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BMC Genomics Apr 2024Pseudoalteromonas viridis strain BBR56 was isolated from seawater at Dutungan Island, South Sulawesi, Indonesia. Bacterial DNA was isolated using Promega Genomic DNA...
Pseudoalteromonas viridis strain BBR56 was isolated from seawater at Dutungan Island, South Sulawesi, Indonesia. Bacterial DNA was isolated using Promega Genomic DNA TM050. DNA purity and quantity were assessed using NanoDrop spectrophotometers and Qubit fluorometers. The DNA library and sequencing were prepared using Oxford Nanopore Technology GridION MinKNOW 20.06.9 with long read, direct, and comprehensive analysis. High accuracy base calling was assessed with Guppy version 4.0.11. Filtlong and NanoPlot were used for filtering and visualizing the FASTQ data. Flye (2.8.1) was used for de novo assembly analysis. Variant calls and consensus sequences were created using Medaka. The annotation of the genome was elaborated by DFAST. The assembled genome and annotation were tested using Busco and CheckM. Herein, we found that the highest similarity of the BBR56 isolate was 98.37% with the 16 S rRNA gene sequence of P. viridis G-1387. The genome size was 5.5 Mb and included chromosome 1 (4.2 Mbp) and chromosome 2 (1.3 Mbp), which encoded 61 pseudogenes, 4 noncoding RNAs, 113 tRNAs, 31 rRNAs, 4,505 coding DNA sequences, 4 clustered regularly interspaced short palindromic repeats, 4,444 coding genes, and a GC content of 49.5%. The sequence of the whole genome of P. viridis BBR56 was uploaded to GenBank under the accession numbers CP072425-CP072426, biosample number SAMN18435505, and bioproject number PRJNA716373. The sequence read archive (SRR14179986) was successfully obtained from NCBI for BBR56 raw sequencing reads. Digital DNA-DNA hybridization results showed that the genome of BBR56 had the potential to be a new species because no other bacterial genomes were similar to the sample. Biosynthetic gene clusters (BGCs) were assessed using BAGEL4 and the antiSMASH bacterial version. The genome harbored diverse BGCs, including genes that encoded polyketide synthase, nonribosomal peptide synthase, RiPP-like, NRP-metallophore, hydrogen cyanide, betalactone, thioamide-NRP, Lant class I, sactipeptide, and prodigiosin. Thus, BBR56 has considerable potential for further exploration regarding the use of its secondary metabolite products in the human and fisheries sectors.
Topics: Humans; Pseudoalteromonas; Pseudogenes; Gene Library; DNA, Bacterial
PubMed: 38615000
DOI: 10.1186/s12864-024-10266-6 -
Heliyon Mar 2024Latest studies indicated that agro-food wastes are considered renewable sources of bioactive compounds. This investigation aimed to utilize natural extracts of citrus...
Latest studies indicated that agro-food wastes are considered renewable sources of bioactive compounds. This investigation aimed to utilize natural extracts of citrus peels as antimicrobial and anti-aflatoxigenic agents for food safety. The bioactivity of two citrus peels was assessed by total phenolic, flavonoids, and antioxidant activity. Nanoemulsions were manufactured using high-speed homogenization. The mean particle size of the nanoemulsions ranged from 29.41 to 66.41 nm with a polydispersity index of 0.11-0.16. The zeta potential values ranged from -14.27 to -26.74 mV, indicating stability between 81.44% and 99.26%. The orange peel extract showed the highest contents of total phenolic and flavonoids compared to the other extracts and nanoemulsions (39.54 mg GAE/g and 79.54 mg CE/100 g, respectively), which agreed with its potential antioxidant activity performed by DPPH free radical-scavenging and ABTS assays. Chlorogenic, caffeic, ferulic, and catechin were the dominant phenolic acids in the extracts and nanoemulsions, while quercitrin, rutin, and hesperidin were the most abundant flavonoids. Limonene was the major volatile component in both oils; however, it was reduced dramatically from 92.52% to 76.62% in orange peel oil and from 91.79 to 79.12% in tangerine peel oil. Consistent with the differences in phenolics, flavonoids, and volatiles between orange and tangerine peel extracts, the antibacterial properties of orange extracts had more potential than tangerine ones. Gram-positive bacteria were more affected by all the examined extracts than Gram-negative ones. The antifungal activity of orange extract and nanoemulsion on seven fungal strains from spp had more potential than tangerine extracts. Additionally, using a simulated media, the orange peel extract and its nanoemulsion had a more anti-aflatoxigenic influence. Molecular docking confirmed the high inhibitory action of flavonoids, especially hesperidin, on the polyketide synthase (-9.3 kcal/mol) and cytochrome P450 monooxygenase (-10.1 kcal/mol) key enzymes of the aflatoxin biosynthetic mechanism.
