Comparative Genomics Analysis of Keratin-Degrading Chryseobacterium Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production

A promising keratin-degrading strain from the genus Chryseobacterium (Chryseobacterium sp. KMC2) was investigated using comparative genomic tools against three publicly available reference genomes to reveal the keratinolytic potential for biosynthesis of valuable secondary metabolites. Genomic features and metabolic potential of four species were compared, showing genomic differences but similar functional categories. Eleven different secondary metabolite gene clusters of interest were mined from the four genomes successfully, including five common ones shared across all genomes. Among the common metabolites, we identified gene clusters involved in biosynthesis of flexirubin-type pigment, microviridin, and siderophore, showing remarkable conservation across the four genomes. Unique secondary metabolite gene clusters were also discovered, for example, ladderane from Chryseobacterium sp. KMC2. Additionally, this study provides a more comprehensive understanding of the potential metabolic pathways of keratin utilization in Chryseobacterium sp. KMC2, with the involvement of amino acid metabolism, TCA cycle, glycolysis/gluconeogenesis, propanoate metabolism, and sulfate reduction. This work uncovers the biosynthesis of secondary metabolite gene clusters from four keratinolytic Chryseobacterium species and shades lights on the keratinolytic potential of Chryseobacterium sp. KMC2 from a genome-mining perspective, can provide alternatives to valorize keratinous materials into high-value bioactive natural products.

Download Full-text

Comparative genomics analysis of Chryseobacterium sp. KMC2 reveals metabolic pathways involved in keratinous utilization and natural product biosynthesis

10.1101/2021.02.23.432615 ◽

2021 ◽

Author(s):

Dingrong Kang ◽

Saeed Shoaie ◽

Samuel Jacquiod ◽

Søren Johannes Sørensen ◽

Rodrigo Ledesma-Amaro

Keyword(s):

Secondary Metabolite ◽

Metabolic Pathways ◽

Genome Mining ◽

Renewable Resource ◽

Gene Clusters ◽

Comparative Genomic ◽

Microbial Conversion ◽

Metabolic Potential ◽

A Genome ◽

Keratinous Materials

Several efforts have been made to valorize keratinous materials, an abundant and renewable resource. Despite these attempts to valorize products generated from keratin hydrolysate, either via chemical or microbial conversion, they generally remain with an overall low value. In this study, a promising keratinolytic strain from the genus Chryseobacterium (Chryseobacteriumsp. KMC2) was investigated using comparative genomic tools against publicly available reference genomes to reveal the metabolic potential for biosynthesis of valuable secondary metabolites. Genome and metabolic features of four species were compared, shows different gene numbers but similar functional categories. We successfully mined eleven different secondary metabolite gene clusters of interest from the four genomes, including five common ones shared across all genomes. Among the common metabolites, we identified gene clusters involved in biosynthesis of flexirubin-type pigment, microviridin, and siderophore, all showing remarkable conservation across the four genomes. Unique secondary metabolite gene clusters were also discovered, for example, ladderane from Chryseobacterium sp. KMC2. Additionally, this study provides a more comprehensive understanding of the potential metabolic pathways of keratin utilization in Chryseobacterium sp. KMC2, with the involvement of amino acid metabolism, TCA cycle, glycolysis/gluconeogenesis, propanoate metabolism, and sulfate reduction. This work uncovers the biosynthesis of secondary metabolite gene clusters from four keratinolytic Chryseobacterium spp. and shades lights on the keratinolytic potential of Chryseobacterium sp. KMC2 from a genome-mining perspective, providing alternatives to valorize keratinous materials into high-value natural products.

Download Full-text

Activation and enhancement of Caerulomycin A biosynthesis in marine-derived Actinoalloteichus sp. AHMU CJ021 by combinatorial genome mining strategies

10.21203/rs.3.rs-27100/v1 ◽

2020 ◽

Author(s):

Yunchang Xie ◽

Jiawen Chen ◽

Bo Wang ◽

Tai Chen ◽

Junyu Chen ◽

...

