scholarly journals Analyzing the biosynthetic potential of antimicrobial-producing actinobacteria originating from Indonesia

2021 ◽  
Vol 26 (3) ◽  
pp. 142
Author(s):  
Anissa Utami ◽  
Pamela Apriliana ◽  
Yudi Kusnadi ◽  
Dewi S. Zilda ◽  
Zidny Ilmiah ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Diversity ◽  
Pcr Amplification ◽  
Type I ◽  
Biosynthetic Pathways ◽  
Biosynthetic Gene ◽  
Cloning And Sequencing ◽  
Potential Source ◽  
Peptide Synthetase ◽  
Insight Into

We investigated the biosynthetic potential of soil-associated actinobacteria originating from Indonesia, identified as Streptomyces luridus and as Streptomyces luteosporeus. Antimicrobial assays indicated inhibitory activity by both strains against the pathogen Pseudomonas aeruginosa, with S. luteosporeus particularly inhibiting the growth of Bacillus subtilis. PCR-amplification, cloning, and sequencing of ketosynthase (KS) domains of type I modular polyketide (PKS-I) and adenylation (AD) domains of non-ribosomal peptide synthetase (NRPS) indicated the diversity of KS and AD domains derived from both Indonesian Streptomyces. Further phylogenetic analysis showed that KS domains from the subclass cis-AT PKS can be classified as being a part of a loading module or an extension module, along with their predicted substrate specificity. The results suggest that both strains are a potential source of novel biosynthetic pathways. This genetic analysis approach can be used as a fast guide to obtain insight into natural product biosynthetic gene diversity in microorganisms.

scholarly journals New Insight into Antimicrobial Compounds from Food and Marine-Sourced Carnobacterium Species through Phenotype and Genome Analyses

2020 ◽  
Vol 8 (7) ◽  
pp. 1093
Author(s):  
Simon Begrem ◽  
Flora Ivaniuk ◽  
Frédérique Gigout-Chevalier ◽  
Laetitia Kolypczuk ◽  
Sandrine Bonnetot ◽  
...  
Keyword(s):  
Polyketide Synthase ◽  
Biosynthetic Gene Cluster ◽  
Ecological Niches ◽  
Antimicrobial Compounds ◽  
Biosynthetic Gene ◽  
Peptide Synthetase ◽  
Seafood Products ◽  
Genome Analyses ◽  
Encoding Genes ◽  
Insight Into

Carnobacterium maltaromaticum and Carnobacterium divergens, isolated from food products, are lactic acid bacteria known to produce active and efficient bacteriocins. Other species, particularly those originating from marine sources, are less studied. The aim of the study is to select promising strains with antimicrobial potential by combining genomic and phenotypic approaches on large datasets comprising 12 Carnobacterium species. The biosynthetic gene cluster (BGCs) diversity of 39 publicly available Carnobacterium spp. genomes revealed 67 BGCs, distributed according to the species and ecological niches. From zero to six BGCs were predicted per strain and classified into four classes: terpene, NRPS (non-ribosomal peptide synthetase), NRPS-PKS (hybrid non-ribosomal peptide synthetase-polyketide synthase), RiPP (ribosomally synthesized and post-translationally modified peptide). In parallel, the antimicrobial activity of 260 strains from seafood products was evaluated. Among the 60% of active strains, three genomes were sequenced and submitted to a dereplication process. C. inhibens MIP2551 produced a high amountof H2O2, probably thanks to the presence of four oxidase-encoding genes. C. maltaromaticum EBP3019 and SF668 strains were highly efficient against Listeria monocytogenes. A new extracellular 16 kDa unmodified bacteriocin in the EBP3019 strain and five different bacteriocins in SF668 were highlighted. In this study, the overview of antimicrobial BGC and inhibitory activities of Carnobacterium spp. allowed the prediction of potential innovative natural products that could be relevant for biotechnological applications.

scholarly journals Shared PKS modules in biosynthesis of synergistic laxaphycins

2020 ◽  
Author(s):  
LMP Heinilä ◽  
DP Fewer ◽  
J Jokela ◽  
M Wahlsten ◽  
A Jortikka ◽  
...  
Keyword(s):  
Natural Products ◽  
Natural Product ◽  
Polyketide Synthase ◽  
Biosynthetic Gene Cluster ◽  
Future Research ◽  
Biosynthetic Pathways ◽  
Biosynthetic Gene ◽  
Wide Range ◽  
Peptide Synthetase ◽  
Antiproliferative Activities

