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Natural Product Reports Jun 2024Covering: 2017.01 to 2023.11Natural products biosynthesized by myxobacteria are appealing due to their sophisticated chemical skeletons, remarkable biological... (Review)
Review
Covering: 2017.01 to 2023.11Natural products biosynthesized by myxobacteria are appealing due to their sophisticated chemical skeletons, remarkable biological activities, and intriguing biosynthetic enzymology. This review aims to systematically summarize the advances in the discovery methods, new structures, and bioactivities of myxobacterial NPs reported in the period of 2017-2023. In addition, the peculiar biosynthetic pathways of several structural families are also highlighted.
Topics: Biological Products; Myxococcales; Molecular Structure; Biosynthetic Pathways; Drug Discovery
PubMed: 38390645
DOI: 10.1039/d3np00062a -
The New Phytologist May 2024Arbuscular mycorrhizal fungi (AMF) transport substantial plant carbon (C) that serves as a substrate for soil organisms, a precursor of soil organic matter (SOM), and a...
Arbuscular mycorrhizal fungi (AMF) transport substantial plant carbon (C) that serves as a substrate for soil organisms, a precursor of soil organic matter (SOM), and a driver of soil microbial dynamics. Using two-chamber microcosms where an air gap isolated AMF from roots, we CO-labeled Avena barbata for 6 wk and measured the C Rhizophagus intraradices transferred to SOM and hyphosphere microorganisms. NanoSIMS imaging revealed hyphae and roots had similar C enrichment. SOM density fractionation, C NMR, and IRMS showed AMF transferred 0.77 mg C g of soil (increasing total C by 2% relative to non-mycorrhizal controls); 33% was found in occluded or mineral-associated pools. In the AMF hyphosphere, there was no overall change in community diversity but 36 bacterial ASVs significantly changed in relative abundance. With stable isotope probing (SIP)-enabled shotgun sequencing, we found taxa from the Solibacterales, Sphingobacteriales, Myxococcales, and Nitrososphaerales (ammonium oxidizing archaea) were highly enriched in AMF-imported C (> 20 atom%). Mapping sequences from C-SIP metagenomes to total ASVs showed at least 92 bacteria and archaea were significantly C-enriched. Our results illustrate the quantitative and ecological impact of hyphal C transport on the formation of potentially protective SOM pools and microbial roles in the AMF hyphosphere soil food web.
Topics: Mycorrhizae; Carbon; Minerals; Food Chain; Hyphae; Soil Microbiology; Carbon Isotopes; Avena; Organic Chemicals; Bacteria; Plant Roots; Soil
PubMed: 38358052
DOI: 10.1111/nph.19560 -
The Science of the Total Environment Apr 2024This study aimed to assess the potential impact of long-term chronic exposure (69 years) to naturally-occurring radionuclides (RNs) and heavy metals on microbial...
This study aimed to assess the potential impact of long-term chronic exposure (69 years) to naturally-occurring radionuclides (RNs) and heavy metals on microbial communities in sediment from a stream flowing through a watershed impacted by an ancient mining site (Rophin, France). Four sediment samples were collected along a radioactivity gradient (for U368 to 1710 Bq.Kg) characterized for the presence of the bioavailable fractions of radionuclides (Ra, Po), and trace metal elements (Th, U, As, Pb, Cu, Zn, Fe). Results revealed that the available fraction of contaminants was significant although it varied considerably from one element to another (0 % for As and Th, 5-59 % for U). Nonetheless, microbial communities appeared significantly affected by such chronic exposure to (radio)toxicities. Several microbial functions carried by bacteria and related with carbon and nitrogen cycling have been impaired. The high values of fungal diversity and richness observed with increasing downstream contamination (H' = 4.4 and Chao1 = 863) suggest that the community had likely shifted toward a more adapted/tolerant one as evidenced, for example, by the presence of the species Thelephora sp. and Tomentella sp. The bacterial composition was also affected by the contaminants with enrichment in Myxococcales, Acidovorax or Nostocales at the most contaminated points. Changes in microbial composition and functional structure were directly related to radionuclide and heavy metal contaminations, but also to organic matter which also significantly affected, directly or indirectly, bacterial and fungal compositions. Although it was not possible to distinguish the specific effects of RNs from heavy metals on microbial communities, it is essential to continue studies considering the available fraction of elements, which is the only one able to interact with microorganisms.