Keyword(s):

Natural Products ◽

Mutant Strain ◽

Genome Mining ◽

Gene Clusters ◽

Immunosuppressive Drug ◽

Biosynthetic Gene ◽

Bioactive Natural Products ◽

Drug Lead ◽

A Genome ◽

Mining Work

Abstract Backgrounds: Activation of silent biosynthetic gene clusters (BGCs) in marine-derived actinomycete strains is a feasible strategy to discover bioactive natural products. Actinoalloteichus sp. AHMU CJ021, isolated from the seashore, was shown to contain an intact but silent caerulomycin A (CRM A) BGC-cam in its genome. Thus, a genome mining work was preformed to activate the strain’s bioproduction of CRM A, an immunosuppressive drug lead with diverse bioactivities.Results: To well activate the expression of cam, ribosomal engineering was adopted to treat the wild type Actinoalloteichus sp. AHMU CJ021. The initial mutant strain XC-11G with gentamycin resistance and CRM A bioproduction titer of 42.51 ± 4.22 mg/L was selected from all generated mutant strains by gene expression comparison of the essential biosynthetic gene-camE. The titer of CRM A bioproduction was then improved by two strain breeding methods via UV mutagenesis and cofactor engineering-directed increasing of intracellular riboflavin, which finally generated the optimal mutant strain XC-11GUR with a CRM A bioproduction titer of 113.91 ± 7.58 mg/L. Subsequently, this titer of strain XC-11GUR was improved to 618.61 ± 16.29 mg/L through medium optimization together with further adjustment derived from response surface methodology. In terms of this 14.7 folds increase in the titer of CRM A compared to the initial value, strain XC-GUR could be a well alternative strain for CRM A development.Conclusions: Our results have constructed an ideal CRM A producer. More importantly, our efforts also have demonstrated the effectiveness of abovementioned combinatorial strategies, which is applicable to the genome mining of bioactive natural products from abundant actinomycetes strains.

Download Full-text

Activation and enhancement of Caerulomycin A biosynthesis in marine-derived Actinoalloteichus sp. AHMU CJ021 by combinatorial genome mining strategies

10.21203/rs.3.rs-27100/v2 ◽

2020 ◽

Author(s):

Yunchang Xie ◽

Jiawen Chen ◽

Bo Wang ◽

Tai Chen ◽

Junyu Chen ◽

...

Keyword(s):

Natural Products ◽

Mutant Strain ◽

Genome Mining ◽

Gene Clusters ◽

Immunosuppressive Drug ◽

Biosynthetic Gene ◽

Bioactive Natural Products ◽

Drug Lead ◽

A Genome ◽

Mining Work

Abstract Backgrounds: Activation of silent biosynthetic gene clusters (BGCs) in marine-derived actinomycete strains is a feasible strategy to discover bioactive natural products. Actinoalloteichus sp. AHMU CJ021, isolated from the seashore, was shown to contain an intact but silent caerulomycin A (CRM A) BGC-cam in its genome. Thus, a genome mining work was preformed to activate the strain’s production of CRM A, an immunosuppressive drug lead with diverse bioactivities.Results: To well activate the expression of cam, ribosome engineering was adopted to treat the wild type Actinoalloteichus sp. AHMU CJ021. The initial mutant strain XC-11G with gentamycin resistance and CRM A production titer of 42.51 ± 4.22 mg/L was selected from all generated mutant strains by gene expression comparison of the essential biosynthetic gene-camE. The titer of CRM A production was then improved by two strain breeding methods via UV mutagenesis and cofactor engineering-directed increase of intracellular riboflavin, which finally generated the optimal mutant strain XC-11GUR with a CRM A production titer of 113.91 ± 7.58 mg/L. Subsequently, this titer of strain XC-11GUR was improved to 618.61 ± 16.29 mg/L through medium optimization together with further adjustment derived from response surface methodology. In terms of this 14.6 folds increase in the titer of CRM A compared to the initial value, strain XC-GUR could be a well alternative strain for CRM A development.Conclusions: Our results have constructed an ideal CRM A producer. More importantly, our efforts also have demonstrated the effectiveness of abovementioned combinatorial strategies, which is applicable to the genome mining of bioactive natural products from abundant actinomycetes strains.

Download Full-text

Activation and enhancement of Caerulomycin A biosynthesis in marine-derived Actinoalloteichus sp. AHMU CJ021 by combinatorial genome mining strategies

10.21203/rs.3.rs-27100/v3 ◽

2020 ◽

Author(s):

Yunchang Xie ◽

Jiawen Chen ◽

Bo Wang ◽

Tai Chen ◽

Junyu Chen ◽

...