AbstractCyanobacteria produce a wide range of lipopeptides that exhibit potent membrane-disrupting activities. Laxaphycins consist of two families of structurally distinct macrocyclic lipopeptides that act in a synergistic manner to produce antifungal and antiproliferative activities. Laxaphycins are produced by range of cyanobacteria but their biosynthetic origins remain unclear. Here, we identified the biosynthetic pathways responsible for the biosynthesis of the laxaphycins produced by Scytonema hofmannii PCC 7110. We show that these laxaphycins, called scytocyclamides, are produced by this cyanobacterium and are encoded in a single biosynthetic gene cluster with shared polyketide synthase enzymes initiating two distinct non-ribosomal peptide synthetase pathways. To our knowledge, laxaphycins are the first clearly distinct polyketide synthase and non-ribosomal peptide synthetase hybrid natural products with shared branched biosynthesis. The unusual mechanism of shared enzymes synthesizing two distinct types of products may aid future research in identifying and expressing natural product biosynthetic pathways and in expanding the known biosynthetic logic of this important family of natural products.

scholarly journals Metagenomic Analysis Reveals Diverse Polyketide Synthase Gene Clusters in Microorganisms Associated with the Marine Sponge Discodermia dissoluta

2005 ◽  
Vol 71 (8) ◽  
pp. 4840-4849 ◽  
Author(s):  
Andreas Schirmer ◽  
Rishali Gadkari ◽  
Christopher D. Reeves ◽  
Fadia Ibrahim ◽  
Edward F. DeLong ◽  
...  
Keyword(s):  
Marine Sponge ◽  
Polyketide Synthase ◽  
Pcr Amplification ◽  
Gene Clusters ◽  
Type I ◽  
Metagenomic Libraries ◽  
Dna Libraries ◽  
Peptide Synthetase ◽  
Sponge Associated Bacteria ◽  
Polyketide Synthase Gene

ABSTRACT Sponge-associated bacteria are thought to produce many novel bioactive compounds, including polyketides. PCR amplification of ketosynthase domains of type I modular polyketide synthases (PKS) from the microbial community of the marine sponge Discodermia dissoluta revealed great diversity and a novel group of sponge-specific PKS ketosynthase domains. Metagenomic libraries totaling more than four gigabases of bacterial genomes associated with this sponge were screened for type I modular PKS gene clusters. More than 90% of the clones in total sponge DNA libraries represented bacterial DNA inserts, and 0.7% harbored PKS genes. The majority of the PKS hybridizing clones carried small PKS clusters of one to three modules, although some clones encoded large multimodular PKSs (more than five modules). The most abundant large modular PKS appeared to be encoded by a bacterial symbiont that made up <1% of the sponge community. Sequencing of this PKS revealed 14 modules that, if expressed and active, is predicted to produce a multimethyl-branched fatty acid reminiscent of mycobacterial lipid components. Metagenomic libraries made from fractions enriched for unicellular or filamentous bacteria differed significantly, with the latter containing numerous nonribosomal peptide synthetase (NRPS) and mixed NRPS-PKS gene clusters. The filamentous bacterial community of D. dissoluta consists mainly of Entotheonella spp., an unculturable sponge-specific taxon previously implicated in the biosynthesis of bioactive peptides.

scholarly journals Genome Mining and Characterization of Biosynthetic Gene Clusters in Two Cave Strains of Paenibacillus sp.

2021 ◽  
Vol 11 ◽  
Author(s):  
Jolanta Lebedeva ◽  
Gabriele Jukneviciute ◽  
Rimvydė Čepaitė ◽  
Vida Vickackaite ◽  
Raminta Pranckutė ◽  
...  
Keyword(s):  
Genome Mining ◽  
Gene Clusters ◽  
Phenotypic Characterization ◽  
Biosynthetic Pathways ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Paenibacillus Sp ◽  
Peptide Synthetase ◽  
Non Ribosomal Peptides

