scholarly journals Natural Product Biosynthetic Gene Diversity in Geographically Distinct Soil Microbiomes

2012 ◽  
Vol 78 (10) ◽  
pp. 3744-3752 ◽  
Author(s):  
Boojala Vijay B. Reddy ◽  
Dimitris Kallifidas ◽  
Jeffrey H. Kim ◽  
Zachary Charlop-Powers ◽  
Zhiyang Feng ◽  
...  
Keyword(s):  
Species Diversity ◽  
Natural Product ◽  
Gene Sequence ◽  
Bacterial Species ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Type I ◽  
Adenylation Domain ◽  
Biosynthetic Gene ◽  
Bacterial Phyla

ABSTRACTThe number of bacterial species estimated to exist on Earth has increased dramatically in recent years. This newly recognized species diversity has raised the possibility that bacterial natural product biosynthetic diversity has also been significantly underestimated by previous culture-based studies. Here, we compare 454-pyrosequenced nonribosomal peptide adenylation domain, type I polyketide ketosynthase domain, and type II polyketide ketosynthase alpha gene fragments amplified from cosmid libraries constructed using DNA isolated from three different arid soils. While 16S rRNA gene sequence analysis indicates these cloned metagenomes contain DNA from similar distributions of major bacterial phyla, we found that they contain almost completely distinct collections of secondary metabolite biosynthetic gene sequences. When grouped at 85% identity, only 1.5% of the adenylation domain, 1.2% of the ketosynthase, and 9.3% of the ketosynthase alpha sequence clusters contained sequences from all three metagenomes. Although there is unlikely to be a simple correlation between biosynthetic gene sequence diversity and the diversity of metabolites encoded by the gene clusters in which these genes reside, our analysis further suggests that sequences in one soil metagenome are so distantly related to sequences in another metagenome that they are, in many cases, likely to arise from functionally distinct gene clusters. The marked differences observed among collections of biosynthetic genes found in even ecologically similar environments suggest that prokaryotic natural product biosynthesis diversity is, like bacterial species diversity, potentially much larger than appreciated from culture-based studies.

scholarly journals Discovery of Novel Biosynthetic Gene Cluster Diversity From a Soil Metagenomic Library

2020 ◽  
Vol 11 ◽  
Author(s):  
Alinne L. R. Santana-Pereira ◽  
Megan Sandoval-Powers ◽  
Scott Monsma ◽  
Jinglie Zhou ◽  
Scott R. Santos ◽  
...  
Keyword(s):  
Natural Product ◽  
Soil Microorganisms ◽  
Polyketide Synthase ◽  
Metagenomic Library ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Type I ◽  
Biosynthetic Gene ◽  
Pcr Screening ◽  
Natural Product Discovery

Soil microorganisms historically have been a rich resource for natural product discovery, yet the majority of these microbes remain uncultivated and their biosynthetic capacity is left underexplored. To identify the biosynthetic potential of soil microorganisms using a culture-independent approach, we constructed a large-insert metagenomic library in Escherichia coli from a topsoil sampled from the Cullars Rotation (Auburn, AL, United States), a long-term crop rotation experiment. Library clones were screened for biosynthetic gene clusters (BGCs) using either PCR or a NGS (next generation sequencing) multiplexed pooling strategy, coupled with bioinformatic analysis to identify contigs associated with each metagenomic clone. A total of 1,015 BGCs were detected from 19,200 clones, identifying 223 clones (1.2%) that carry a polyketide synthase (PKS) and/or a non-ribosomal peptide synthetase (NRPS) cluster, a dramatically improved hit rate compared to PCR screening that targeted type I polyketide ketosynthase (KS) domains. The NRPS and PKS clusters identified by NGS were distinct from known BGCs in the MIBiG database or those PKS clusters identified by PCR. Likewise, 16S rRNA gene sequences obtained by NGS of the library included many representatives that were not recovered by PCR, in concordance with the same bias observed in KS amplicon screening. This study provides novel resources for natural product discovery and circumvents amplification bias to allow annotation of a soil metagenomic library for a more complete picture of its functional and phylogenetic diversity.

scholarly journals The natural product biosynthetic potential of Red Sea nudibranch microbiomes

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10525
Author(s):  
Samar M. Abdelrahman ◽  
Nastassia V. Patin ◽  
Amro Hanora ◽  
Akram Aboseidah ◽  
Shimaa Desoky ◽  
...  
Keyword(s):  
Antitumor Activity ◽  
16S Rrna ◽  
Microbial Communities ◽  
Natural Product ◽  
Red Sea ◽  
High Throughput Sequencing ◽  
Marine Invertebrates ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Biosynthetic Gene

