Expanding our understanding of sequence-function relationships of type II polyketide biosynthetic gene clusters: bioinformatics-guided identification of Frankiamicin A from Frankia sp. EAN1pec

Is Pseudofrankia, the non-nitrogen-fixing and/or non-nodulating actinorhizal nodule dweller, mutualistic or parasitic? Insights from genome-predictive analysis

This study re-evaluates Pseudofrankia strains, traditionally regarded as parasitic dwellers of actinorhizal root nodules due to their inability to fix nitrogen (Fix -) and/or nodulate (Nod -), as potential plant growth-promoting bacteria (PGPB). We compared plant growth-promoting traits (PGPTs) between Pseudofrankia strains, including one newly sequenced strain BMG5.37 in this study and typical (Fix + /Nod +) Frankia, Protofrankia, and Parafrankia, as well as non-frankia actinorhizal species Nocardia and Micromonospora, and the phytopathogenic Streptomyces. Although lacking nitrogen-fixing genes typically found in mutualistic Frankiaceae strains, Pseudofrankia may compensate through predicted pathways for denitrification and nitrate utilization. Functional profiling suggests potential for phosphorus solubilization, gibberellin production, and vitamin metabolism, as well as bioremediation of pollutants. Pseudofrankia strains are predicted to show moderate resistance to heavy metals, with a stronger tolerance to arsenic and tellurium compared to Frankia. Furthermore, they are anticipated to exhibit significant biotic and abiotic stress resistance, including oxidative and osmotic stress. Predictive data also indicate that Pseudofrankia strains may have root colonization abilities and may play a role in plant signaling and phytohormone production, particularly in auxin and gibberellin pathways. Secretion systems, especially CE-Type VI, are predicted to be highly developed in Pseudofrankia, suggesting potential for effective plant interactions. These findings position Pseudofrankia strains as promising candidates for plant growth promotion, although experimental validation and the integration of transcriptomic or proteomic data are needed to confirm these predictions.

ActVI-ORFA directs metabolic flux towards actinorhodin by preventing intermediate degradation

The biosynthetic pathway of actinorhodin in Streptomyces coelicolor A3(2) has been studied for decades as a model system of type II polyketide biosynthesis. The actinorhodin biosynthetic gene cluster includes a gene, actVI-orfA, that encodes a protein that belongs to the nuclear transport factor-2-like (NTF-2-like) superfamily. The function of this ActVI-ORFA protein has been a long-standing question in this field. Several hypothetical functions, including pyran ring cyclase, enzyme complex stability enhancer, and gene transcription regulator, have been proposed for ActVI-ORFA in previous studies. However, although the recent structural analysis of ActVI-ORFA revealed a solvent-accessible cavity, the protein displayed structural differences to the well-characterized cyclase SnoaL and did not possess a DNA-binding domain. The obtained crystal structure facilitates an inspection of the previous hypotheses regarding the function of ActVI-ORFA. In the present study, we investigated the effects of a series of actVI-orfA test plasmids with different mutations in an established vector/host system. Time-course analysis of dynamic metabolism profiles demonstrated that ActVI-ORFA prevented formation of shunt metabolites and may have a metabolic flux directing function, which shepherds the flux of unstable intermediates towards actinorhodin. The expression studies resulted in the isolation and structure elucidation of two new shunt metabolites from the actinorhodin pathway. Next, we utilized computational modeling to probe the active site of ActVI-ORFA and confirmed the importance of residues R76 and H78 in the flux directing functionality by expression studies. This is the first time such a function has been observed for a member of NTF-2-like superfamily in Streptomyces secondary metabolism.