The genome sequencing and mining of microorganisms from unexplored and extreme environments has become important in the process of identifying novel biosynthetic pathways. In the present study, the biosynthetic potential of Paenibacillus sp. strains 23TSA30-6 and 28ISP30-2 was investigated. Both strains were isolated from the deep oligotrophic Krubera-Voronja Cave and were found to be highly active against both Gram-positive and Gram-negative bacteria. Genome mining revealed a high number of biosynthetic gene clusters in the cave strains: 21 for strain 23TSA30-6 and 19 for strain 28ISP30-2. Single clusters encoding the biosynthesis of phosphonate, terpene, and siderophore, as well as a single trans-AT polyketide synthase/non-ribosomal peptide synthetase, were identified in both genomes. The most numerous clusters were assigned to the biosynthetic pathways of non-ribosomal peptides and ribosomally synthesized and post-translationally modified peptides. Although four non-ribosomal peptide synthetase gene clusters were predicted to be involved in the biosynthesis of known compounds (fusaricidin, polymyxin B, colistin A, and tridecaptin) of the genus Paenibacillus, discrepancies in the structural organization of the clusters, as well as in the substrate specificity of some adenylation domains, were detected between the reference pathways and the clusters in our study. Among the clusters involved in the biosynthesis of ribosomally synthesized peptides, only one was predicted to be involved in the biosynthesis of a known compound: paenicidin B. Most biosynthetic gene clusters in the genomes of the cave strains showed a low similarity with the reference pathways and were predicted to represent novel biosynthetic pathways. In addition, the cave strains differed in their potential to encode the biosynthesis of a few unique, previously unknown compounds (class II lanthipeptides and three non-ribosomal peptides). The phenotypic characterization of proteinaceous and volatile compounds produced by strains 23TSA30-6 and 28ISP30-2 was also performed, and the results were compared with those of genome mining.

scholarly journals Identification and Characterization of Biosynthetic Gene Clusters from Halophilic Marine Fungus Eurotium rubrum

2020 ◽  
Author(s):  
Obul Reddy Bandapali ◽  
Frederik Teilfeldt Hansen ◽  
Alisha Parveen ◽  
Pradeep Phule ◽  
Emmagouni Sharath Kumar Goud ◽  
...  
Keyword(s):  
Polyketide Synthase ◽  
Gene Clusters ◽  
Marine Fungus ◽  
Type I ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Peptide Synthetase ◽  
Future Drug ◽  
Identification And Characterization

Eurotium rubrum is a halophilic marine ascomycete, which can bear the hypersalinities of the Red Sea and proliferate, while most living entities cannot bear this condition. Recently, a 26.2 Mb assembled genome of this fungus had become available. Marine fungi are fascinating organisms capable of harboring several biosynthetic gene clusters (BGCs), which enables them to produce several natural compounds with antibiotic and anticancerous properties. Understanding the BGCs are critically important for the development of biotechnological applications and the discovery of future drugs. There is no knowledge available on the BGCs of this halophilic marine ascomycete. Herein, we set out to explore and characterize BGCs and the corresponding genes from E. rubrum using bioinformatic methods. We deciphered 36 BGCs in the genome of E. rubrum. These 36 BGCs can be grouped into four non-ribosomal peptide synthetase (NRPS) clusters, eight NRPS-like (NRPSL) BGCs, eight type I polyketide synthase (T1PKS), 11 terpene BGCs including one &beta;-lactone cluster, four hybrid BGCs, and two siderophore BGCs. This study is an example of marine genomics application into potential future drug-like compound discovery.

scholarly journals Population genetic variation analysis of bitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae in China using inter simple sequence repeats (ISSR) molecular markers

2021 ◽  
Author(s):  
Rui Zang ◽  
Ying Zhao ◽  
Kangdi Guo ◽  
Kunqi Hong ◽  
Huijun Xi ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Fusarium Oxysporum ◽  
Diversity Index ◽  
Gene Diversity ◽  
Pcr Amplification ◽  
Bitter Gourd ◽  
Diseased Plant ◽  
Variation Analysis ◽  
Group I