Background Antibiotic resistance is a growing problem that can be ameliorated by the discovery of novel drug candidates. Bacterial associates are often the source of pharmaceutically active natural products isolated from marine invertebrates, and thus, important targets for drug discovery. While the microbiomes of many marine organisms have been extensively studied, microbial communities from chemically-rich nudibranchs, marine invertebrates that often possess chemical defences, are relatively unknown. Methods We applied both culture-dependent and independent approaches to better understand the biochemical potential of microbial communities associated with nudibranchs. Gram-positive microorganisms isolated from nudibranchs collected in the Red Sea were screened for antibacterial and antitumor activity. To assess their biochemical potential, the isolates were screened for the presence of natural product biosynthetic gene clusters, including polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes, using PCR. The microbiomes of the nudibranchs were investigated by high-throughput sequencing of 16S rRNA amplicons. Results In screens against five model microorganisms, 51% of extracts displayed antimicrobial activity against more than one organism, and 19% exhibited antitumor activity against Ehrlich’s ascites carcinoma. Sixty-four percent of isolates contained PKS and NRPS genes, suggesting their genomes contain gene clusters for natural product biosynthesis. Thirty-five percent were positive for more than one class of biosynthetic gene. These strains were identified as belonging to the Firmicutes and Actinobacteria phyla via 16S rRNA gene sequencing. In addition, 16S rRNA community amplicon sequencing revealed all bacterial isolates were present in the uncultured host-associated microbiome, although they were a very small percentage of the total community. Taken together, these results indicate that bacteria associated with marine nudibranchs are potentially a rich source of bioactive compounds and natural product biosynthetic genes.

Distribution and diversity of glycocin biosynthesis gene clusters beyond Firmicutes

Glycobiology ◽  
2020 ◽  
Author(s):  
Vaidhvi Singh ◽  
Alka Rao
Keyword(s):  
Disulfide Bonds ◽  
Pathogenic Bacteria ◽  
Bacterial Species ◽  
Gene Clusters ◽  
Type I ◽  
Event Analysis ◽  
Bacterial Phyla ◽  
Spoilage Bacteria ◽  
Biosynthesis Gene ◽  
Promising Source

Abstract Glycocins are the ribosomally synthesized glycosylated bacteriocins discovered and characterized in Firmicutes, only. These peptides have antimicrobial activity against several pathogenic bacteria, including Streptococcus pyogenes , methicillin-resistant Staphylococcus aureus and food-spoilage bacteria Listeria monocytogenes. Glycocins exhibit immunostimulatory properties and make a promising source of new antibiotics and food preservatives akin to Nisin. Biochemical studies of Sublancin, Glycocin F, Pallidocin and ASM1 prove that the nested disulfide-bonds are essential for their bioactivities. Using in silico approach of genome mining coupled with manual curation, here we identify 220 new putative glycocin biosynthesis gene clusters (PGBCs) spread across 153 bacterial species belonging to seven different bacterial phyla. Based on gene composition, we have grouped these PGBCs into five distinct conserved cluster Types I–V. All experimentally identified glycocins belong to Type I PGBCs. From protein sequence based phylograms, tanglegrams, global similarity heat-maps and cumulative mutual information analysis, it appears that glycocins may have originated from closely related bacteriocins, whereas recruitment of cognate glycosyltransferases (GTs) might be an independent event. Analysis further suggests that GTs may have coevolved with glycocins in cluster-specific manner to define distinctive donor specificities of GTs or to contribute to glycocin diversity across these clusters. We further identify 162 hitherto unreported PGBCs wherein the corresponding product glycocins have three or less than three cysteines. Secondary structure predictions suggest that these putative glycocins may not form di-nested disulfide-bonds. Therefore, production of such glycocins in heterologous host Escherichia coli is feasible and may provide novel antimicrobial spectrum and or mechanism of action for varied applications.

Reclassification of Streptomyces costaricanus and Streptomyces phaeogriseichromatogenes as later heterotypic synonyms of Streptomyces murinus

2021 ◽  
Author(s):  
Hisayuki Komaki
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Biosynthetic Gene ◽  
Rrna Gene Sequence ◽  
Biosynthetic Gene Clusters ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

This study aimed to clarify the taxonomic relationships among Streptomyces costaricanus , Streptomyces graminearus, Streptomyces murinus and Streptomyces phaeogriseichromatogenes . These strains share the same 16S rRNA gene sequence. Multilocus sequence analysis revealed that S. costaricanus , S. murinus and S. phaeogriseichromatogenes belong to the same species, but S. graminearus does not. Digital DNA–DNA relatedness and average nucleotide identity among S. costaricanus, S. murinus and S. phaeogriseichromatogenes were 70.9–74.6% and 96.5–97.0 %, respectively. In addition to the previously reported phenotypic data, the presence of a similar set of secondary metabolite-biosynthetic gene clusters for polyketides and nonribosomal peptides supported the similarity among the three species. Therefore, S. costaricanus and S. phaeogriseichromatogenes should be reclassified as later heterotypic synonyms of S. murinus .

scholarly journals Nanopore-Sequencing Characterization of the Gut Microbiota of Melolontha melolontha Larvae: Contribution to Protection against Entomopathogenic Nematodes?