Topics: Metals, Heavy; Microbiota; Bacteria; Radioisotopes; France
PubMed: 38325491
DOI: 10.1016/j.scitotenv.2024.170692 -
International Journal of Systematic and... Feb 2024Three microaerophilic bacterial strains, designated SG22, SG63 and SG29 were isolated from paddy soils in PR China. Cells of these strains were Gram-staining-negative...
Three microaerophilic bacterial strains, designated SG22, SG63 and SG29 were isolated from paddy soils in PR China. Cells of these strains were Gram-staining-negative and long rod-shaped. SG22, SG63 and SG29 showed the highest 16S rRNA gene sequence similarities with the members of the genus . The results of phylogenetic and phylogenomic analysis also indicated that these strains clustered with members of the genus . The main respiratory menaquinone of SG22, SG63 and SG29 was MK-8 and the major fatty acids were iso-C, iso-C and C. SG22, SG29 and SG63 not only possessed iron reduction ability but also harboured genes () encoding nitrogenase. The genomic DNA G+C contents of SG22, SG63 and SG29 ranged from 73.3 to 73.5 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values between SG22, SG63 and SG29 and the closely related species of the genus were lower than the cut-off values (dDDH 70 % and ANI 95-96 %) for prokaryotic species delineation. On the basis of these results, strains SG22, SG63 and SG29 represent three novel species within the genus , for which the names sp. nov., sp. nov. and sp. nov., are proposed. The type strains are SG22 (= GDMCC 1.3185 = JCM 35581), SG63 (= GDMCC 1.2914 = JCM 35124) and SG29 (= GDMCC 1.2911 = JCM 35123).
Topics: Nitrogen-Fixing Bacteria; Ferric Compounds; Phylogeny; RNA, Ribosomal, 16S; Base Composition; Fatty Acids; Sequence Analysis, DNA; DNA, Bacterial; Bacterial Typing Techniques; Myxococcales; Nucleotides; Soil
PubMed: 38323900
DOI: 10.1099/ijsem.0.006268 -
Science (New York, N.Y.) Feb 2024The generation of cyclic oligoadenylates and subsequent allosteric activation of proteins that carry sensory domains is a distinctive feature of type III CRISPR-Cas...
The generation of cyclic oligoadenylates and subsequent allosteric activation of proteins that carry sensory domains is a distinctive feature of type III CRISPR-Cas systems. In this work, we characterize a set of associated genes of a type III-B system from that contains two caspase-like proteases, SAVED-CHAT and PCaspase (prokaryotic caspase), co-opted from a cyclic oligonucleotide-based antiphage signaling system (CBASS). Cyclic tri-adenosine monophosphate (AMP)-induced oligomerization of SAVED-CHAT activates proteolytic activity of the CHAT domains, which specifically cleave and activate PCaspase. Subsequently, activated PCaspase cleaves a multitude of proteins, which results in a strong interference phenotype in vivo in Taken together, our findings reveal how a CRISPR-Cas-based detection of a target RNA triggers a cascade of caspase-associated proteolytic activities.
Topics: Bacterial Proteins; Caspases; CRISPR-Associated Proteins; CRISPR-Cas Systems; Escherichia coli; RNA; Proteolysis; Myxococcales; Protein Domains
PubMed: 38301007
DOI: 10.1126/science.adk0378 -
Microbiology Spectrum Mar 2024In the past century, microbial natural products have proven themselves to be substantial and fruitful sources of anti-infectives. In addition to the well-studied...
