knowledge on metallosensing regulators and trace metal action, as well as discuss the possible application in natural product discovery.
Subject(s)
Metals/pharmacology , Streptomyces/drug effects , Trace Elements/pharmacology , Streptomyces/growth & developmentABSTRACT
In the biosynthesis of diverse natural bioactive products the adenylation domains (ADs) of nonribosomal peptide synthetases select specific precursors from the cellular pool and activate them for further incorporation into the scaffold of the final compound. Therefore, the drug discovery programs employing PCR-based screening studies of microbial collections or metagenomic libraries often use AD-coding genes as markers of relevant biosynthetic gene clusters. However, due to significant sequence diversity of ADs, the conventional approach using only one primer pair in a single screening experiment could be insufficient for maximal coverage of AD abundance. In this study, the widely used primer pair A3F/A7R was compared with the newly designed aa194F/aa413R one by 454 pyrosequencing of two sets of actinomycete strains from highly dissimilar environments: subseafloor sediments and forest soil. Individually, none of the primer pairs was able to cover the overall diversity of ADs. However, due to slightly shifted specificity of the primer pairs, the total number and diversity of identified ADs were noticeably extended when both primer pairs were used in a single assay. Additionally, the efficiency of AD detection by different primer combinations was confirmed on the model of Salinispora tropica genomic DNA of known sequence.
Subject(s)
Actinobacteria/genetics , DNA Primers , High-Throughput Screening Assays , Peptide Synthases/genetics , Protein Interaction Domains and Motifs/genetics , Actinobacteria/classification , Actinobacteria/isolation & purification , Base Sequence , Consensus Sequence , Peptide Synthases/chemistry , Polymerase Chain Reaction , Position-Specific Scoring Matrices , Soil MicrobiologyABSTRACT
BACKGROUND: Distribution and evolutionary history of resistance genes in environmental actinobacteria provide information on intensity of antibiosis and evolution of specific secondary metabolic pathways at a given site. To this day, actinobacteria producing biologically active compounds were isolated mostly from soil but only a limited range of soil environments were commonly sampled. Consequently, soil remains an unexplored environment in search for novel producers and related evolutionary questions. RESULTS: Ninety actinobacteria strains isolated at contrasting soil sites were characterized phylogenetically by 16S rRNA gene, for presence of erm and ABC transporter resistance genes and antibiotic production. An analogous analysis was performed in silico with 246 and 31 strains from Integrated Microbial Genomes (JGI_IMG) database selected by the presence of ABC transporter genes and erm genes, respectively. In the isolates, distances of erm gene sequences were significantly correlated to phylogenetic distances based on 16S rRNA genes, while ABC transporter gene distances were not. The phylogenetic distance of isolates was significantly correlated to soil pH and organic matter content of isolation sites. In the analysis of JGI_IMG datasets the correlation between phylogeny of resistance genes and the strain phylogeny based on 16S rRNA genes or five housekeeping genes was observed for both the erm genes and ABC transporter genes in both actinobacteria and streptomycetes. However, in the analysis of sequences from genomes where both resistance genes occurred together the correlation was observed for both ABC transporter and erm genes in actinobacteria but in streptomycetes only in the erm gene. CONCLUSIONS: The type of erm resistance gene sequences was influenced by linkage to 16S rRNA gene sequences and site characteristics. The phylogeny of ABC transporter gene was correlated to 16S rRNA genes mainly above the genus level. The results support the concept of new specific secondary metabolite scaffolds occurring more likely in taxonomically distant producers but suggest that the antibiotic selection of gene pools is also influenced by site conditions.
