scholarly journals ­Genomic data mining of the marine actinobacteriaStreptomycessp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2912 ◽  
Author(s):  
Agustina Undabarrena ◽  
Juan A. Ugalde ◽  
Michael Seeger ◽  
Beatriz Cámara
Keyword(s):  
Oxidative Stress ◽  
Culture Media ◽  
Genome Mining ◽  
Gene Clusters ◽  
Heavy Metal Resistance ◽  
Morphological Characterization ◽  
Metal Resistance ◽  
Biological Traits ◽  
Strong Response ◽  
Metabolic Versatility

Streptomycessp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureusandL. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search inStreptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derivedStreptomycessp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described forStreptomyces. In addition,Streptomycessp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strainStreptomyces violaceoruberA3(2). Moreover,Streptomycessp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility ofStreptomycessp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment.

scholarly journals Comparative whole-genome analysis of a Thar desert strain Streptomyces sp. JB150 provides deep insights into the encoded parvome and adaptations to desert edaphic system

2021 ◽  
Author(s):  
Dharmesh Harwani ◽  
Jyotsna Begani ◽  
Jyoti Lakhani
Keyword(s):  
Genome Mining ◽  
Compatible Solutes ◽  
Gene Clusters ◽  
Flavin Mononucleotide ◽  
Thar Desert ◽  
Secretion Systems ◽  
Desert Ecosystems ◽  
Whole Genome Analysis ◽  
Genetic Traits ◽  
Metabolic Versatility

AbstractWe sequenced the genome of Streptomyces sp. JB150, isolated from a unique site of the Thar desert in India. Genome mining of the JB150 genome revealed the presence of many interesting secondary metabolic biosynthetic gene clusters (BGCs). The encoded parvome of JB150 includes non-ribosomal peptides, polyketides including β-lactone, butyrolactone, ectoine, lantipeptides, lasso peptides, melanin, resorcinol, siderophores, terpenoids, thiopeptides, and other types of hybrid compounds. Among them, ~30% BGCs displayed a high degree of novelty. The genome of JB150 was enriched for a large assortment of specialized genes coding for the production of many interesting biomolecules comprising compatible solutes, multiple stress-response regulators, transport proteins, protein secretion systems, signaling molecules, chaperones and storage reserves, etc. The presence of diverse members of CAZymes enzyme families, high numbers of riboflavin, flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), trehalose and aromatic compounds synthesis genes, putative orthologues to several of the classical fatty acid synthesis components, prototrophy for many essential amino acids exhibit metabolic versatility of JB150 to inhabit in the extreme desert environment. Besides, the genome of JB150 was observed to specifically encode thiazole-oxazole-modified thiazolemicrocin (TOMM) and ectoine. The comparison of the complete genomes of Streptomyces sp. JB150 and seven other actinomycete strains belonging to different desert ecosystems unveiled the presence of many previously undetected, distinctive, biological, and genomic signatures. We propose that these genetic traits endowed by these strains are essential for their adaptation in the highly underprivileged, extreme ecosystem of the Thar desert to cope with multiple abiotic stressors, oligotrophic nutrient conditions and to produce a huge repertoire of diverse secondary metabolites.

scholarly journals Genomic and Metabolomic Analysis of Antarctic Bacteria Revealed Culture and Elicitation Conditions for the Production of Antimicrobial Compounds

Biomolecules ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 673
Author(s):  
Kattia Núñez-Montero ◽  
Damián Quezada-Solís ◽  
Zeinab G. Khalil ◽  
Robert J. Capon ◽  
Fernando D. Andreote ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
Secondary Metabolites ◽  
Culture Media ◽  
Genome Mining ◽  
Gene Clusters ◽  
Culture Conditions ◽  
Bioactive Metabolites ◽  
Bacterial Strains ◽  
Antarctic Bacteria ◽  
New Antibiotics

Concern about finding new antibiotics against drug-resistant pathogens is increasing every year. Antarctic bacteria have been proposed as an unexplored source of bioactive metabolites; however, most biosynthetic gene clusters (BGCs) producing secondary metabolites remain silent under common culture conditions. Our work aimed to characterize elicitation conditions for the production of antibacterial secondary metabolites from 34 Antarctic bacterial strains based on MS/MS metabolomics and genome mining approaches. Bacterial strains were cultivated under different nutrient and elicitation conditions, including the addition of lipopolysaccharide (LPS), sodium nitroprusside (SNP), and coculture. Metabolomes were obtained by HPLC-QTOF-MS/MS and analyzed through molecular networking. Antibacterial activity was determined, and seven strains were selected for genome sequencing and analysis. Biosynthesis pathways were activated by all the elicitation treatments, which varies among strains and dependents of culture media. Increased antibacterial activity was observed for a few strains and addition of LPS was related with inhibition of Gram-negative pathogens. Antibiotic BGCs were found for all selected strains and the expressions of putative actinomycin, carotenoids, and bacillibactin were characterized by comparison of genomic and metabolomic data. This work established the use of promising new elicitors for bioprospection of Antarctic bacteria and highlights the importance of new “-omics” comparative approaches for drug discovery.