PubMed: 38509881
DOI: 10.1016/j.heliyon.2024.e27737 -
Frontiers in Microbiology 2023A novel marine actinomycete, designated strain MCN248, was isolated from the coastal sediment in Songkhla Province, Thailand. Based on the 16S rRNA gene sequences, the...
A novel marine actinomycete, designated strain MCN248, was isolated from the coastal sediment in Songkhla Province, Thailand. Based on the 16S rRNA gene sequences, the new isolate was closely related to DSM45887 (99.2%) and DSM43553 (98.6%). Phylogenetic analyzes based on the 16S rRNA gene sequences showed that strain MCN248 was clustered with DSM45887 and DSM43553. However, the digital DNA-DNA hybridization analyzes presented a low relatedness of 40.2% between strain MCN248 and the above closely related strains. This strain contained meso-diaminopimelic acid. The acyl type of the peptidoglycan was acetyl, and mycolic acids were absent. The major menaquinones were MK-9(H) and MK-9(H). The whole cell sugars consisted of madurose, ribose, mannose, and glucose. Diphosphatidylglycerol, hydroxyl-phosphatidylethanolamine, phosphatidylethanolamine, phosphatidylinositol, and phosphatidylglycerol were detected as the major phospholipids. The predominant cellular fatty acids were -C (40.4%), 10-methyl-C (22.1%), and C8c (10.9%). The DNA G + C content of the genomic DNA was 71.7%. With analyzes, the antiSMASH platform uncovered a diverse 29 secondary metabolite biosynthesis arsenal, including non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) of strain MCN248, with a high prevalence of gene cluster encoding pathways for the production of anticancer and cytotoxic compounds. Consistently, the crude extract could inhibit colorectal HCT-116 cancer cells at a final concentration of 50 μg/mL. Based on the polyphasic approach, strain MCN248 was designated as a novel species of the genus , for which the name sp. nov. is proposed. The type strain of the type species is MCN248 (=NBRC115966 = TBRC17110).
PubMed: 38053561
DOI: 10.3389/fmicb.2023.1226945 -
The Plant Pathology Journal Oct 2023Recently, strategies for controlling Fusarium oxysporum f. sp. lycopersici (Fol), the causal agent of Fusarium wilt of tomato, focus on using effective biocontrol...
Recently, strategies for controlling Fusarium oxysporum f. sp. lycopersici (Fol), the causal agent of Fusarium wilt of tomato, focus on using effective biocontrol agents. In this study, an analysis of the biocontrol and plant growth promoting (PGP) attributes of 11 isolates of loamy soil Bacillus spp. has been conducted. Among them, the isolates B.PNR1 and B.PNR2 inhibited the mycelial growth of Fol by inducing abnormal fungal cell wall structures and cell wall collapse. Moreover, broad-spectrum activity against four other plant pathogenic fungi, F. oxysporum f. sp. cubense race 1 (Foc), Sclerotium rolfsii, Colletotrichum musae, and C. gloeosporioides were noted for these isolates. These two Bacillus isolates produced indole acetic acid, phosphate solubilization enzymes, and amylolytic and cellulolytic enzymes. In the pot experiment, the culture filtrate from B.PNR1 showed greater inhibition of the fungal pathogens and significantly promoted the growth of tomato plants more than those of the other treatments. Isolate B.PNR1, the best biocontrol and PGP, was identified as Bacillus stercoris by its 16S rRNA gene sequence and whole genome sequencing analysis (WGS). The WGS, through genome mining, confirmed that the B.PNR1 genome contained genes/gene cluster of a nonribosomal peptide synthetase/polyketide synthase, such as fengycin, surfactin, bacillaene, subtilosin A, bacilysin, and bacillibactin, which are involved in antagonistic and PGP activities. Therefore, our finding demonstrates the effectiveness of B. stercoris strain B.PNR1 as an antagonist and for plant growth promotion, highlighting the use of this microorganism as a biocontrol agent against the Fusarium wilt pathogen and PGP abilities in tomatoes.
PubMed: 37817491
DOI: 10.5423/PPJ.OA.01.2023.0018 -
PeerJ 2023Chytridiomycosis, caused by (Bd), is a skin disease associated with worldwide amphibian declines. Symbiotic microbes living on amphibian skin interact with Bd and may...