Subject(s)
ATP-Binding Cassette Transporters/genetics , Actinobacteria/classification , Actinobacteria/genetics , Drug Resistance, Bacterial , Methyltransferases/genetics , Phylogeny , RNA, Ribosomal, 16S/genetics , Actinobacteria/drug effects , Actinobacteria/isolation & purification , Anti-Bacterial Agents/biosynthesis , Cluster Analysis , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Genes, rRNA , Molecular Sequence Data , Sequence Analysis, DNA , Soil MicrobiologyABSTRACT
In the biosynthesis of lincosamide antibiotics lincomycin and celesticetin, the amino acid and amino sugar units are linked by an amide bond. The respective condensing enzyme lincosamide synthetase (LS) is expected to be an unusual system combining nonribosomal peptide synthetase (NRPS) components with so far unknown amino sugar related activities. The biosynthetic gene cluster of celesticetin was sequenced and compared to the lincomycin one revealing putative LS coding ORFs shared in both clusters. Based on a bioassay and production profiles of S. lincolnensis strains with individually deleted putative LS coding genes, the proteins LmbC, D, E, F and V were assigned to LS function. Moreover, the newly recognized N-terminal domain of LmbN (LmbN-CP) was also assigned to LS as a NRPS carrier protein (CP). Surprisingly, the homologous CP coding sequence in celesticetin cluster is part of ccbZ gene adjacent to ccbN, the counterpart of lmbN, suggesting the gene rearrangement, evident also from still active internal translation start in lmbN, and indicating the direction of lincosamide biosynthesis evolution. The in vitro test with LmbN-CP, LmbC and the newly identified S. lincolnensis phosphopantetheinyl transferase Slp, confirmed the cooperation of the previously characterized NRPS A-domain LmbC with a holo-LmbN-CP in activation of a 4-propyl-L-proline precursor of lincomycin. This result completed the functional characterization of LS subunits resembling NRPS initiation module. Two of the four remaining putative LS subunits, LmbE/CcbE and LmbV/CcbV, exhibit low but significant homology to enzymes from the metabolism of mycothiol, the NRPS-independent system processing the amino sugar and amino acid units. The functions of particular LS subunits as well as cooperation of both NRPS-based and NRPS-independent LS blocks are discussed. The described condensing enzyme represents a unique hybrid system with overall composition quite dissimilar to any other known enzyme system.
Subject(s)
Cysteine/metabolism , Glycopeptides/metabolism , Inositol/metabolism , Lincomycin/biosynthesis , Lincosamides/biosynthesis , Peptide Synthases/metabolismABSTRACT
Subseafloor sediments present an untapped source of novel bacterial species with industrially important bioactivities. Subseafloor core samples collected during the Integrated Ocean Drilling Program Expeditions 315, 316, and 331 and stored in Kochi Core Center at -80 °C for 1 to 4 years were used for cultivation-based study of viable actinomycetes. In total, more than 100 actinomycete-like colonies were isolated from two deep-frozen subseafloor sediment samples. Isolated actinomycetes showed close similarity to known Actinotalea, Dietzia, Gordonia, Isoptericola, Microbacterium, Nocardia, Rhodococcus, Pseudonocardia, Streptomyces, and Tsukamurella species and were halotolerant. Bioactivity assays revealed that two of the isolates were producing potent antibacterial compound(s) and one isolate was having antifungal activity. Our study demonstrated that deep-frozen subseafloor core samples could be a potential source of viable actinomycetes, which may be used in drug discovery.
Subject(s)
Actinobacteria/isolation & purification , Biodiversity , Geologic Sediments/microbiology , Actinobacteria/chemistry , Actinobacteria/classification , Actinobacteria/genetics , Cold Temperature , DNA, Bacterial/genetics , Geologic Sediments/chemistry , RNA, Ribosomal, 16S/geneticsABSTRACT
A linear polyketide, amphirionin-4 (1), has been isolated from cultivated algal cells of the marine dinoflagellate Amphidinium species. The structure was elucidated on the basis of detailed analyses of 1D and 2D NMR data, and the absolute configurations of C-4 and C-8 were determined using the modified Mosher's method. Amphirionin-4 (1) exhibited extremely potent proliferation-promoting activity on murine bone marrow stromal ST-2 cells (950% promotion) at a concentration of 0.1 ng/mL.