scholarly journals Molecular Characterization of Copper and Cadmium Resistance Determinants in the Biomining Thermoacidophilic ArchaeonSulfolobus metallicus

Archaea ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-16 ◽  
Author(s):  
Alvaro Orell ◽  
Francisco Remonsellez ◽  
Rafaela Arancibia ◽  
Carlos A. Jerez
Keyword(s):  
Heavy Metals ◽  
Gene Cluster ◽  
Stress Responses ◽  
Gene Clusters ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Cadmium Resistance ◽  
Resistance Determinants ◽  
Thermophilic Archaeon ◽  
General Response

Sulfolobus metallicusis a thermoacidophilic crenarchaeon used in high-temperature bioleaching processes that is able to grow under stressing conditions such as high concentrations of heavy metals. Nevertheless, the genetic and biochemical mechanisms responsible for heavy metal resistance inS. metallicusremain uncharacterized. Proteomic analysis ofS. metallicuscells exposed to 100 mM Cu revealed that 18 out of 30 upregulated proteins are related to the production and conversion of energy, amino acids biosynthesis, and stress responses. Ten of these last proteins were also up-regulated inS. metallicustreated in the presence of 1 mM Cd suggesting that at least in part, a common general response to these two heavy metals. TheS. metallicusgenome contained two completecopgene clusters, each encoding a metallochaperone (CopM), a Cu-exporting ATPase (CopA), and a transcriptional regulator (CopT). Transcriptional expression analysis revealed thatcopMandcopAfrom eachcopgene cluster were cotranscribed and their transcript levels increased whenS. metallicuswas grown either in the presence of Cu or using chalcopyrite (CuFeS2) as oxidizable substrate. This study shows for the first time the presence of a duplicated version of thecopgene cluster inArchaeaand characterizes some of the Cu and Cd resistance determinants in a thermophilic archaeon employed for industrial biomining.

scholarly journals Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil

2020 ◽  
Author(s):  
Agnieszka Klonowska ◽  
Lionel Moulin ◽  
Julie Kaye Ardley ◽  
Florence Braun ◽  
Margaret Mary Gollagher ◽  
...  
Keyword(s):  
Heavy Metal ◽  
New Species ◽  
New Caledonia ◽  
Draft Genome ◽  
Gene Clusters ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Mimosa Pudica ◽  
Protein Coding ◽  
A New Species

Abstract Background Cupriavidus strain STM 6070 was isolated from nickel-rich soil collected near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly effective at fixing nitrogen with M. pudica. Here we have provided an updated taxonomy for STM 6070 and described salient features of the annotated genome, focusing on heavy metal resistance (HMR) loci and heavy metal efflux (HME) systems.Results The 6,771,773 bp high-quality-draft genome consists of 107 scaffolds containing 6,118 protein-coding genes. ANI values show that STM 6070 is a new species of Cupriavidus. The STM 6070 symbiotic region was syntenic with that of the M. pudica-nodulating Cupriavidus taiwanensis LMG 19424T. In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni2+ and Zn2+ concentrations. The STM 6070 genome contains 55 genes, located in 12 clusters, that encode HMR structural proteins belonging to the RND, MFS, CHR, ARC3, CDF and P-ATPase protein superfamilies. These HMR molecular determinants are putatively involved in arsenic (ars), chromium (chr), cobalt-zinc-cadmium (czc), copper (cop, cup), nickel (nie and nre), and silver and/or copper (sil) resistance. Seven of these HMR clusters were common to symbiotic and non-symbiotic Cupriavidus species, while four clusters were specific to STM 6070, with three of these being associated with insertion sequences. Within the specific STM 6070 HMR clusters, three novel HME-RND systems (nieIC cep nieBA, czcC2B2A2, and hmxB zneAC zneR hmxS) were identified, which constitute new candidate genes for nickel and zinc resistance.Conclusions STM 6070 belongs to a new Cupriavidus species, for which we have proposed the name Cupriavidus neocaledonicus sp. nov.. STM6070 harbours a pSym with a high degree of gene conservation to the pSyms of M. pudica-nodulating C. taiwanensis strains, probably as a result of recent horizontal transfer. The presence of specific HMR clusters, associated with transposase genes, suggests that the selection pressure of the New Caledonian ultramafic soils has driven the specific adaptation of STM 6070 to heavy-metal-rich soils via horizontal gene transfer.