Frankia nepalensis sp. nov., a non-infective non-nitrogen-fixing isolate from root nodules of Coriaria nepalensis Wall

Strains CN4T, CN6, CN7 and CNm7 were isolated from root nodules of Coriaria nepalensis from Murree in Pakistan. They do not form root nodules on C. nepalensis nor on Alnus glutinosa although they deformed root hairs of Alnus. The colonies are bright red-pigmented, the strains form hyphae and sporangia but no N2-fixing vesicles and do not fix nitrogen in vitro. The peptidoglycan of strain CN4T contains meso-diaminopimelic acid; whole cell sugars consist of ribose, mannose, glucose, galactose and rhamnose. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unknown lipids represent the major polar lipids; MK-9(H4) and MK-9(H6) are the predominant menaquinones (>15 %), and iso-C16 : 0 and C17 : 1ω8c are the major fatty acids (>15 %). The results of comparative 16S rRNA gene sequence analyses indicated that strain CN4T is most closely related to Frankia saprophytica CN 3T. An MLSA phylogeny using amino acids sequences of AtpD, DnaA, FtsZ, Pgk and RpoB, assigned the strain to cluster 4 non-nodulating species, close to F. saprophytica CN 3T , Frankia asymbiotica M16386T and Frankia inefficax EuI1cT with 0.04 substitutions per site, while that value was 0.075 with other strains. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between CN4T and all species of the genus Frankia with validly published names were below the defined threshold for prokaryotic species demarcation, with dDDH and ANI values at or below 27.8 and 83.7 %, respectively. The four strains CN4T, CN6, CN7 and CNm7 had dDDH (98.6-99.6 %) and ANI values that grouped them as representing a single species. CN4T has a 10.76 Mb genome. CN4T was different from its close phylogenetic neighbours with validly published names in being red-pigmented, in having several lantibiotic-coding clusters, a carbon monoxide dehydrogenase cluster and a clustered regularly interspaced short palindromic repeats (CRISPR) cluster. The results of phenotypic, physiological and phylogenomic analyses confirmed the assignment of strain CN4T (=DSM 114740T = LMG 32595T) to a novel species, with CN4T as type strain, for which the name Frankia nepalensis sp. nov. is proposed.

Frankia colletiae sp. nov., a nitrogen-fixing actinobacterium isolated from Colletia cruciata

A nitrogen-fixing actinobacterium strain (Cc1.17^T) isolated from a root nodule of Colletia cruciata was subjected to polyphasic taxonomic studies. The strain was characterized by the presence of meso-diaminopimelic acid in its peptidoglycan, galactose, glucose, mannose, rhamnose, ribose and xylose as cell-wall sugars, phosphatidylinositol, diphosphatidylglycerol, glycophospholipids, phosphatidylglycerol, glycophospholipid and uncharacterized lipids as its polar lipids, and C_16 : 0, iso-C_16 : 0, C_{17 : 1} ω9 and C_18 : 1 ω9 as major fatty acids (>10 %). Strain Cc1.17^T showed 16S rRNA gene sequence similarities of 97.4-99.8 % to validly named Frankia species. Phylogenetic trees based on 16S rRNA gene and genome sequences placed strain Cc1.17^T in a new lineage within the genus Frankia. Digital DNA-DNA hybridization and average nucleotide identity values between strain Cc1.17^T and its closest phylogenomic neighbours were well below the thresholds recommended for prokaryotic species delineation. Therefore, strain Cc1.17^T (=DSM 43829^T=CECT 9313^T) merits recognition as the type strain of a new species for which the name Frankia colletiae sp. nov. is proposed.

Novel species of Frankia, Frankia gtarii sp. nov. and Frankia tisai sp. nov., isolated from a root nodule of Alnus glutinosa

