scholarly journals Two Angular Dioxygenases Contribute to the Metabolic Versatility of Dibenzofuran-Degrading Rhodococcus sp. Strain HA01

2008 ◽  
Vol 74 (12) ◽  
pp. 3812-3822 ◽  
Author(s):  
Hamdy A. H. Aly ◽  
Nguyen B. Huu ◽  
Victor Wray ◽  
Howard Junca ◽  
Dietmar H. Pieper
Keyword(s):  
Angular Position ◽  
Gene Clusters ◽  
The Novel ◽  
High Similarity ◽  
Complementary Activity ◽  
Metabolic Versatility ◽  
Oxygenase Activity ◽  
Angular Dioxygenation ◽  
Low Activity ◽  
Rhodococcus Sp

ABSTRACT Rhodococcus sp. strain HA01, isolated through its ability to utilize dibenzofuran (DBF) as the sole carbon and energy source, was also capable, albeit with low activity, of transforming dibenzo-p-dioxin (DD). This strain could also transform 3-chlorodibenzofuran (3CDBF), mainly by angular oxygenation at the ether bond-carrying carbon (the angular position) and an adjacent carbon atom, to 4-chlorosalicylate as the end product. Similarly, 2-chlorodibenzofuran (2CDBF) was transformed to 5-chlorosalicylate. However, lateral oxygenation at the 3,4-positions was also observed and yielded the novel product 2-chloro-3,4-dihydro-3,4-dihydroxydibenzofuran. Two gene clusters encoding enzymes for angular oxygenation (dfdA1A2A3A4 and dbfA1A2) were isolated, and expression of both was observed during growth on DBF. Heterologous expression revealed that both oxygenase systems catalyze angular oxygenation of DBF and DD but exhibited complementary substrate specificity with respect to CDBF transformation. While DfdA1A2A3A4 oxygenase, with high similarity to DfdA1A2A3A4 oxygenase from Terrabacter sp. strain YK3, transforms 3CDBF by angular dioxygenation at a rate of 29% ± 4% that of DBF, 2CDBF was not transformed. In contrast, DbfA1A2 oxygenase, with high similarity to the DbfA1A2 oxygenase from Terrabacter sp. strain DBF63, exhibited complementary activity with angular oxygenase activity against 2CDBF but negligible activity against 3CDBF. Thus, Rhodococcus sp. strain HA01 constitutes the first described example of a bacterial strain where coexpression of two angular dioxygenases was observed. Such complementary activity allows for the efficient transformation of chlorinated DBFs.

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.

Updated analysis of the surface carbohydrate gene clusters in the diverse panel of Acinetobacter baumannii isolates.

2021 ◽  
Author(s):  
Johanna J Kenyon ◽  
Ruth M. Hall
Keyword(s):  
Acinetobacter Baumannii ◽  
Capsular Polysaccharide ◽  
Gene Clusters ◽  
Outer Core ◽  
The Novel

To enhance the utility of the genetically diverse panel of Acinetobacter baumannii isolates reported recently by Galac and co-workers (AAC 64: e00840-20) and to identify the novel KL and OCL, all of the gene clusters that direct the biosynthesis of capsular polysaccharide and of the outer core of lipooligosaccharide, respectively, were re-examined. The nine KL and one OCL previously recorded as novel were identified and nine further novel KL and two OCL were found.

scholarly journals Draft Genome Sequence of Lactobacillus rhamnosus OSU-PECh-69, a Cheese Isolate with Antibacterial Activity

2020 ◽  
Vol 9 (37) ◽  
Author(s):  
Israel García-Cano ◽  
Walaa E. Hussein ◽  
Diana Rocha-Mendoza ◽  
Ahmed E. Yousef ◽  
Rafael Jiménez-Flores
Keyword(s):  
Genome Sequence ◽  
Antimicrobial Agents ◽  
Draft Genome ◽  
Lactobacillus Rhamnosus ◽  
Gc Content ◽  
Gene Clusters ◽  
Gram Negative Bacteria ◽  
The Novel ◽  
Content Type ◽  
A Genome

ABSTRACT The novel strain Lactobacillus rhamnosus OSU-PECh-69 was isolated from provolone cheese. It produces antimicrobial agents having a molecular mass of 5 to 10 kDa that are active against Gram-positive and Gram-negative bacteria. The strain has a genome sequence of 3,057,669 bp, a GC content of 46.6%, and up to two gene clusters encoding bacteriocins.

scholarly journals Genetic Characterization and Evolutionary Implications of a car Gene Cluster in the Carbazole Degrader Pseudomonas sp. Strain CA10