scholarly journals Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil

2020 ◽  
Author(s):  
Agnieszka Klonowska ◽  
Lionel Moulin ◽  
Julie Ardley ◽  
Florence Braun ◽  
Margaret Gollagher ◽  
...  
Keyword(s):  
Heavy Metal ◽  
New Species ◽  
New Caledonia ◽  
Draft Genome ◽  
Gene Clusters ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Mimosa Pudica ◽  
Protein Coding ◽  
A New Species

Abstract Background Cupriavidus strain STM 6070 was isolated from nickel-rich soil collected near Koniambo massif, New Caledonia, using the invasive legume trap host Mimosa pudica. STM 6070 is a heavy metal-tolerant strain that is highly effective at fixing nitrogen with M. pudica. Here we have provided an updated taxonomy for STM 6070 and described salient features of the annotated genome, focusing on heavy metal resistance (HMR) loci and heavy metal efflux (HME) systems.Results The 6,771,773 bp high-quality-draft genome consists of 107 scaffolds containing 6,118 protein-coding genes. ANI values show that STM 6070 is a new species of Cupriavidus. The STM 6070 symbiotic region was syntenic with that of the M. pudica-nodulating Cupriavidus taiwanensis LMG 19424T. In contrast to the nickel and zinc sensitivity of C. taiwanensis strains, STM 6070 grew at high Ni2+ and Zn2+ concentrations. The STM 6070 genome contains 55 genes, located in 12 clusters, that encode HMR structural proteins belonging to the RND, MFS, CHR, ARC3, CDF and P-ATPase protein superfamilies. These HMR molecular determinants are putatively involved in arsenic (ars), chromium (chr), cobalt-zinc-cadmium (czc), copper (cop, cup), nickel (nie and nre), and silver and/or copper (sil) resistance. Seven of these HMR clusters were common to symbiotic and non-symbiotic Cupriavidus species, while four clusters were specific to STM 6070, with three of these being associated with insertion sequences. Within the specific STM 6070 HMR clusters, three novel HME-RND systems (nieIC cep nieBA, czcC2B2A2, and hmxB zneAC zneR hmxS) were identified, which constitute new candidate genes for nickel and zinc resistance.Conclusions STM 6070 belongs to a new Cupriavidus species, for which we have proposed the name Cupriavidus neocaledonicus sp. nov.. STM6070 harbours a pSym with a high degree of gene conservation to the pSyms of M. pudica-nodulating C. taiwanensis strains, probably as a result of recent horizontal transfer. The presence of specific HMR clusters, associated with transposase genes, suggests that the selection pressure of the New Caledonian ultramafic soils has driven the specific adaptation of STM 6070 to heavy-metal-rich soils via horizontal gene transfer.

scholarly journals Integrase-Controlled Excision of Metal-Resistance Genomic Islands in Acinetobacter baumannii

Genes ◽  
2018 ◽  
Vol 9 (7) ◽  
pp. 366 ◽  
Author(s):  
Zaaima AL-Jabri ◽  
Roxana Zamudio ◽  
Eva Horvath-Papp ◽  
Joseph Ralph ◽  
Zakariya AL-Muharrami ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Acinetobacter Baumannii ◽  
Core Genome ◽  
Susceptibility Testing ◽  
Gene Clusters ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Genomic Islands ◽  
Genome Plasticity ◽  
E Coli

Genomic islands (GIs) are discrete gene clusters encoding for a variety of functions including antibiotic and heavy metal resistance, some of which are tightly associated to lineages of the core genome phylogenetic tree. We have investigated the functions of two distinct integrase genes in the mobilization of two metal resistant GIs, G08 and G62, of Acinetobacter baumannii. Real-time PCR demonstrated integrase-dependent GI excision, utilizing isopropyl β-d-1-thiogalactopyranoside IPTG-inducible integrase genes in plasmid-based mini-GIs in Escherichia coli. In A. baumannii, integrase-dependent excision of the original chromosomal GIs could be observed after mitomycin C induction. In both E. coli plasmids and A. baumannii chromosome, the rate of excision and circularization was found to be dependent on the expression level of the integrases. Susceptibility testing in A. baumannii strain ATCC 17978, A424, and their respective ΔG62 and ΔG08 mutants confirmed the contribution of the GI-encoded efflux transporters to heavy metal decreased susceptibility. In summary, the data evidenced the functionality of two integrases in the excision and circularization of the two Acinetobacter heavy-metal resistance GIs, G08 and G62, in E. coli, as well as when chromosomally located in their natural host. These recombination events occur at different frequencies resulting in genome plasticity and may participate in the spread of resistance determinants in A. baumannii.