The status of four Frankia strains isolated from a root nodule of Alnus glutinosa was established in a polyphasic study. Taxogenomics and phenotypic features show that the isolates belong to the genus Frankia. All four strains form extensively branched substrate mycelia, multilocular sporangia, vesicles, lack aerial hyphae, but contain meso-diaminopimelic acid as the diamino acid of the peptidoglycan, galactose, glucose, mannose, ribose, xylose and traces of rhamnose as cell wall sugars, iso-C_16:0 as the predominant fatty acid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol as the major polar lipids, have comparable genome sizes to other cluster 1, Alnus-infective strains with structural and accessory genes associated with nitrogen fixation. The genome sizes of the isolates range from 7.0 to 7.7 Mbp and the digital DNA G + C contents from 71.3 to 71.5 %. The four sequenced genomes are rich in biosynthetic gene clusters predicted to express for novel specialized metabolites, notably antibiotics. 16S rRNA gene and whole genome sequence analyses show that the isolates fall into two lineages that are closely related to the type strains of Frankia alni and Frankia torreyi. All of these taxa are separated by combinations of phenotypic properties and by digital DNA:DNA hybridization scores which indicate that they belong to different genomic species. Based on these results, it is proposed that isolates Agncl-4^T and Agncl-10, and Agncl-8^T and Agncl-18, be recognised as Frankia gtarii sp. nov. and Frankia tisai sp. nov. respectively, with isolates Agncl-4^T (=DSM 107976^T = CECT 9711^T) and Agncl-8^T (=DSM 107980^T = CECT 9715^T) as the respective type strains.

Streptomyces humicola sp. nov., a novel actinobacterium isolated from peat swamp forest soil in Thailand

A polyphasic approach was used to describe strain RB6PN25^T, an actinobacterium isolated from peat swamp forest soil in Rayong Province, Thailand. The strain was a Gram-stain-positive and filamentous bacterium that contained ll-diaminopimelic acid, mannose and ribose in whole-cell hydrolysates. MK-9(H₈) was the major menaquinone. The major fatty acids were iso-C_16 : 0, anteiso-C_15 : 0 and iso-C_15 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, two unidentified glycophospholipids, two unidentified aminolipids and an unidentified phospholipid. The 16S rRNA gene sequences analysis indicated that it was most closely related to Streptomyces rubrisoli DSM 42083^T (97.6 %) and Streptomyces palmae TBRC 1999^T (97.4 %). Strain RB6PN25^T exhibited low average nucleotide identity and digital DNA-DNA hybridization values with S. rubrisoli DSM 42083^T (78.6 %, 23.2 %) and S. palmae TBRC 1999^T (76.0 %, 22.6 %). The DNA G+C content of strain RB6PN25^T was 69.9%. The results of phenotypic, chemotaxonomic, genotypic and phylogenetic analyses reveal that strain RB6PN25^T represents a novel species of the genus Streptomyces, for which the name Streptomyces humicola sp. nov. is proposed. The type strain is RB6PN25^T (=TBRC 14819^T=NBRC 115204^T).

Biotechnological and Ecological Potential of Micromonospora provocatoris sp. nov., a Gifted Strain Isolated from the Challenger Deep of the Mariana Trench

A Micromonospora strain, isolate MT25^T, was recovered from a sediment collected from the Challenger Deep of the Mariana Trench using a selective isolation procedure. The isolate produced two major metabolites, n-acetylglutaminyl glutamine amide and desferrioxamine B, the chemical structures of which were determined using 1D and 2D-NMR, including ¹H-¹⁵N HSQC and ¹H-¹⁵N HMBC 2D-NMR, as well as high resolution MS. A whole genome sequence of the strain showed the presence of ten natural product-biosynthetic gene clusters, including one responsible for the biosynthesis of desferrioxamine B. Whilst 16S rRNA gene sequence analyses showed that the isolate was most closely related to the type strain of Micromonospora chalcea, a whole genome sequence analysis revealed it to be most closely related to Micromonospora tulbaghiae 45142^T. The two strains were distinguished using a combination of genomic and phenotypic features. Based on these data, it is proposed that strain MT25^T (NCIMB 15245^T, TISTR 2834^T) be classified as Micromonospora provocatoris sp. nov. Analysis of the genome sequence of strain MT25^T (genome size 6.1 Mbp) revealed genes predicted to responsible for its adaptation to extreme environmental conditions that prevail in deep-sea sediments.