Chytridiomycosis, caused by (Bd), is a skin disease associated with worldwide amphibian declines. Symbiotic microbes living on amphibian skin interact with Bd and may alter infection outcomes. We completed whole genome sequencing of 40 bacterial isolates cultured from the skin of four amphibian species in the Eastern US. Each isolate was tested for the ability to inhibit Bd growth. The aim of this study was to identify genomic differences among the isolates and generate hypotheses about the genomic underpinnings of Bd growth inhibition. We identified sixty-five gene families that were present in all 40 isolates. Screening for common biosynthetic gene clusters revealed that this set of isolates contained a wide variety of clusters; the two most abundant clusters with potential antifungal activity were siderophores (N=17 isolates) and Type III polyketide synthases (N=22 isolates). We then examined various subsets of the 22 isolates in the phylum Proteobacteria for genes encoding specific compounds that may inhibit fungal growth, including chitinase and violacein. We identified differences in and isolates in the chitinase genes that showed some association with anti-Bd activity, as well as variation in the violacein genes in the isolates. Using a comparative genomics approach, we generated several testable hypotheses about differences among bacterial isolates from amphibian skin communities that could contribute to variation in the ability to inhibit Bd growth. Further work is necessary to explore and uncover the various mechanisms utilized by amphibian skin bacterial isolates to inhibit Bd.
Topics: Animals; Batrachochytrium; Bacteria; Genomics; Amphibians; Chitinases
PubMed: 37637170
DOI: 10.7717/peerj.15714 -
International Journal of Molecular... May 2024Utilizing bioinformatics tools, this study expands our understanding of secondary metabolism in , identifying novel genes within polyketide synthase (PKS), non-ribosomal...
Utilizing bioinformatics tools, this study expands our understanding of secondary metabolism in , identifying novel genes within polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), sesquiterpene cyclase (STC), diterpene cyclase (DTC), and dimethylallyltryptophan synthase (DMATS) families. These findings enrich the genetic framework associated with 's pathogenicity and ecological adaptation, offering insights into uncharted metabolic pathways. Significantly, the discovery of previously unannotated genes provides new molecular targets for developing targeted antifungal strategies, promising to enhance crop protection and advance our understanding of fungal biochemistry. This research not only broadens the scope of known secondary metabolites but also opens avenues for future exploration into 's biosynthetic capabilities, potentially leading to novel antifungal compounds. Our work underscores the importance of integrating bioinformatics and genomics for fungal research, paving the way for sustainable agricultural practices by pinpointing precise molecular interventions against . This study sets a foundation for further investigations into the fungus's secondary metabolism, with implications for biotechnology and crop disease management.
Topics: Botrytis; Secondary Metabolism; Peptide Synthases; Polyketide Synthases; Fungal Proteins; Computational Biology; Multigene Family; Genes, Fungal
PubMed: 38892087
DOI: 10.3390/ijms25115900 -
International Journal of Molecular... Nov 2023is a major pathogen causing anthracnose in Chinese flowering cabbage (), posing a significant threat to the Chinese flowering cabbage industry. The conidia of...
is a major pathogen causing anthracnose in Chinese flowering cabbage (), posing a significant threat to the Chinese flowering cabbage industry. The conidia of germinate and form melanized infection structures called appressoria, which enable penetration of the host plant's epidermal cells. However, the molecular mechanism underlying melanin biosynthesis in remains poorly understood. In this study, we identified two enzymes related to DHN-melanin biosynthesis in : ChPks and ChThr1. Our results demonstrate that the expression levels of genes and were significantly up-regulated during hyphal and appressorial melanization processes. Furthermore, knockout of the gene resulted in a blocked DHN-melanin biosynthetic pathway in hyphae and appressoria, leading to increased sensitivity of the Δ mutant to cell-wall-interfering agents as well as decreased turgor pressure and pathogenicity. It should be noted that although the Δ mutant still exhibited melanin accumulation in colonies and appressoria, its sensitivity to cell-wall-interfering agents and turgor pressure decreased compared to wild-type strains; however, complete loss of pathogenicity was not observed. In conclusion, our results indicate that DHN-melanin plays an essential role in both pathogenicity and cell wall integrity in . Specifically, ChPks is crucial for DHN-melanin biosynthesis while deficiency of ChThr1 does not completely blocked melanin production.
Topics: Virulence; Melanins; Colletotrichum; Cell Wall
PubMed: 37958874
DOI: 10.3390/ijms242115890 -
Microbial Biotechnology May 2024Avermectins (AVEs), a family of macrocyclic polyketides produced by Streptomyces avermitilis, have eight components, among which B1a is noted for its strong insecticidal...
