Non-canonical substrates for terpene synthases in bacteria are synthesized by a new family of methyltransferases

FEMS Microbiology Reviews ◽

10.1093/femsre/fuab024 ◽

2021 ◽

Author(s):

Birgit Piechulla ◽

Chi Zhang ◽

Daniela Eisenschmidt-Bönn ◽

Feng Chen ◽

Nancy Magnus

Keyword(s):

Structural Diversity ◽

Gene Clusters ◽

Chemical Diversity ◽

Terpenoid Biosynthesis ◽

Bacterial Genomes ◽

Terpene Synthases ◽

Sequence Comparisons ◽

New Family ◽

Organismal Fitness ◽

Isoprenyl Diphosphate

ABSTRACT The ‘biogenetic isoprene rule’, formulated in the mid 20th century, predicted that terpenoids are biosynthesized via polymerization of C5 isoprene units. The polymerizing enzymes have been identified to be isoprenyl diphosphate synthases, products of which are catalyzed by terpene synthases (TPSs) to achieve vast structural diversity of terpene skeletons. Irregular terpenes (e.g, C11, C12, C16 and C17) are also frequently observed, and they have presumed to be synthesized by the modification of terpene skeletons. This review highlights the exciting discovery of an additional route to the biosynthesis of irregular terpenes which involves the action of a newly discovered enzyme family of isoprenyl diphosphate methyltransferases (IDMTs). These enzymes methylate, and sometimes cyclize, the classical isoprenyl diphosphate substrates to produce modified, non-canonical substrates for specifically evolved TPSs. So far, this new pathway has been found only in bacteria. Structure and sequence comparisons of the IDMTs strongly indicate a conservation of their active pockets and overall topologies. Some bacterial IDMTs and TPSs appear in small gene clusters, which may facilitate future mining of bacterial genomes for identification of irregular terpene-producing enzymes. The IDMT-TPS route for terpenoid biosynthesis presents another example of nature's ingenuity in creating chemical diversity, particularly terpenoids, for organismal fitness.

Download Full-text

Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool

10.1101/494286 ◽

2018 ◽

Cited By ~ 3

Author(s):

Javier Santos-Aberturas ◽

Govind Chandra ◽

Luca Frattaruolo ◽

Rodney Lacret ◽

Thu H. Pham ◽

...

Keyword(s):

Genome Mining ◽

Gene Clusters ◽

Chemical Diversity ◽

Bioactive Molecules ◽

Post Translational Modification ◽

Biosynthetic Gene Clusters ◽

New Family ◽

The Family ◽

Modified Peptides ◽

Mining Tool

ABSTRACTThe rational discovery of new specialized metabolites by genome mining represents a very promising strategy in the quest for new bioactive molecules. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a major class of natural product that derive from genetically encoded precursor peptides. However, RiPP gene clusters are particularly refractory to reliable bioinformatic predictions due to the absence of a common biosynthetic feature across all pathways. Here, we describe RiPPER, a new tool for the family-independent identification of RiPP precursor peptides and apply this methodology to search for novel thioamidated RiPPs in Actinobacteria. Until now, thioamidation was believed to be a rare post-translational modification, which is catalyzed by a pair of proteins (YcaO and TfuA) in Archaea. In Actinobacteria, the thioviridamide-like molecules are a family of cytotoxic RiPPs that feature multiple thioamides, and it has been proposed that a YcaO-TfuA pair of proteins also catalyzes their formation. Potential biosynthetic gene clusters encoding YcaO and TfuA protein pairs are common in Actinobacteria but the chemical diversity generated by these pathways is almost completely unexplored. A RiPPER analysis reveals a highly diverse landscape of precursor peptides encoded in previously undescribed gene clusters that are predicted to make thioamidated RiPPs. To illustrate this strategy, we describe the first rational discovery of a new family of thioamidated natural products, the thiovarsolins from Streptomyces varsoviensis.