Biosynthesis of Diverse Type II Polyketide Core Structures in Streptomyces coelicolor M1152

Synthetic biology-based approaches have been employed to generate advanced natural product (NP) pathway intermediates to overcome obstacles in NP drug discovery and production. Type II polyketides (PK-IIs) comprise a major subclass of NPs that provide attractive structures for antimicrobial and anticancer drug development. Herein, we have assembled five biosynthetic pathways using a generalized operon design strategy in Streptomyces coelicolor M1152 to allow comparative analysis of metabolite production in an improved heterologous host. The work resulted in production of four distinct PK-II core structures, namely benzoisochromanequinone, angucycline, tetracenomycin, and pentangular compounds, which serve as precursors to diverse pharmaceutically important NPs. Our bottom-up design strategy provided evidence that the biosynthetic pathway of BE-7585A proceeds via an angucycline core structure, instead of rearrangement of an anthracycline aglycone, and led to the discovery of a novel 26-carbon pentangular polyketide. The synthetic biology platform presented here provides an opportunity for further controlled production of diverse PK-IIs in a heterologous host.

Micromonospora radicis sp. nov., isolated from roots of Azadirachta indica var. siamensis Valenton, and reclassification of Jishengella zingiberis as Micromonospora zingiberis comb. nov

A novel endophytic actinomycete strain AZ1-13^T was isolated from roots of Azadirachta indica, and its taxonomic position was investigated using a polyphasic approach. Pairwise 16S rRNA gene sequence similarities of strain AZ1-13^T and its closest species, Jishegella zingiberis PLAI1-1^T and Micromonospora endophytica 202201^T, were 99.7 and 99.2 %, respectively. Phylogenetic analyses of the family Micromonosporaceae based on 16S rRNA gene sequences indicated strains AZ1-13^T and J. zingiberis PLAI1-1^Tare located within the genus Micromonospora. The approximate genome size of the strain was 5.96 Mb with 71.9 mol% of G+C content. The strain AZ1-13^T exhibited ANIb values of 87.4 % with J. zingiberis PLAI1-1^T and 85.1 % with M. endophytica 202201^T. Chemotaxonomic characteristics of strain AZ1-13^T were consistent within the genus Micromonospora: cell-wall peptidoglycan of the strain contained meso-diaminopimelic acid; glucose, mannose, ribose and xylose are presented as the whole-cell sugars; the predominant menaquinones were MK-9(H₄) and MK-9(H₆); major cellular fatty acids were iso-C_15 : 0, 10-methyl C_17 : 0, C_17 : 0, anteiso-C_17 : 0 and iso-C_17 : 1ω8c; diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol were detected as distinguished phospholipids. Based on phenotypic properties, phylogeny and genomic data, the strain AZ1-13^T could be distinguished from its closest neighbours, representing a novel species of the genus Micromonospora, for which the name Micromonospora radicis sp. nov. is proposed. The type strain is AZ1-13^T (=KCTC 39786^T=NBRC 112324^T=JCM 32147^T = TISTR 2404^T). This study also proposed that J. zingiberisis transferred to the genus Micromonospora as Micromonospora zingiberis comb. nov. (type strain PLAI1-1^T=TBRC 7644^T=NBRC 113144^T=JCM 32592^T).