In the past century, microbial natural products have proven themselves to be substantial and fruitful sources of anti-infectives. In addition to the well-studied Actinobacteria, understudied bacterial taxa like the Gram-negative myxobacteria have increasingly gained attention in the ongoing search for novel and biologically active natural products. In the course of a regional sampling campaign to source novel myxobacteria, we recently uncovered new myxobacterial strains MCy12716 and MCy12733 belonging to the clade. Early bioactivity screens of the bacterial extracts revealed the presence of bioactive natural products that were identified as angiolam A and several novel derivatives. Sequencing of the corresponding producer strains allowed the identification of the angiolam biosynthetic gene cluster, which was verified by targeted gene inactivation. Based on bioinformatic analysis of the biosynthetic gene cluster, a concise biosynthesis model was devised to explain angiolam biosynthesis. Importantly, novel angiolam derivatives uncovered in this study named angiolams B, C, and D were found to display promising antiparasitic activities against the malaria pathogen in the 0.3-0.8 µM range.IMPORTANCEThe COVID-19 pandemic and continuously emerging antimicrobial resistance (AMR) have recently raised awareness about limited treatment options against infectious diseases. However, the shortage of treatment options against protozoal parasitic infections, like malaria, is much more severe, especially for the treatment of so-called neglected tropical diseases. The detection of anti-parasitic bioactivities of angiolams produced by MCy12716 and MCy12733 displays the hidden potential of scarcely studied natural products to have promising biological activities in understudied indications. Furthermore, the improved biological activities of novel angiolam derivatives against and the evaluation of its biosynthesis display the opportunities of the angiolam scaffold on route to treat protozoal parasitic infections as well as possible ways to increase the production of derivatives with improved bioactivities.
Topics: Humans; Myxococcales; Antiparasitic Agents; Pandemics; Malaria, Falciparum; Plasmodium falciparum; Biological Products
PubMed: 38298128
DOI: 10.1128/spectrum.03689-23 -
PLoS Biology Jan 2024Ecological variation influences the character of many biotic interactions, but examples of predator-prey reversal mediated by abiotic context are few. We show that the...
Ecological variation influences the character of many biotic interactions, but examples of predator-prey reversal mediated by abiotic context are few. We show that the temperature at which prey grow before interacting with a bacterial predator can determine the very direction of predation, reversing predator and prey identities. While Pseudomonas fluorescens reared at 32°C was extensively killed by the generalist predator Myxococcus xanthus, P. fluorescens reared at 22°C became the predator, slaughtering M. xanthus to extinction and growing on its remains. Beyond M. xanthus, diffusible molecules in P. fluorescens supernatant also killed 2 other phylogenetically distant species among several examined. Our results suggest that the sign of lethal microbial antagonisms may often change across abiotic gradients in natural microbial communities, with important ecological and evolutionary implications. They also suggest that a larger proportion of microbial warfare results in predation-the killing and consumption of organisms-than is generally recognized.
Topics: Animals; Predatory Behavior; Antibiosis; Biological Evolution; Microbiota; Myxococcus xanthus
PubMed: 38261596
DOI: 10.1371/journal.pbio.3002454 -
Applied Microbiology and Biotechnology Dec 2024The myxobacteria are an attractive bioresource for bioactive compounds since the large size genome contains many biosynthetic gene clusters of secondary metabolites. The...