Keyword(s):

Natural Products ◽

Mutant Strain ◽

Genome Mining ◽

Gene Clusters ◽

Immunosuppressive Drug ◽

Biosynthetic Gene ◽

Bioactive Natural Products ◽

Drug Lead ◽

A Genome ◽

Mining Work

Abstract Backgrounds: Activation of silent biosynthetic gene clusters (BGCs) in marine-derived actinomycete strains is a feasible strategy to discover bioactive natural products. Actinoalloteichus sp. AHMU CJ021, isolated from the seashore, was shown to contain an intact but silent caerulomycin A (CRM A) BGC- cam in its genome. Thus, a genome mining work was preformed to activate the strain’s production of CRM A, an immunosuppressive drug lead with diverse bioactivities.Results: To well activate the expression of cam , ribosome engineering was adopted to treat the wild type Actinoalloteichus sp. AHMU CJ021. The initial mutant strain XC-11G with gentamycin resistance and CRM A production titer of 42.51 ± 4.22 mg/L was selected from all generated mutant strains by gene expression comparison of the essential biosynthetic gene-camE. The titer of CRM A production was then improved by two strain breeding methods via UV mutagenesis and cofactor engineering-directed increase of intracellular riboflavin, which finally generated the optimal mutant strain XC-11GUR with a CRM A production titer of 113.91 ± 7.58 mg/L. Subsequently, this titer of strain XC-11GUR was improved to 618.61 ± 16.29 mg/L through medium optimization together with further adjustment derived from response surface methodology. In terms of this 14.6 folds increase in the titer of CRM A compared to the initial value, strain XC-GUR could be a well alternative strain for CRM A development.Conclusions: Our results have constructed an ideal CRM A producer. More importantly, our efforts also have demonstrated the effectiveness of abovementioned combinatorial strategies, which is applicable to the genome mining of bioactive natural products from abundant actinomycetes strains.

Download Full-text

Genome mining and biosynthesis of a polyketide from a biofertilizer fungus that can facilitate reductive iron assimilation in plant

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1819998116 ◽

2019 ◽

Vol 116 (12) ◽

pp. 5499-5504 ◽

Cited By ~ 5

Author(s):

Mengbin Chen ◽

Qikun Liu ◽

Shu-Shan Gao ◽

Abbegayle E. Young ◽

Steven E. Jacobsen ◽

...

Keyword(s):

Acyl Carrier Protein ◽

Genome Mining ◽

Gene Clusters ◽

Bioactive Molecules ◽

Bioactive Natural Products ◽

Redox Active ◽

A Genome ◽

Iron Deficient ◽

Iron Assimilation ◽

Polyketide Chain

Fungi have the potential to produce a large repertoire of bioactive molecules, many of which can affect the growth and development of plants. Genomic survey of sequenced biofertilizer fungi showed many secondary metabolite gene clusters are anchored by iterative polyketide synthases (IPKSs), which are multidomain enzymes noted for generating diverse small molecules. Focusing on the biofertilizerTrichoderma harzianumt-22, we identified and characterized a cryptic IPKS-containing cluster that synthesizes tricholignan A, a redox-activeortho-hydroquinone. Tricholignan A is shown to reduce Fe(III) and may play a role in promoting plant growth under iron-deficient conditions. The construction of tricholignan by a pair of collaborating IPKSs was investigated using heterologous reconstitution and biochemical studies. A regioselective methylation step is shown to be a key step in formation of theortho-hydroquinone. The responsible methyltransferase (MT) is fused with an N-terminal pseudo-acyl carrier protein (ψACP), in which theapostate of the ACP is essential for methylation of the growing polyketide chain. The ψACP is proposed to bind to the IPKS and enable thetransMT to access the growing polyketide. Our studies show that a genome-driven approach to discovering bioactive natural products from biofertilizer fungi can lead to unique compounds and biosynthetic knowledge.

Download Full-text

Activation and enhancement of caerulomycin A biosynthesis in marine-derived Actinoalloteichus sp. AHMU CJ021 by combinatorial genome mining strategies

Microbial Cell Factories ◽

10.1186/s12934-020-01418-w ◽

2020 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Yunchang Xie ◽

Jiawen Chen ◽

Bo Wang ◽

Tai Chen ◽

Junyu Chen ◽

...