Genomic Insights Into Plant-Growth-Promoting Potentialities of the Genus Frankia

This study was designed to determine the plant growth promoting (PGP) potential of members of the genus Frankia. To this end, the genomes of 21 representative strains were examined for genes associated directly or indirectly with plant growth. All of the Frankia genomes contained genes that encoded for products associated with the biosynthesis of auxins [indole-3-glycerol phosphate synthases, anthranilate phosphoribosyltransferases (trpD), anthranilate synthases, and aminases (trpA and B)], cytokinins (11 well-conserved genes within the predicted biosynthetic gene cluster), siderophores, and nitrogenases (nif operon except for atypical Frankia) as well as genes that modulate the effects of biotic and abiotic environmental stress (e.g., alkyl hydroperoxide reductases, aquaporin Z, heat shock proteins). In contrast, other genes were associated with strains assigned to one or more of four host-specific clusters. The genes encoding for phosphate solubilization (e.g., low-affinity inorganic phosphate transporters) and lytic enzymes (e.g., cellulases) were found in Frankia cluster 1 genomes, while other genes were found only in cluster 3 genomes (e.g., alkaline phosphatases, extracellular endoglucanases, pectate lyases) or cluster 4 and subcluster 1c genomes (e.g., NAD(P) transhydrogenase genes). Genes encoding for chitinases were found only in the genomes of the type strains of Frankia casuarinae, F. inefficax, F. irregularis, and F. saprophytica. In short, these in silico genome analyses provide an insight into the PGP abilities of Frankia strains of known taxonomic provenance. This is the first study designed to establish the underlying genetic basis of cytokinin production in Frankia strains. Also, the discovery of additional genes in the biosynthetic gene cluster involved in cytokinin production opens up the prospect that Frankia may have novel molecular mechanisms for cytokinin biosynthesis.

Lysoquinone-TH1, a New Polyphenolic Tridecaketide Produced by Expressing the Lysolipin Minimal PKS II in Streptomyces albus

The structural repertoire of bioactive naphthacene quinones is expanded by engineering Streptomyces albus to express the lysolipin minimal polyketide synthase II (PKS II) genes from Streptomyces tendae Tü 4042 (llpD-F) with the corresponding cyclase genes llpCI-CIII. Fermentation of the recombinant strain revealed the two new polyaromatic tridecaketides lysoquinone-TH1 (7, identified) and TH2 (8, postulated structure) as engineered congeners of the dodecaketide lysolipin (1). The chemical structure of 7, a benzo[a]naphthacene-8,13-dione, was elucidated by NMR and HR-MS and confirmed by feeding experiments with [1,2-¹³C₂]-labeled acetate. Lysoquinone-TH1 (7) is a pentangular polyphenol and one example of such rare extended polyaromatic systems of the benz[a]napthacene quinone type produced by the expression of a minimal PKS II in combination with cyclases in an artificial system. While the natural product lysolipin (1) has antimicrobial activity in nM-range, lysoquinone-TH1 (7) showed only minor potency as inhibitor of Gram-positive microorganisms. The bioactivity profiling of lysoquinone-TH1 (7) revealed inhibitory activity towards phosphodiesterase 4 (PDE4), an important target for the treatment in human health like asthma or chronic obstructive pulmonary disease (COPD). These results underline the availability of pentangular polyphenolic structural skeletons from biosynthetic engineering in the search of new chemical entities in drug discovery.

Permanent Draft Genome Sequences of Three Frankia sp. Strains That Are Atypical, Noninfective, Ineffective Isolates

Here, we present draft genome sequences for three atypical Frankia strains (lineage 4) that were isolated from root nodules but are unable to reinfect actinorhizal plants. The genome sizes of Frankia sp. strains EUN1h, BMG5.36, and NRRL B16386 were 9.91, 11.20, and 9.43 Mbp, respectively.

Non-ribosomal peptide synthetases: Identifying the cryptic gene clusters and decoding the natural product

Non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) present in bacteria and fungi are the major multi-modular enzyme complexes which synthesize secondary metabolites like the pharmacologically important antibiotics and siderophores. Each of the multiple modules of an NRPS activates a different amino or aryl acid, followed by their condensation to synthesize a linear or cyclic natural product. The studies on NRPS domains, the knowledge of their gene cluster architecture and tailoring enzymes have helped in the in silico genetic screening of the ever-expanding sequenced microbial genomic data for the identification of novel NRPS/PKS clusters and thus deciphering novel non-ribosomal peptides (NRPs). Adenylation domain is an integral part of the NRPSs and is the substrate selecting unit for the final assembled NRP. In some cases, it also requires a small protein, the MbtH homolog, for its optimum activity. The presence of putative adenylation domain and MbtH homologs in a sequenced genome can help identify the novel secondary metabolite producers. The role of the adenylation domain in the NRPS gene clusters and its characterization as a tool for the discovery of novel cryptic NRPS gene clusters are discussed.