Download Full-text

Genome sequence of Aspergillus flavus A7, a marine-derived fungus with antibacterial activity

Genome ◽

10.1139/gen-2020-0066 ◽

2020 ◽

Author(s):

Yaru Gao ◽

Xinyang Du ◽

Huanhuan Li ◽

Ying Wang

Keyword(s):

Aspergillus Flavus ◽

Structural Diversity ◽

Gene Clusters ◽

Illumina Miseq ◽

Physicochemical Characteristics ◽

Antibacterial Activities ◽

Chemical Diversity ◽

Genome Comparison ◽

Marine Microorganisms ◽

Sequencing Platform

Due to the specific properties of the marine environment, marine microorganisms have exclusive physicochemical characteristics that are different from those of terrestrial microorganisms, which can produce various secondary metabolites (SMs) with considerable structural diversity and biological activity. In this study, three strains of coepiphytic Aspergillus with potential antibacterial activities, A7 (Aspergillus flavus), B27 (Aspergillus flavipes) and R12 (Aspergillus sydowii), were isolated from the South China Sea. Via the Illumina MiSeq sequencing platform, the genomes of the three strains were sequenced, and genome comparison showed the highest diversity of the biosynthetic gene clusters (BGCs) in A7. Meanwhile, a comparison of physiological and genomic characteristics between A7 and other Aspergillus flavus strains demonstrated the superior environmental adaptability of A7, which is apparently consistent with the genetic richness of BGCs. By assigning reads to known BGCs, putative BGCs were allocated in A7 that corresponded to various SMs, including naphthopyrone, pyranonigrin E, cyclopiazonic acids, etc. Based on gene homology analysis, we surmise that a region is involved in the biosynthesis of ustiloxin-like RiPPs, a less thoroughly studied SM in fungi. Our results provide genetic information for the investigation of marine Aspergillus sp., which may help to elucidate their chemical diversity and adaptive strategies.

Download Full-text

A global survey of specialized metabolic diversity encoded in bacterial genomes

10.1101/2021.08.11.455920 ◽

2021 ◽

Author(s):

Athina Gavriilidou ◽

Satria A Kautsar ◽

Nestor Zaburannyi ◽

Daniel Krug ◽

Rolf Mueller ◽

...

Keyword(s):

Secondary Metabolites ◽

Evolutionary History ◽

Gene Clusters ◽

Chemical Diversity ◽

Metabolic Diversity ◽

Bacterial Genomes ◽

Biosynthetic Gene Clusters ◽

Taxonomic Rank ◽

New Antibiotics ◽

Biosynthetic Machinery

Bacterial secondary metabolites have been studied for decades for their usefulness as drugs, such as antibiotics. However, the identification of new structures has been decelerating, in part due to rediscovery of known compounds. Meanwhile, multi-resistant pathogens continue to emerge, urging the need for new antibiotics. It is unclear how much chemical diversity exists in Nature and whether discovery efforts should be focused on established antibiotic producers or rather on understudied taxa. Here, we surveyed around 170,000 bacterial genomes as well as several thousands of Metagenome Assembled Genomes (MAGs) for their diversity in Biosynthetic Gene Clusters (BGCs) known to encode the biosynthetic machinery for producing secondary metabolites. We used two distinct algorithms to provide a global overview of the biosynthetic diversity present in the sequenced part of the bacterial kingdom. Our results indicate that only 3% of genomic potential for natural products has been experimentally discovered. We connect the emergence of most biosynthetic diversity in evolutionary history close to the taxonomic rank of genus. Despite enormous differences in potential among taxa, we identify Streptomyces as by far the most biosynthetically diverse based on currently available data. Simultaneously, our analysis highlights multiple promising high-producing taxas that have thus far escaped investigation.

Download Full-text

Correlational networking guides the discovery of cryptic proteases for lanthipeptide maturation

10.1101/2021.07.26.453782 ◽

2021 ◽

Author(s):

Dan Xue ◽

Ethan A. Older ◽

Zheng Zhong ◽

Zhuo Shang ◽

Nanzhu Chen ◽

...

Keyword(s):

Biological Function ◽

Gene Clusters ◽

Biosynthetic Gene ◽

Class Iii ◽

Bacterial Genomes ◽

Biosynthetic Gene Clusters ◽

Drug Candidates ◽

New Class ◽

New Family ◽

Global Correlation

Proteases required for lanthipeptide maturation are not encoded in many of their respective biosynthetic gene clusters. These cryptic proteases hinder the study and application of lanthipeptides as promising drug candidates. Here, we establish a global correlation network bridging the gap between lanthipeptide precursors and cryptic proteases. Applying our analysis to 161,954 bacterial genomes, we establish 6,041 correlations between precursors and cryptic proteases, with 91 prioritized. We use network predictions and co-expression analysis to reveal a previously missing protease for the maturation of class I lanthipeptide paenilan. We further discover widely distributed bacterial M16B metallopeptidases of previously unclear biological function as a new family of lanthipeptide proteases. We show the involvement of a pair of bifunctional M16B proteases in the production of new class III lanthipeptides with high substrate specificity. Together, these results demonstrate the strength of our correlational networking approach to the discovery of cryptic lanthipeptide proteases.