Keyword(s):

Natural Products ◽

Mutant Strain ◽

Genome Mining ◽

Gene Clusters ◽

Immunosuppressive Drug ◽

Biosynthetic Gene ◽

Bioactive Natural Products ◽

Drug Lead ◽

A Genome ◽

Mining Work

Abstract Background Activation of silent biosynthetic gene clusters (BGCs) in marine-derived actinomycete strains is a feasible strategy to discover bioactive natural products. Actinoalloteichus sp. AHMU CJ021, isolated from the seashore, was shown to contain an intact but silent caerulomycin A (CRM A) BGC-cam in its genome. Thus, a genome mining work was preformed to activate the strain’s production of CRM A, an immunosuppressive drug lead with diverse bioactivities. Results To well activate the expression of cam, ribosome engineering was adopted to treat the wild type Actinoalloteichus sp. AHMU CJ021. The initial mutant strain XC-11G with gentamycin resistance and CRM A production titer of 42.51 ± 4.22 mg/L was selected from all generated mutant strains by gene expression comparison of the essential biosynthetic gene-camE. The titer of CRM A production was then improved by two strain breeding methods via UV mutagenesis and cofactor engineering-directed increase of intracellular riboflavin, which finally generated the optimal mutant strain XC-11GUR with a CRM A production titer of 113.91 ± 7.58 mg/L. Subsequently, this titer of strain XC-11GUR was improved to 618.61 ± 16.29 mg/L through medium optimization together with further adjustment derived from response surface methodology. In terms of this 14.6 folds increase in the titer of CRM A compared to the initial value, strain XC-GUR could be a well alternative strain for CRM A development. Conclusions Our results had constructed an ideal CRM A producer. More importantly, our efforts also had demonstrated the effectiveness of abovementioned combinatorial strategies, which is applicable to the genome mining of bioactive natural products from abundant actinomycetes strains.

Download Full-text

Integrated metabolomic, molecular networking and genome mining analyses uncover novel angucyclines from Streptomyces sp. RO-S4 isolated from Bejaia Bay, Algeria

10.1101/2021.12.21.473593 ◽

2021 ◽

Author(s):

Rima Ouchene ◽

Didier Stien ◽

Juliette Segret ◽

Mouloud Kecha ◽

Alice MS Rodrigues ◽

...

Keyword(s):

Ring Opening ◽

Draft Genome ◽

Genome Mining ◽

Gene Clusters ◽

Diffusion Method ◽

Biosynthetic Gene ◽

Metabolic Potential ◽

Molecular Networking ◽

Streptomyces Sp ◽

A Genome

Multi-omic approaches have recently made big strides towards the effective exploration of microorganisms and accelerating the discovery of new bioactive compounds. We combined metabolomic, molecular networking, and genomic-based approaches to investigate the metabolic potential of the Streptomyces sp. RO-S4 strain isolated from the polluted waters of Bejaia Bay in Algeria. Antagonistic assays against methicillin-resistant Staphylococcus aureus with RO-S4 organic extracts showed an inhibition zone of 20 mm by the agar diffusion method, and its minimum inhibitory concentration was 16 μg/mL. A molecular network was created using GNPS and annotated through the comparison of MS/MS spectra against several databases. The predominant compounds in the RO-S4 extract belonged to the angucyclines family. Three compounds were annotated as known metabolites, while all the others were putatively new to Science. Notably, all compounds had fridamycin-like aglycones, and several of them had a lactonized D ring analogous to that of urdamycin L. The whole genome of Streptomyces RO-S4 was sequenced to identify the biosynthetic gene cluster (BGC) encoding for these angucyclines, which yielded a draft genome of 7,497,846 bp with 72.4% G+C content. Subsequently, a genome mining analysis revealed 19 putative biosynthetic gene clusters, including a grincamycin-like BGC with a high similarity to that of Streptomyces sp. CZN-748 previously reported to also produce mostly open fridamycin-like aglycones. As the ring-opening process leading to these compounds is still not defined, we performed comparative analysis with other angucycline BGCs and advanced some hypotheses to explain the ring-opening and lactone formation, possibly linked to the uncoupling between the activity of GcnE and GcnM homologues in the RO-S4 strain. The combination of metabolomic and genomic approaches greatly improved the interpretation of the metabolic potential of the RO-S4 strain.

Download Full-text

Comparative genomic analysis of Flavobacteriaceae: insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis.

10.21203/rs.3.rs-15750/v1 ◽

2020 ◽

Author(s):

Asimenia Gavriilidou ◽

Johanna Gutleben ◽

Dennis Versluis ◽

Francesca Forgiarini ◽

Mark WJ van Passel ◽

...