2001 ◽  
Vol 183 (12) ◽  
pp. 3663-3679 ◽  
Author(s):  
Hideaki Nojiri ◽  
Hiroyo Sekiguchi ◽  
Kana Maeda ◽  
Masaaki Urata ◽  
Sei-Ichiro Nakai ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Insertion Sequence ◽  
Gene Clusters ◽  
Open Reading Frames ◽  
The Novel ◽  
Gene Duplications ◽  
Homology Searching ◽  
Reading Frames ◽  
Strain Ca10 ◽  
Recombination Gene

ABSTRACT The nucleotide sequences of the 27,939-bp-long upstream and 9,448-bp-long downstream regions of thecarAaAaBaBbCAc(ORF7)Ad genes of carbazole-degrading Pseudomonas sp. strain CA10 were determined. Thirty-two open reading frames (ORFs) were identified, and the car gene cluster was consequently revealed to consist of 10 genes (carAaAaBaBbCAcAdDFE) encoding the enzymes for the three-step conversion of carbazole to anthranilate and the degradation of 2-hydroxypenta-2,4-dienoate. The high identities (68 to 83%) with the enzymes involved in 3-(3-hydroxyphenyl)propionic acid degradation were observed only for CarFE. This observation, together with the fact that two ORFs are inserted between carDand carFE, makes it quite likely that thecarFE genes were recruited from another locus. In the 21-kb region upstream from carAa, aromatic-ring-hydroxylating dioxygenase genes (ORF26, ORF27, and ORF28) were found. Inductive expression in carbazole-grown cells and the results of homology searching indicate that these genes encode the anthranilate 1,2-dioxygenase involved in carbazole degradation. Therefore, these ORFs were designated antABC. Four homologous insertion sequences, IS5car1 to IS5car4, were identified in the neighboring regions ofcar and ant genes. IS5car2and IS5car3 constituted the putative composite transposon containing antABC. One-ended transposition of IS5car2 together with the 5′ portion ofantA into the region immediately upstream ofcarAa had resulted in the formation of IS5car1 and ORF9. In addition to the insertion sequence-dependent recombination, gene duplications and presumed gene fusion were observed. In conclusion, through the above gene rearrangement, the novel genetic structure of the cargene cluster has been constructed. In addition, it was also revealed that the car and ant gene clusters are located on the megaplasmid pCAR1.

scholarly journals Biodegradation of Tetralin: Genomics, Gene Function and Regulation

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 339 ◽  
Author(s):  
Belén Floriano ◽  
Eduardo Santero ◽  
Francisca Reyes-Ramírez
Keyword(s):  
Gene Expression ◽  
Current Knowledge ◽  
Gene Clusters ◽  
Sole Source ◽  
Regulatory Elements ◽  
Catabolic Pathway ◽  
Regulatory Systems ◽  
Biochemical Genetic ◽  
Complex Regulation ◽  
Rhodococcus Sp

Tetralin (1,2,3,4-tetrahydonaphthalene) is a recalcitrant compound that consists of an aromatic and an alicyclic ring. It is found in crude oils, produced industrially from naphthalene or anthracene, and widely used as an organic solvent. Its toxicity is due to the alteration of biological membranes by its hydrophobic character and to the formation of toxic hydroperoxides. Two unrelated bacteria, Sphingopyxis granuli strain TFA and Rhodococcus sp. strain TFB were isolated from the same niche as able to grow on tetralin as the sole source of carbon and energy. In this review, we provide an overview of current knowledge on tetralin catabolism at biochemical, genetic and regulatory levels in both strains. Although they share the same biodegradation strategy and enzymatic activities, no evidences of horizontal gene transfer between both bacteria have been found. Moreover, the regulatory elements that control the expression of the gene clusters are completely different in each strain. A special consideration is given to the complex regulation discovered in TFA since three regulatory systems, one of them involving an unprecedented communication between the catabolic pathway and the regulatory elements, act together at transcriptional and posttranscriptional levels to optimize tetralin biodegradation gene expression to the environmental conditions.

scholarly journals Biosynthetic Potential of a Novel Antarctic Actinobacterium Marisediminicola antarctica ZS314T Revealed by Genomic Data Mining and Pigment Characterization

Marine Drugs ◽  
2019 ◽  
Vol 17 (7) ◽  
pp. 388 ◽  
Author(s):  
Li Liao ◽  
Shiyuan Su ◽  
Bin Zhao ◽  
Chengqi Fan ◽  
Jin Zhang ◽  
...  
Keyword(s):  
Data Mining ◽  
Natural Products ◽  
Gene Cluster ◽  
Genomic Data ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
The Novel ◽  
Biosynthetic Gene ◽  
Base Pairs ◽  
Peptide Synthetase