Download Full-text

Recapitulation of the evolution of biosynthetic gene clusters reveals hidden chemical diversity on bacterial genomes

10.1101/020503 ◽

2015 ◽

Cited By ~ 6

Author(s):

Pablo Cruz-Morales ◽

Christian E. Martínez-Guerrero ◽

Marco A. Morales-Escalante ◽

Luis Yáñez-Guerra ◽

Johannes Florian Kopp ◽

...

Keyword(s):

Natural Products ◽

Chemical Space ◽

Streptomyces Coelicolor ◽

Genome Mining ◽

Gene Clusters ◽

Biosynthetic Gene Cluster ◽

Chemical Diversity ◽

Biosynthetic Gene ◽

Bacterial Genomes ◽

Biosynthetic Gene Clusters

AbstractNatural products have provided humans with antibiotics for millennia. However, a decline in the pace of chemical discovery exerts pressure on human health as antibiotic resistance spreads. The empirical nature of current genome mining approaches used for natural products research limits the chemical space that is explored. By integration of evolutionary concepts related to emergence of metabolism, we have gained fundamental insights that are translated into an alternative genome mining approach, termed EvoMining. As the founding assumption of EvoMining is the evolution of enzymes, we solved two milestone problems revealing unprecedented conversions. First, we report the biosynthetic gene cluster of the ‘orphan’ metabolite leupeptin in Streptomyces roseus. Second, we discover an enzyme involved in formation of an arsenic-carbon bond in Streptomyces coelicolor and Streptomyces lividans. This work provides evidence that bacterial chemical repertoire is underexploited, as well as an approach to accelerate the discovery of novel antibiotics from bacterial genomes.

Download Full-text

A biaryl-linked tripeptide from Planomonospora leads to widespread class of minimal RiPP gene clusters

10.1101/2020.07.21.214643 ◽

2020 ◽

Author(s):

Mitja M. Zdouc ◽

Mohammad M. Alanjary ◽

Guadalupe S. Zarazúa ◽

Sonia I. Maffioli ◽

Max Crüsemann ◽

...

Keyword(s):

Cytochrome P450 ◽

Structural Diversity ◽

Gene Clusters ◽

Bioinformatic Analysis ◽

Cytochrome P450 Monooxygenases ◽

Bacterial Genomes ◽

P450 Monooxygenase ◽

Linked Gene ◽

P450 Monooxygenases ◽

Microbial Natural Products

AbstractMicrobial natural products impress by their bioactivity, structural diversity and ingenious biosynthesis. While screening the rare actinobacterial genus Planomonospora, cyclopeptides 1A and 1B were discovered, featuring an unusual Tyr-His biaryl-bridging across a tripeptide scaffold, with the sequences N-acetyl-Tyr-Tyr-His (1A) and N-acetyl-Tyr-Phe-His (1B). Genome analysis of the 1A producing strain pointed to-wards a ribosomal synthesis of 1A, from a pentapeptide precursor encoded by the tiny 18-nucleotide gene bycA, to our knowledge the smallest gene ever reported. Further, biaryl instalment is performed by the closely linked gene bycB, encoding a cytochrome P450 monooxygenase. Biosynthesis of 1A was confirmed by heterologous production in Streptomyces, yielding the mature product. Bioinformatic analysis of related cytochrome P450 monooxygenases indicated that they constitute a widespread family of pathways, associated to 5-aa coding sequences in approximately 200 (actino)bacterial genomes, all with potential for a biaryl linkage between amino acids 1 and 3. We propose the name biarylicins for this newly discovered family of RiPPs.

Download Full-text

Bioactive Metabolites From Acid-Tolerant Fungi in a Thai Mangrove Sediment

Frontiers in Microbiology ◽

10.3389/fmicb.2020.609952 ◽

2021 ◽

Vol 11 ◽

Author(s):

Hai Gao ◽

Yanan Wang ◽

Qiao Luo ◽

Liyuan Yang ◽

Xingxing He ◽

...