Keyword(s):

Antimicrobial Activity ◽

Carbohydrate Metabolism ◽

Secondary Metabolite ◽

Gene Clusters ◽

Gliding Motility ◽

Ecological Niches ◽

Comparative Genomic ◽

Rrna Gene ◽

Metabolic Potential ◽

Secondary Metabolite Biosynthesis

Abstract BackgroundMembers of the bacterial family Flavobacteriaceae are widely distributed in the marine environment and often found associated with algae, fish, detritus or marine invertebrates. Yet, little is known about the characteristics that drive their ubiquity in diverse ecological niches. Here, we provide an overview of functional traits common to taxonomically diverse members of the family Flavobacteriaceae from different environmental sources, with a focus on the Marine clade. We include seven newly sequenced marine sponge-derived strains that were also tested for gliding motility and antimicrobial activity. ResultsComparative genomics revealed that genome similarities appeared to be correlated to 16S rRNA gene phylogeny, while differences were mostly associated with nutrient acquisition, such as carbohydrate metabolism and gliding motility. The high frequency and diversity of genes encoding polymer-degrading enzymes support the capacity of marine Flavobacteriaceae to utilize diverse carbon sources. Homologs of gliding proteins were widespread among all studied Flavobacteriaceae in contrast to members of other phyla, highlighting the particular presence of this feature within the Bacteroidetes. Notably, not all gliding bacteria formed spreading colonies. Genome mining uncovered a diverse secondary metabolite biosynthesis arsenal of Flavobacteriaceae with high prevalence of gene clusters encoding pathways for the production of antimicrobial, antioxidant and cytotoxic compounds. Antimicrobial activity tests showed, however, that the phenotype differed from the genome-derived predictions for the seven tested strains.ConclusionsOur study elucidates the functional repertoire of marine Flavobacteriaceae and highlights the need to combine genomic and experimental data while using the appropriate stimuli to unlock their uncharted metabolic potential.

Download Full-text

Genome-scale determination of 5´ and 3´ boundaries of RNA transcripts in Streptomyces genomes

Scientific Data ◽

10.1038/s41597-020-00775-w ◽

2020 ◽

Vol 7 (1) ◽

Author(s):

Yongjae Lee ◽

Namil Lee ◽

Soonkyu Hwang ◽

Woori Kim ◽

Yujin Jeong ◽

...

Keyword(s):

Secondary Metabolite ◽

Genome Mining ◽

Gene Clusters ◽

Regulatory Elements ◽

Laboratory Culture ◽

Culture Conditions ◽

Practical Applications ◽

Rna Transcripts ◽

A Genome ◽

Genome Scale

AbstractStreptomyces species are gram-positive bacteria with GC-rich linear genomes and they serve as dominant reservoirs for producing clinically and industrially important secondary metabolites. Genome mining of Streptomyces revealed that each Streptomyces species typically encodes 20–50 secondary metabolite biosynthetic gene clusters (smBGCs), emphasizing their potential for novel compound discovery. Unfortunately, most of smBGCs are uncharacterized in terms of their products and regulation since they are silent under laboratory culture conditions. To translate the genomic potential of Streptomyces to practical applications, it is essential to understand the complex regulation of smBGC expression and to identify the underlying regulatory elements. To progress towards these goals, we applied two Next-Generation Sequencing methods, dRNA-Seq and Term-Seq, to industrially relevant Streptomyces species to reveal the 5´ and 3´ boundaries of RNA transcripts on a genome scale. This data provides a fundamental resource to aid our understanding of Streptomyces’ regulation of smBGC expression and to enhance their potential for secondary metabolite synthesis.

Download Full-text

Draft Genome Sequences of Fungus Aspergillus calidoustus

Genome Announcements ◽

10.1128/genomea.00102-16 ◽

2016 ◽

Vol 4 (2) ◽

Cited By ~ 6

Author(s):

Fabian Horn ◽

Jörg Linde ◽

Derek J. Mattern ◽

Grit Walther ◽

Reinhard Guthke ◽

...

Keyword(s):

Secondary Metabolite ◽

Genome Sequence ◽

Functional Annotation ◽

Draft Genome ◽

Genome Mining ◽

Gene Clusters ◽

Draft Genome Sequence ◽

Genome Sequences

Here, we report the draft genome sequence of Aspergillus calidoustus (strain SF006504) . The functional annotation of A. calidoustus predicts a relatively large number of secondary metabolite gene clusters. The presented genome sequence builds the basis for further genome mining.

Download Full-text