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 396
Author(s):  
Ewa Sajnaga ◽  
Marcin Skowronek ◽  
Agnieszka Kalwasińska ◽  
Waldemar Kazimierczak ◽  
Karolina Ferenc ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Entomopathogenic Nematodes ◽  
Bacterial Species ◽  
Antagonistic Activity ◽  
Rrna Gene ◽  
Nanopore Sequencing ◽  
Bacterial Phyla ◽  
Melolontha Melolontha

This study focused on the potential relationships between midgut microbiota of the common cockchafer Melolontha melolontha larvae and their resistance to entomopathogenic nematodes (EPN) infection. We investigated the bacterial community associated with control and unsusceptible EPN-exposed insects through nanopore sequencing of the 16S rRNA gene. Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant bacterial phyla within the complex and variable midgut microbiota of the wild M. melolontha larvae. The core microbiota was found to include 82 genera, which accounted for 3.4% of the total number of identified genera. The EPN-resistant larvae differed significantly from the control ones in the abundance of many genera belonging to the Actinomycetales, Rhizobiales, and Clostridiales orders. Additionally, the analysis of the microbiome networks revealed different sets of keystone midgut bacterial genera between these two groups of insects, indicating differences in the mutual interactions between bacteria. Finally, we detected Xenorhabdus and Photorhabdus as gut residents and various bacterial species exhibiting antagonistic activity against these entomopathogens. This study paves the way to further research aimed at unravelling the role of the host gut microbiota on the output of EPN infection, which may contribute to enhancement of the efficiency of nematodes used in eco-friendly pest management.

scholarly journals Salicylic Acid Biosynthesis and Metabolism: A Divergent Pathway for Plants and Bacteria

Biomolecules ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 705
Author(s):  
Awdhesh Kumar Mishra ◽  
Kwang-Hyun Baek
Keyword(s):  
Salicylic Acid ◽  
Bacterial Species ◽  
Shikimate Pathway ◽  
Gene Clusters ◽  
Defense Responses ◽  
Biosynthetic Gene ◽  
Biosynthetic Enzyme ◽  
Biosynthetic Gene Clusters ◽  
Acid Biosynthesis ◽  
Common Precursor

Salicylic acid (SA) is an active secondary metabolite that occurs in bacteria, fungi, and plants. SA and its derivatives (collectively called salicylates) are synthesized from chorismate (derived from shikimate pathway). SA is considered an important phytohormone that regulates various aspects of plant growth, environmental stress, and defense responses against pathogens. Besides plants, a large number of bacterial species, such as Pseudomonas, Bacillus, Azospirillum, Salmonella, Achromobacter, Vibrio, Yersinia, and Mycobacteria, have been reported to synthesize salicylates through the NRPS/PKS biosynthetic gene clusters. This bacterial salicylate production is often linked to the biosynthesis of small ferric-ion-chelating molecules, salicyl-derived siderophores (known as catecholate) under iron-limited conditions. Although bacteria possess entirely different biosynthetic pathways from plants, they share one common biosynthetic enzyme, isochorismate synthase, which converts chorismate to isochorismate, a common precursor for synthesizing SA. Additionally, SA in plants and bacteria can undergo several modifications to carry out their specific functions. In this review, we will systematically focus on the plant and bacterial salicylate biosynthesis and its metabolism.

scholarly journals Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia

2020 ◽  
Vol 295 (44) ◽  
pp. 14826-14839
Author(s):  
Serina L. Robinson ◽  
Barbara R. Terlouw ◽  
Megan D. Smith ◽  
Sacha J. Pidot ◽  
Timothy P. Stinear ◽  
...  
Keyword(s):  
Machine Learning ◽  
Natural Product ◽  
Global Analysis ◽  
Gene Clusters ◽  
Divergent Evolution ◽  
Acid Activation ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Predictive Tool ◽  
Wide Range

Enzymes that cleave ATP to activate carboxylic acids play essential roles in primary and secondary metabolism in all domains of life. Class I adenylate-forming enzymes share a conserved structural fold but act on a wide range of substrates to catalyze reactions involved in bioluminescence, nonribosomal peptide biosynthesis, fatty acid activation, and β-lactone formation. Despite their metabolic importance, the substrates and functions of the vast majority of adenylate-forming enzymes are unknown without tools available to accurately predict them. Given the crucial roles of adenylate-forming enzymes in biosynthesis, this also severely limits our ability to predict natural product structures from biosynthetic gene clusters. Here we used machine learning to predict adenylate-forming enzyme function and substrate specificity from protein sequences. We built a web-based predictive tool and used it to comprehensively map the biochemical diversity of adenylate-forming enzymes across >50,000 candidate biosynthetic gene clusters in bacterial, fungal, and plant genomes. Ancestral phylogenetic reconstruction and sequence similarity networking of enzymes from these clusters suggested divergent evolution of the adenylate-forming superfamily from a core enzyme scaffold most related to contemporary CoA ligases toward more specialized functions including β-lactone synthetases. Our classifier predicted β-lactone synthetases in uncharacterized biosynthetic gene clusters conserved in >90 different strains of Nocardia. To test our prediction, we purified a candidate β-lactone synthetase from Nocardia brasiliensis and reconstituted the biosynthetic pathway in vitro to link the gene cluster to the β-lactone natural product, nocardiolactone. We anticipate that our machine learning approach will aid in functional classification of enzymes and advance natural product discovery.

Sign in / Sign up

Export Citation Format

Share Document