AbstractBitter gourd wilt caused by Fusarium oxysporum f. sp. momordicae (FOM) is a devastating crop disease in China. A total of 173 isolates characteristic of typical Fusarium oxysporum with abundant microconidia and macroconidia on white or ruby colonies were obtained from diseased plant tissues. BLASTn analysis of the rDNA-ITS of the isolates showed 99% identity with F. oxysporum species. Among the tested isolates, three were infectious toward tower gourd and five were pathogenic to bottle gourd. However, all of the isolates were pathogenic to bitter gourd. For genetic differences analysis, 40 ISSR primers were screened and 11 primers were used for ISSR-PCR amplification. In total, 127 loci were detected, of which 76 were polymorphic at a rate of 59.84%. POPGENE analysis showed that Nei’s gene diversity index (H) and Shannon’s information index (I) were 0.09 and 0.15, respectively, which indicated that the genetic diversity of the 173 isolates was low. The coefficient of gene differentiation (Gst = 0.33 > 0.15) indicated that genetic differentiation was mainly among populations. The strength of gene flow (Nm = 1.01 > 1.0) was weak, indicating that the population differentiation caused by gene drift was blocked to some degree. The dendrogram based on ISSR markers showed that the nine geographical populations were clustered into two groups at the threshold of genetic similarity coefficient of 0.96. The Shandong and Henan populations were clustered into Group I, while the Guangdong, Hainan, Guangxi, Fujian, Jiangxi, and Hubei populations constituted Group II. Results of the genetic variation analysis showed that the Hunan and Guangxi populations had the highest degree of genetic differentiation, while the Hubei population had the lowest genetic differentiation. Our findings enrich the knowledge of the genetic variation characteristics of FOM populations with the goal of developing effective disease-management programs and resistance breeding programs.

scholarly journals Genetic Diversity and Phylogenetic Analysis of Citrus tristeza virus Isolates from Turkey

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Gözde Erkiş-Güngör ◽  
Bayram Çevik
Keyword(s):  
Phylogenetic Analysis ◽  
Citrus Tristeza Virus ◽  
Molecular Characteristics ◽  
Cloning And Sequencing ◽  
Phylogenetic Groups ◽  
The 1960S ◽  
Tristeza Virus ◽  
Virus Isolates ◽  
Stem Pitting ◽  
Citrus Tristeza

The presence of Citrus tristeza virus (CTV) in Turkey has been known since the 1960s and the virus was detected in all citrus growing regions of the country. Even though serological and biological characteristics of CTV have been studied since the 1980s, molecular characteristics of CTV isolates have not been studied to date in Turkey. In this study, molecular characteristics of 15 CTV isolates collected from different citrus growing regions of Turkey were determined by amplification, cloning, and sequencing of their major coat protein (CP) genes. The sequence analysis showed that the CP genes were highly conserved among Turkish isolates. However, isolates from different regions showed more genetic variation than isolates from the same region. Turkish isolates were clustered into three phylogenetic groups showing no association with geographical origins, host, or symptoms induced in indicator plants. Phylogenetic analysis of Turkish isolates with isolates from different citrus growing regions of the world including well-characterized type isolates of previously established strain specific groups revealed that some Turkish isolates were closely related to severe quick decline or stem pitting isolates. The results demonstrated that although CTV isolates from Turkey are considered biologically mild, majority of them contain severe components potentially causing quick decline or stem pitting.

scholarly journals Pentaminomycins F and G, First Non-Ribosomal Peptides Containing 2-Pyridylalanine

2020 ◽  
Author(s):  
Daniel Carretero Molina ◽  
Francisco Javier Ortiz-Lopez ◽  
Jesús Martín ◽  
Ignacio González ◽  
Marina Sánchez-Hidalgo ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Gene Cluster ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Peptide Synthetase ◽  
Non Ribosomal Peptides

Pentaminomycins F-H, a group of three new hydroxyarginine-containing cyclic pentapeptides, were isolated from cultures of a <i>Streptomyces cacaoi</i> subsp. <i>cacaoi</i> strain along with the known pentaminomycins A-E. The structures of the new peptides were determined by a combination of mass spectrometry and NMR and Marfey's analyses. Among them, pentaminomycins F and G were shown to contain in their structures the rare amino acid 3-(2-pyridyl)-alanine. This finding represents the first reported example of non-ribosomal peptides containing this residue. The LDLLD chiral sequence found for the three compounds was in agreement with that reported for previously isolated pentaminomycins and consistent with the epimerization domains present in the putative non-robosomal peptide synthetase (NRPS) biosynthetic gene cluster.<br>

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