Complete Genome Sequence of Streptomyces venezuelae ATCC 15439, Producer of the Methymycin/Pikromycin Family of Macrolide Antibiotics, Using PacBio Technology

Here, we report the complete genome sequence of Streptomyces venezuelae ATCC 15439, a producer of the methymycin/pikromycin family of macrolide antibiotics and a model host for natural product studies, obtained exclusively using PacBio sequencing technology. The 9.03-Mbp genome harbors 8,775 genes and 11 polyketide and nonribosomal peptide natural product gene clusters.

Evolution of chemical diversity by coordinated gene swaps in type II polyketide gene clusters

Natural product biosynthetic pathways generate molecules of enormous structural complexity and exquisitely tuned biological activities. Studies of natural products have led to the discovery of many pharmaceutical agents, particularly antibiotics. Attempts to harness the catalytic prowess of biosynthetic enzyme systems, for both compound discovery and engineering, have been limited by a poor understanding of the evolution of the underlying gene clusters. We developed an approach to study the evolution of biosynthetic genes on a cluster-wide scale, integrating pairwise gene coevolution information with large-scale phylogenetic analysis. We used this method to infer the evolution of type II polyketide gene clusters, tracing the path of evolution from the single ancestor to those gene clusters surviving today. We identified 10 key gene types in these clusters, most of which were swapped in from existing cellular processes and subsequently specialized. The ancestral type II polyketide gene cluster likely comprised a core set of five genes, a roster that expanded and contracted throughout evolution. A key C24 ancestor diversified into major classes of longer and shorter chain length systems, from which a C20 ancestor gave rise to the majority of characterized type II polyketide antibiotics. Our findings reveal that (i) type II polyketide structure is predictable from its gene roster, (ii) only certain gene combinations are compatible, and (iii) gene swaps were likely a key to evolution of chemical diversity. The lessons learned about how natural selection drives polyketide chemical innovation can be applied to the rational design and guided discovery of chemicals with desired structures and properties.

Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM)

Microbial natural products are an invaluable source of evolved bioactive small molecules and pharmaceutical agents. Next-generation and metagenomic sequencing indicates untapped genomic potential, yet high rediscovery rates of known metabolites increasingly frustrate conventional natural product screening programs. New methods to connect biosynthetic gene clusters to novel chemical scaffolds are therefore critical to enable the targeted discovery of genetically encoded natural products. Here, we present PRISM, a computational resource for the identification of biosynthetic gene clusters, prediction of genetically encoded nonribosomal peptides and type I and II polyketides, and bio- and cheminformatic dereplication of known natural products. PRISM implements novel algorithms which render it uniquely capable of predicting type II polyketides, deoxygenated sugars, and starter units, making it a comprehensive genome-guided chemical structure prediction engine. A library of 57 tailoring reactions is leveraged for combinatorial scaffold library generation when multiple potential substrates are consistent with biosynthetic logic. We compare the accuracy of PRISM to existing genomic analysis platforms. PRISM is an open-source, user-friendly web application available at http://magarveylab.ca/prism/.

High-Quality Draft Genome Sequence of Actinobacterium Kibdelosporangium sp. MJ126-NF4, Producer of Type II Polyketide Azicemicins, Using Illumina and PacBio Technologies

Here, we report the high-quality draft genome sequence of actinobacterium Kibdelosporangium sp. MJ126-NF4, producer of the type II polyketide azicemicins, obtained using Illumina and PacBio sequencing technologies. The 11.75-Mbp genome contains >11,000 genes and 22 polyketide and nonribosomal peptide natural product gene clusters.