scholarly journals Genomic and Physiological Properties of a Facultative Methane-Oxidizing Bacterial Strain of Methylocystis sp. from a Wetland

2020 ◽  
Vol 8 (11) ◽  
pp. 1719
Author(s):  
Gi-Yong Jung ◽  
Sung-Keun Rhee ◽  
Young-Soo Han ◽  
So-Jeong Kim
Keyword(s):  
Methane Oxidation ◽  
Carbon Sources ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Phylogenomic Analysis ◽  
Atmospheric Methane ◽  
Methane Oxidizing Bacteria ◽  
Metabolic Versatility ◽  
Physiological Properties ◽  
Ph Range

Methane-oxidizing bacteria are crucial players in controlling methane emissions. This study aimed to isolate and characterize a novel wetland methanotroph to reveal its role in the wetland environment based on genomic information. Based on phylogenomic analysis, the isolated strain, designated as B8, is a novel species in the genus Methylocystis. Strain B8 grew in a temperature range of 15 °C to 37 °C (optimum 30–35 °C) and a pH range of 6.5 to 10 (optimum 8.5–9). Methane, methanol, and acetate were used as carbon sources. Hydrogen was produced under oxygen-limited conditions. The assembled genome comprised of 3.39 Mbp and 59.9 mol% G + C content. The genome contained two types of particulate methane monooxygenases (pMMO) for low-affinity methane oxidation (pMMO1) and high-affinity methane oxidation (pMMO2). It was revealed that strain B8 might survive atmospheric methane concentration. Furthermore, the genome had various genes for hydrogenase, nitrogen fixation, polyhydroxybutyrate synthesis, and heavy metal resistance. This metabolic versatility of strain B8 might enable its survival in wetland environments.

scholarly journals Metagenomics Revealing Molecular Profiling of Microbial Community Structure and Metabolic Capacity In Bamucuo, Tibet

2021 ◽  
Author(s):  
Cai Wei ◽  
Dan Sun ◽  
Wenliang Yuan ◽  
Lei Li ◽  
Chaoxu Dai ◽  
...  
Keyword(s):  
Microbial Community ◽  
Carbon Fixation ◽  
Microbial Community Composition ◽  
Gene Clusters ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Tibet Plateau ◽  
Metabolic Capacity ◽  
Bioactive Substances ◽  
Bacterial Phyla

Abstract Background: The Qinghai-Tibet Plateau (QTP) is the highest plateau in the world, and the microorganisms there play vital ecological roles in the global biogeochemical cycle; however, detailed information on the microbial communities in QTP is still lacking. Results: Here, we performed a landscape survey of the microorganisms in Bamucuo, Tibet, resulting in 160,212 (soil) and 135,994 (water) contigs by shotgun metagenomic methods, and generated 75 nearly complete metagenome-assembled genomes (MAGs). Proteobacteria, Actinobacteria and Firmicutes were found to be the three most dominant bacterial phyla, while Euryarchaeota was the most dominant archaeal phylum. Surprisingly, Pandoravirus salinus was found in the soil microbial community. The KEGG annotations showed that the genes related to metabolism accounted for 62.9% (soil) and 58.4% (water), respectively. Of the 75 MAGs, 63 were found to contain the genes related to all the six carbon fixation pathways, and the heavy metal resistance genes, the pressure response subsystem, and the secondary metabolite biosynthesis gene clusters (BGCs) were discovered to be abundant. Conclusions: We concluded that the microorganisms in Bamucuo fix carbon mainly through the 3-hydroxypropionic bi-cycle pathway; this study, for the first time, characterized the microbial community composition and metabolic capacity in QTP high-altitude areas (with an altitude of 4,555 meters), confirmed that QTP is a huge and valuable resource bank in which more new non-resistant antibiotics and many other bioactive substances could be developed, and provided the expanded information for further microbial community studies in QTP.

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