Subject(s)
Dinoflagellida/chemistry , Mesenchymal Stem Cells/drug effects , Polyketides/isolation & purification , Polyketides/pharmacology , Animals , Cell Proliferation/drug effects , Macrolides/chemistry , Marine Biology , Mice , Molecular Structure , Nuclear Magnetic Resonance, Biomolecular , Polyketides/chemistryABSTRACT
The biosynthetic gene cluster of porothramycin, a sequence-selective DNA alkylating compound, was identified in the genome of producing strain Streptomyces albus subsp. albus (ATCC 39897) and sequentially characterized. A 39.7 kb long DNA region contains 27 putative genes, 18 of them revealing high similarity with homologous genes from biosynthetic gene cluster of closely related pyrrolobenzodiazepine (PBD) compound anthramycin. However, considering the structures of both compounds, the number of differences in the gene composition of compared biosynthetic gene clusters was unexpectedly high, indicating participation of alternative enzymes in biosynthesis of both porothramycin precursors, anthranilate, and branched L-proline derivative. Based on the sequence analysis of putative NRPS modules Por20 and Por21, we suppose that in porothramycin biosynthesis, the methylation of anthranilate unit occurs prior to the condensation reaction, while modifications of branched proline derivative, oxidation, and dimethylation of the side chain occur on already condensed PBD core. Corresponding two specific methyltransferase encoding genes por26 and por25 were identified in the porothramycin gene cluster. Surprisingly, also methyltransferase gene por18 homologous to orf19 from anthramycin biosynthesis was detected in porothramycin gene cluster even though the appropriate biosynthetic step is missing, as suggested by ultra high-performance liquid chromatography-diode array detection-mass spectrometry (UHPLC-DAD-MS) analysis of the product in the S. albus culture broth.
Subject(s)
Anthramycin/analogs & derivatives , Bacterial Proteins/genetics , Multigene Family , Streptomyces/genetics , Streptomyces/metabolism , Anthramycin/biosynthesis , Anthramycin/chemistry , Bacterial Proteins/metabolism , Molecular Sequence Data , Molecular Structure , Sequence Analysis , Streptomyces/chemistryABSTRACT
The obligate marine actinobacterium Salinispora arenicola was successfully cultured from temperate sediments of the Pacific Ocean (Tosa Bay, offshore Kochi Prefecture, Japan) with the highest latitude of 33°N ever reported for this genus. Based on 16S rRNA gene sequence analysis, the Tosa Bay strains are of the same phylotype as the type strain S. arenicola NBRC105043. However, sequence analysis of their 16S-23S rRNA intergenic spacer (ITS) revealed novel sequence variations. In total, five new ITS sequences were discovered and further phylogenetic analyses using gyrase B and rifamycin ketosynthase (KS) domain sequences supported the phylogenetic diversity of the novel Salinispora isolates. Screening of secondary metabolite genes in these strains revealed the presence of KS1 domain sequences previously reported in S. arenicola strains isolated from the Sea of Cortez, the Bahamas and the Red Sea. Moreover, salinosporamide biosynthetic genes, which are highly homologous to those of Bahamas-endemic S. tropica, were detected in several Tosa Bay isolates, making this report the first detection of salinosporamide genes in S. arenicola. The results of this study provide evidence of a much wider geographical distribution and secondary metabolism diversity in this genus than previously projected.
Subject(s)
Bacterial Proteins/genetics , Geologic Sediments/microbiology , Micromonosporaceae/genetics , Micromonosporaceae/isolation & purification , Seawater/microbiology , Bacterial Proteins/metabolism , DNA, Bacterial/genetics , DNA, Ribosomal Spacer/genetics , Genetic Variation , Geologic Sediments/chemistry , Micromonosporaceae/classification , Micromonosporaceae/metabolism , Molecular Sequence Data , Phylogeny , RNA, Ribosomal, 16S/genetics , Seawater/chemistry , Secondary Metabolism , TemperatureABSTRACT
The SAV3339 (SdrA) protein of Streptomyces avermitilis, a member of the DeoR family of regulators, was assessed to determine its in vivo function by gene knockdown through the use of cis-encoded noncoding RNA and knockout of the sdrA gene. These analyses revealed that SdrA represents another class of Streptomyces regulator that controls morphological development and antibiotic production.