The myxobacteria are an attractive bioresource for bioactive compounds since the large size genome contains many biosynthetic gene clusters of secondary metabolites. The genome of the myxobacterium Melittangium boletus contains three biosynthetic gene clusters for lanthipeptide production. One of the gene clusters includes genes coding lanthipeptide precursor (melA), class II lanthipeptide synthetase (melM), and transporter (melT). The amino acid sequence of melA indicated similarity with that of known lanthipeptides mersacidin and lichenicidin A1 by the alignment. To perform heterologous production of new lanthipeptides, the expression vector containing the essential genes (melA and melM) was constructed by utilizing codon-optimized synthetic genes. The co-expression of two genes in the host bacterial cells of Escherichia coli BL21 (DE3) afforded new lanthipeptides named melittapeptins A-C. The structures of melittapeptins A-C including lanthionine/methyllanthionine bridge pattern were proposed based on protease digestion and MS/MS experiments. The native strain of M. boletus did not produce melittapeptins A-C, so heterologous production using the biosynthetic gene cluster was effective in obtaining the lanthipeptides. Melittapeptins A-C showed specific and potent antibacterial activity to the Gram-positive bacterium Micrococcus luteus. To the best of our knowledge, this is the first report of antibacterial lanthipeptides derived from myxobacterial origin. KEY POINTS: • New lanthipeptides melittapeptins were heterologously produced in Escherichia coli. • Melittapeptins showed specific antibacterial activity against Micrococcus luteus. • Melittapeptins were the first antibacterial lanthipeptides of myxobacterial origin.
Topics: Tandem Mass Spectrometry; Bacteriocins; Amino Acid Sequence; Anti-Bacterial Agents; Myxococcales; Escherichia coli
PubMed: 38229328
DOI: 10.1007/s00253-023-12834-4 -
Molecular Omics Feb 2024The outer membrane vesicles (OMVs) secreted by some Gram-negative bacteria contain RNA cargo, which can be introduced into target cells, affecting their cellular...
The outer membrane vesicles (OMVs) secreted by some Gram-negative bacteria contain RNA cargo, which can be introduced into target cells, affecting their cellular processes. To test whether the antimicrobial OMVs secreted by predatory myxobacteria might contain cargo RNA with a role in prey killing, we purified OMVs and cells from four different strains of spp. for RNA-seq transcriptome sequencing. Myxobacterial OMVs contained distinct sets of RNA molecules. The abundance of major cellular transcripts correlated strongly with their abundance in OMVs, suggesting non-specific packaging into OMVs. However, many major cellular transcripts were absent entirely from OMVs and some transcripts were found exclusively in OMVs, suggesting OMV RNA cargo loading is not simply a consequence of sampling the cellular transcriptome. Despite considerable variation in OMV RNA cargo between biological replicates, a small number of transcripts were found consistently in replicate OMV preparations. These 'core' OMV transcripts were often found in the OMVs from multiple strains, and sometimes enriched relative to their abundance in cellular transcriptomes. In addition to providing the first transcriptomes for myxobacterial OMVs, and the first cellular transcriptomes for three strains of spp., we highlight five transcripts for further study. These transcripts are 'core' for at least two of the three strains of studied, and encode two alkyl hydroperoxidase proteins (AhpC and AhpD), two ribosome-associated inhibitors (RaiA-like) and a DO-family protease. It will be interesting to test whether the transcripts serve a biological function within OMVs, potentially being transported into prey cells for translation into toxic proteins.
Topics: Myxococcus; RNA
PubMed: 38098456
DOI: 10.1039/d3mo00222e -
International Journal of Molecular... Oct 2023The co-culturing of microorganisms is a well-known strategy to study microbial interactions in the laboratory. This approach facilitates the identification of new...
The co-culturing of microorganisms is a well-known strategy to study microbial interactions in the laboratory. This approach facilitates the identification of new signals and molecules produced by one species that affects other species' behavior. In this work, we have studied the effects of the interaction of nine species (, , , , , , , , and ) with the predator bacteria , five of which (, , , , and ) induce mound formation of on complex media (Casitone Yeast extract (CYE) and Casitone tris (CTT); media on which does not form these aggregates under normal culture conditions. An in-depth study on - interactions (the strain producing the strongest effect) has allowed the identification of two siderophores produced by , demethylenenocardamine and nocardamine, responsible for this grouping effect over . Experiments using pure commercial nocardamine and different concentrations of FeSO show that iron depletion is responsible for the behavior of . Additionally, it was found that molecules, smaller than 3 kDa, produced by can induce the production of DK-xanthenes by .
Topics: Myxococcus; Myxococcus xanthus; Streptomyces; Microbial Interactions; Iron
PubMed: 37958645
DOI: 10.3390/ijms242115659