Rare actinobacterial species are considered as potential resources of new natural products. Marisediminicola antarctica ZS314T is the only type strain of the novel actinobacterial genus Marisediminicola isolated from intertidal sediments in East Antarctica. The strain ZS314T was able to produce reddish orange pigments at low temperatures, showing characteristics of carotenoids. To understand the biosynthetic potential of this strain, the genome was completely sequenced for data mining. The complete genome had 3,352,609 base pairs (bp), much smaller than most genomes of actinomycetes. Five biosynthetic gene clusters (BGCs) were predicted in the genome, including a gene cluster responsible for the biosynthesis of C50 carotenoid, and four additional BGCs of unknown oligosaccharide, salinixanthin, alkylresorcinol derivatives, and NRPS (non-ribosomal peptide synthetase) or amino acid-derived compounds. Further experimental characterization indicated that the strain may produce C.p.450-like carotenoids, supporting the genomic data analysis. A new xanthorhodopsin gene was discovered along with the analysis of the salinixanthin biosynthetic gene cluster. Since little is known about this genus, this work improves our understanding of its biosynthetic potential and provides opportunities for further investigation of natural products and strategies for adaptation to the extreme Antarctic environment.

scholarly journals Transcriptome Analysis of Aspergillus flavus RevealsveA-Dependent Regulation of Secondary Metabolite Gene Clusters, Including the Novel Aflavarin Cluster

2015 ◽  
Vol 14 (10) ◽  
pp. 983-997 ◽  
Author(s):  
J. W. Cary ◽  
Z. Han ◽  
Y. Yin ◽  
J. M. Lohmar ◽  
S. Shantappa ◽  
...  
Keyword(s):  
Secondary Metabolism ◽  
Secondary Metabolite ◽  
Aspergillus Flavus ◽  
Gene Clusters ◽  
Fungal Species ◽  
The Novel ◽  
Content Type ◽  
Expression Of Genes ◽  
Number Of Genes ◽  
Fungal Secondary Metabolism

ABSTRACTThe global regulatoryveAgene governs development and secondary metabolism in numerous fungal species, includingAspergillus flavus. This is especially relevant sinceA. flavusinfects crops of agricultural importance worldwide, contaminating them with potent mycotoxins. The most well-known are aflatoxins, which are cytotoxic and carcinogenic polyketide compounds. The production of aflatoxins and the expression of genes implicated in the production of these mycotoxins areveAdependent. The genes responsible for the synthesis of aflatoxins are clustered, a signature common for genes involved in fungal secondary metabolism. Studies of theA. flavusgenome revealed many gene clusters possibly connected to the synthesis of secondary metabolites. Many of these metabolites are still unknown, or the association between a known metabolite and a particular gene cluster has not yet been established. In the present transcriptome study, we show thatveAis necessary for the expression of a large number of genes. Twenty-eight out of the predicted 56 secondary metabolite gene clusters include at least one gene that is differentially expressed depending on presence or absence ofveA. One of the clusters under the influence ofveAis cluster 39. The absence ofveAresults in a downregulation of the five genes found within this cluster. Interestingly, our results indicate that the cluster is expressed mainly in sclerotia. Chemical analysis of sclerotial extracts revealed that cluster 39 is responsible for the production of aflavarin.

scholarly journals Targeted induction of a silent fungal gene cluster encoding the bacteria-specific germination inhibitor fumigermin

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Maria Cristina Stroe ◽  
Tina Netzker ◽  
Kirstin Scherlach ◽  
Thomas Krüger ◽  
Christian Hertweck ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Polyketide Synthase ◽  
Biological Activities ◽  
Gene Clusters ◽  
Ecological Function ◽  
The Novel ◽  
Ecological Context ◽  
Fungal Metabolite ◽  
Silent Gene ◽  
Encoding Gene

Microorganisms produce numerous secondary metabolites (SMs) with various biological activities. Many of their encoding gene clusters are silent under standard laboratory conditions because for their activation they need the ecological context, such as the presence of other microorganisms. The true ecological function of most SMs remains obscure, but understanding of both the activation of silent gene clusters and the ecological function of the produced compounds is of importance to reveal functional interactions in microbiomes. Here, we report the identification of an as-yet uncharacterized silent gene cluster of the fungus Aspergillus fumigatus, which is activated by the bacterium Streptomyces rapamycinicus during the bacterial-fungal interaction. The resulting natural product is the novel fungal metabolite fumigermin, the biosynthesis of which requires the polyketide synthase FgnA. Fumigermin inhibits germination of spores of the inducing S. rapamycinicus, and thus helps the fungus to defend resources in the shared habitat against a bacterial competitor.

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