Subject(s)
Anti-Bacterial Agents/biosynthesis , Gene Expression Regulation, Bacterial , Streptomyces/cytology , Streptomyces/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Gene Knockdown Techniques , Gene Knockout Techniques , Streptomyces/geneticsABSTRACT
Clinically used lincosamide antibiotic lincomycin incorporates in its structure 4-propyl-L-proline (PPL), an unusual amino acid, while celesticetin, a less efficient related compound, makes use of proteinogenic L-proline. Biochemical characterization, as well as phylogenetic analysis and homology modelling combined with the molecular dynamics simulation were employed for complex comparative analysis of the orthologous protein pair LmbC and CcbC from the biosynthesis of lincomycin and celesticetin, respectively. The analysis proved the compared proteins to be the stand-alone adenylation domains strictly preferring their own natural substrate, PPL or L-proline. The LmbC substrate binding pocket is adapted to accommodate a rare PPL precursor. When compared with L-proline specific ones, several large amino acid residues were replaced by smaller ones opening a channel which allowed the alkyl side chain of PPL to be accommodated. One of the most important differences, that of the residue corresponding to V306 in CcbC changing to G308 in LmbC, was investigated in vitro and in silico. Moreover, the substrate binding pocket rearrangement also allowed LmbC to effectively adenylate 4-butyl-L-proline and 4-pentyl-L-proline, substrates with even longer alkyl side chains, producing more potent lincosamides. A shift of LmbC substrate specificity appears to be an integral part of biosynthetic pathway adaptation to the PPL acquisition. A set of genes presumably coding for the PPL biosynthesis is present in the lincomycin--but not in the celesticetin cluster; their homologs are found in biosynthetic clusters of some pyrrolobenzodiazepines (PBD) and hormaomycin. Whereas in the PBD and hormaomycin pathways the arising precursors are condensed to another amino acid moiety, the LmbC protein is the first functionally proved part of a unique condensation enzyme connecting PPL to the specialized amino sugar building unit.
Subject(s)
Bacterial Proteins/chemistry , Dipeptides/chemistry , Evolution, Molecular , Lincomycin/biosynthesis , Lincosamides/biosynthesis , Molecular Dynamics Simulation , Streptomyces/enzymology , Lincomycin/chemistry , Lincosamides/chemistry , Protein Structure, TertiaryABSTRACT
A fingerprinting method for chemical screening of microbial metabolites, potential antibiotics, in spent cultivation broths is described. The method is based on high-throughput ultra-high-performance liquid chromatography (UHPLC) separation with UV detection (photodiode array detector). Thirteen antibiotic standards and four cultivation broths were used for the method development. The comparison of ten liquid-liquid and solid phase extraction protocols for sample clean-up and pre-concentration revealed that Oasis HLB C18 sorbent gives the best recoveries. The Acquity BEH C18 chromatographic column was chosen for the samples separation with respect to its universality, selectivity, efficiency and robustness. The method is presented by two 3D fingerprints for every sample that was obtained under different, acidic and alkaline, UHPLC conditions. The acidic mobile phase consisted of 0.5% phosphoric acid with methanol and the alkaline mobile phase of 1mM ammonium formate, pH 9 with acetonitrile. Each pair of 3D fingerprints includes the following physico-chemical information: polarity (retention time), presence and characterization of chromophores (UV spectra), compound concentration (detector response), and acid-base properties (influence of different pH of the aqueous parts of mobile phases on retention times). The sample extraction and method validation were assessed with relative standard deviation (RSD) of 0.5, 5.0 and 20.0% for retention times, peak areas and minor compound peak areas, respectively.
Subject(s)
Actinobacteria/metabolism , Anti-Bacterial Agents/analysis , Chromatography, High Pressure Liquid/methods , Culture Media/chemistry , Actinobacteria/chemistry , Anti-Bacterial Agents/metabolism , Culture Media/metabolism , Fermentation , Solid Phase ExtractionABSTRACT
The lincomycin biosynthetic gene lmbX was deleted in Streptomyces lincolnensis ATCC 25466, and deletion of this gene led to abolition of lincomycin production. The results of complementation experiments proved the blockage in the biosynthesis of lincomycin precursor 4-propyl-L-proline. Feeding this mutant strain with precursor derivatives resulted in production of 4'-butyl-4'-depropyllincomycin and 4'-pentyl-4'-depropyllincomycin in high titers and without lincomycin contamination. Moreover, 4'-pentyl-4'-depropyllincomycin was found to be more active than lincomycin against clinical Staphylococcus isolates with genes determining low-level lincosamide resistance.