Avermectins (AVEs), a family of macrocyclic polyketides produced by Streptomyces avermitilis, have eight components, among which B1a is noted for its strong insecticidal activity. Biosynthesis of AVE "a" components requires 2-methylbutyryl-CoA (MBCoA) as starter unit, and malonyl-CoA (MalCoA) and methylmalonyl-CoA (MMCoA) as extender units. We describe here a novel strategy for increasing B1a production by enhancing acyl-CoA precursor supply. First, we engineered meilingmycin (MEI) polyketide synthase (PKS) for increasing MBCoA precursor supply. The loading module (using acetyl-CoA as substrate), extension module 7 (using MMCoA as substrate) and TE domain of MEI PKS were assembled to produce 2-methylbutyrate, providing the starter unit for B1a production. Heterologous expression of the newly designed PKS (termed Mei-PKS) in S. avermitilis wild-type (WT) strain increased MBCoA level, leading to B1a titer 262.2 μg/mL - 4.36-fold higher than WT value (48.9 μg/mL). Next, we separately inhibited three key nodes in essential pathways using CRISPRi to increase MalCoA and MMCoA levels in WT. The resulting strains all showed increased B1a titer. Combined inhibition of these key nodes in Mei-PKS expression strain increased B1a titer to 341.9 μg/mL. Overexpression of fatty acid β-oxidation pathway genes in the strain further increased B1a titer to 452.8 μg/mL - 8.25-fold higher than WT value. Finally, we applied our precursor supply strategies to high-yield industrial strain A229. The strategies, in combination, led to B1a titer 8836.4 μg/mL - 37.8% higher than parental A229 value. These findings provide an effective combination strategy for increasing AVE B1a production in WT and industrial S. avermitilis strains, and our precursor supply strategies can be readily adapted for overproduction of other polyketides.
Topics: Polyketide Synthases; Metabolic Engineering; Acyl Coenzyme A; Streptomyces; Metabolic Networks and Pathways; Ivermectin; Bacterial Proteins
PubMed: 38683675
DOI: 10.1111/1751-7915.14470 -
Journal of Fungi (Basel, Switzerland) May 2024pigments (MPs), a class of secondary metabolites produced by spp., can be classified into yellow, orange, and red MPs according to their differences in the wavelength...
pigments (MPs), a class of secondary metabolites produced by spp., can be classified into yellow, orange, and red MPs according to their differences in the wavelength of the maximum absorption. However, the biosynthetic sequence and cellular biosynthesis mechanism of different MPs components are still not yet completely clear in spp. In this study, the subcellular localization of five MPs synthases was investigated using fluorescent protein fusion expression. The results revealed that the proteins encoded by the MPs biosynthetic gene cluster were compartmentalized in various subcellular locations, including the mitochondrial polyketide synthase MrPigA, cytosolic enzymes consisting of the ketoreductase MrPigC, the oxidoreductase MrPigE, and the monooxygenase MrPigN, and the cell-wall-bound oxidoreductase MrPigF. Moreover, the correct localization of MrPigF to the cell wall was crucial for the synthesis of orange MPs. Lastly, we discussed the compartmentalized biosynthetic pathway of MPs. This study will not only be helpful in clarifying the biosynthetic sequence and biosynthesis mechanism of different MPs but also provides new insights into the cellular biosynthesis of secondary metabolites in filamentous fungi.
PubMed: 38921362
DOI: 10.3390/jof10060375 -
BMC Cancer Jan 2024Colibactin, a genotoxin produced by polyketide synthase harboring (pks) bacteria, induces double-strand breaks and chromosome aberrations. Consequently, enrichment of...
BACKGROUND
Colibactin, a genotoxin produced by polyketide synthase harboring (pks) bacteria, induces double-strand breaks and chromosome aberrations. Consequently, enrichment of pksEscherichia coli in colorectal cancer and polyposis suggests a possible carcinogenic effect in the large intestine. Additionally, specific colibactin-associated mutational signatures; SBS88 and ID18 in the Catalogue of Somatic Mutations in Cancer database, are detected in colorectal carcinomas. Previous research showed that a recurrent APC splice variant perfectly fits SBS88.
METHODS
In this study, we explore the presence of colibactin-associated signatures and fecal pks in an unexplained polyposis cohort. Somatic targeted Next-Generation Sequencing (NGS) was performed for 379 patients. Additionally, for a subset of 29 patients, metagenomics was performed on feces and mutational signature analyses using Whole-Genome Sequencing (WGS) on Formalin-Fixed Paraffin Embedded (FFPE) colorectal tissue blocks.
RESULTS
NGS showed somatic APC variants fitting SBS88 or ID18 in at least one colorectal adenoma or carcinoma in 29% of patients. Fecal metagenomic analyses revealed enriched presence of pks genes in patients with somatic variants fitting colibactin-associated signatures compared to patients without variants fitting colibactin-associated signatures. Also, mutational signature analyses showed enrichment of SBS88 and ID18 in patients with variants fitting these signatures in NGS compared to patients without.
CONCLUSIONS
These findings further support colibactins ability to mutagenize colorectal mucosa and contribute to the development of colorectal adenomas and carcinomas explaining a relevant part of patients with unexplained polyposis.
Topics: Humans; Mutation; Colorectal Neoplasms; Peptides; Polyketides; Escherichia coli; Adenoma; Carcinoma
PubMed: 38238650
DOI: 10.1186/s12885-024-11849-y