Keyword(s):

Acid Stress ◽

A549 Cells ◽

Gene Clusters ◽

Chemical Diversity ◽

Bioactive Metabolites ◽

Mangrove Sediment ◽

Mangrove Sediments ◽

Sequence Comparisons ◽

Chemical Screening ◽

Acid Tolerant

Despite being potentially useful extremophile resources, there have been few reports on acid-tolerant fungi and their bioactive metabolites. Acidophilic/aciduric fungi (n = 237) were isolated from Thai mangrove sediments in an acidic medium. Using fungal identification technology (including morphologic observation, chemical screening, and sequence comparisons) all the isolates were identified and 41 representative isolates were selected for analysis of the phylogenetic relationships (ITS rDNA, β-tubulin, calmodulin, and actin gene sequences). There were seven genera identified – Penicillium; Aspergillus; Talaromyces; Cladosporium; Allophoma; Alternaria; and Trichoderma – in four taxonomic orders of the phylum Ascomycota, and Penicillium, Aspergillus, and Talaromyces were the dominant genera. Acidity tolerance was evaluated and 95% of the isolates could grow under extremely acidic conditions (pH 2). Six strains were classed as acidophilic fungi that cannot survive under pH 7, all of which had an extraordinarily close genetic relationship and belonged to the genus Talaromyces. This is the first report on the acidophilic characteristics of this genus. The antimicrobial, anti-tumor, and antiviral activities of the fermentation extracts were evaluated. Nearly three-quarters of the extracts showed cytotoxic activity, while less than a quarter showed antimicrobial or anti-H1N1 activity. The typical aciduric fungus Penicillium oxalicum OUCMDZ-5207 showed similar growth but completely different chemical diversity at pH 3 and 7. The metabolites of OUCMDZ-5207 that were obtained only at pH 3 were identified as tetrahydroauroglaucin (1), flavoglaucin (2), and auroglaucin (3), among which auroglaucin showed strong selective inhibition of A549 cells with an IC50 value of 5.67 μM. These results suggest that acid stress can activate silent gene clusters to expand the diversity of secondary metabolites, and the bioprospecting of aciduric/acidophilic microorganism resources in Thai mangrove sediments may lead to the discovery of compounds with potential medicinal applications.

Download Full-text

Meroterpenoids: A Comprehensive Update Insight on Structural Diversity and Biology

Biomolecules ◽

10.3390/biom11070957 ◽

2021 ◽

Vol 11 (7) ◽

pp. 957

Author(s):

Mamona Nazir ◽

Muhammad Saleem ◽

Muhammad Imran Tousif ◽

Muhammad Aijaz Anwar ◽

Frank Surup ◽

...

Keyword(s):

Amino Acids ◽

Secondary Metabolites ◽

Biological Effects ◽

Structural Diversity ◽

Chemical Diversity ◽

Biosynthetic Pathways ◽

Natural Sources ◽

Hybrid Compounds ◽

Anti Inflammatory

Meroterpenoids are secondary metabolites formed due to mixed biosynthetic pathways which are produced in part from a terpenoid co-substrate. These mixed biosynthetically hybrid compounds are widely produced by bacteria, algae, plants, and animals. Notably amazing chemical diversity is generated among meroterpenoids via a combination of terpenoid scaffolds with polyketides, alkaloids, phenols, and amino acids. This review deals with the isolation, chemical diversity, and biological effects of 452 new meroterpenoids reported from natural sources from January 2016 to December 2020. Most of the meroterpenoids possess antimicrobial, cytotoxic, antioxidant, anti-inflammatory, antiviral, enzyme inhibitory, and immunosupressive effects.

Download Full-text

Recombinant transfer in the basic genome ofEscherichia coli

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1510839112 ◽

2015 ◽

Vol 112 (29) ◽

pp. 9070-9075 ◽

Cited By ~ 59

Author(s):

Purushottam D. Dixit ◽

Tin Yau Pang ◽

F. William Studier ◽

Sergei Maslov

Keyword(s):

Common Ancestor ◽

Recipient Cell ◽

Gene Clusters ◽

Selective Advantage ◽

Last Common Ancestor ◽

Genome Sequences ◽

Bacterial Genomes ◽

Basic Genome ◽

Single Base Pair ◽

Generalized Transduction

An approximation to the ∼4-Mbp basic genome shared by 32 strains ofEscherichia colirepresenting six evolutionary groups has been derived and analyzed computationally. A multiple alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ∼90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single base-pair mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly between genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome pairs have one or two recombinant transfers of length ∼40–115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. Moderately diverged genome pairs (0.4–1% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying lengths throughout the basic genome, whereas more highly diverged pairs within an evolutionary group or pairs between evolutionary groups having >1.3% SNPs have few clonal matches longer than a few kilobase pairs. Many recombinant transfers appear to incorporate fragments of the entering DNA produced by restriction systems of the recipient cell. A simple computational model can closely fit the data. Most recombinant transfers seem likely to be due to generalized transduction by coevolving populations of phages, which could efficiently distribute variability throughout bacterial genomes.

Download Full-text