Isoeugenol monooxygenase and its putative regulatory gene are located in the eugenol metabolic gene cluster in Pseudomonas nitroreducens Jin1

ABSTRACTThe biosynthetic gene cluster of FK228, an FDA-approved anticancer natural product, was identified and sequenced previously. The genetic organization of this gene cluster has now been delineated through systematic gene deletion and transcriptional analysis. As a result, the gene cluster is redefined to contain 12 genes:depAthroughdepJ,depM, and a newly identified pathway regulatory gene,depR.

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The algT Gene of Pseudomonas syringae pv. glycinea andNew Insights into the Transcriptional Organization of thealgT-muc Gene Cluster

Journal of Bacteriology ◽

10.1128/jb.01160-06 ◽

2006 ◽

Vol 188 (23) ◽

pp. 8013-8021 ◽

Cited By ~ 14

Author(s):

Alexander Schenk ◽

Michael Berger ◽

Lisa M. Keith ◽

Carol L. Bender ◽

Georgi Muskhelishvili ◽

...

Keyword(s):

Gene Cluster ◽

Pseudomonas Syringae ◽

Azotobacter Vinelandii ◽

Regulatory Gene ◽

In Planta ◽

Phytopathogenic Bacterium ◽

Reverse Transcription Pcr ◽

Alginate Production ◽

Alginate Biosynthesis

ABSTRACT The phytopathogenic bacterium Pseudomonas syringae pv. glycinea infects soybean plants and causes bacterial blight. In addition to P. syringae, the human pathogen Pseudomonas aeruginosa and the soil bacterium Azotobacter vinelandii produce the exopolysaccharide alginate, a copolymer of d-mannuronic and l-guluronic acids. Alginate production in P. syringae has been associated with increased fitness and virulence in planta. Alginate biosynthesis is tightly controlled by proteins encoded by the algT-muc regulatory gene cluster in P. aeruginosa and A. vinelandii. These genes encode the alternative sigma factor AlgT (σ22), its anti-sigma factors MucA and MucB, MucC, a protein with a controversial function that is absent in P. syringae, and MucD, a periplasmic serine protease and homolog of HtrA in Escherichia coli. We compared an alginate-deficient algT mutant of P. syringae pv. glycinea with an alginate-producing derivative in which algT is intact. The alginate-producing derivative grew significantly slower in vitro growth but showed increased epiphytic fitness and better symptom development in planta. Evaluation of expression levels for algT, mucA, mucB, mucD, and algD, which encodes an alginate biosynthesis gene, showed that mucD transcription is not dependent on AlgT in P. syringae in vitro. Promoter mapping using primer extension experiments confirmed this finding. Results of reverse transcription-PCR demonstrated that algT, mucA, and mucB are cotranscribed as an operon in P. syringae. Northern blot analysis revealed that mucD was expressed as a 1.75-kb monocistronic mRNA in P. syringae.

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The Glucuronic Acid Utilization Gene Cluster from Bacillus stearothermophilus T-6

Journal of Bacteriology ◽

10.1128/jb.181.12.3695-3704.1999 ◽

1999 ◽

Vol 181 (12) ◽

pp. 3695-3704 ◽

Cited By ~ 106

Author(s):

Smadar Shulami ◽

Orit Gat ◽

Abraham L. Sonenshein ◽

Yuval Shoham

Keyword(s):

Gene Cluster ◽

Transport System ◽

Bacillus Stearothermophilus ◽

Glucuronic Acid ◽

Genomic Library ◽

Regulatory Gene ◽

Sugar Transport ◽

Transcriptional Unit ◽

Transport Systems ◽

Potential Operator

ABSTRACT A λ-EMBL3 genomic library of Bacillus stearothermophilus T-6 was screened for hemicellulolytic activities, and five independent clones exhibiting β-xylosidase activity were isolated. The clones overlap each other and together represent a 23.5-kb chromosomal segment. The segment contains a cluster of xylan utilization genes, which are organized in at least three transcriptional units. These include the gene for the extracellular xylanase, xylanase T-6; part of an operon coding for an intracellular xylanase and a β-xylosidase; and a putative 15.5-kb-long transcriptional unit, consisting of 12 genes involved in the utilization of α-d-glucuronic acid (GlcUA). The first four genes in the potential GlcUA operon (orf1, -2, -3, and -4) code for a putative sugar transport system with characteristic components of the binding-protein-dependent transport systems. The most likely natural substrate for this transport system is aldotetraouronic acid [2-O-α-(4-O-methyl-α-d-glucuronosyl)-xylotriose] (MeGlcUAXyl3). The following two genes code for an intracellular α-glucuronidase (aguA) and a β-xylosidase (xynB). Five more genes (kdgK,kdgA, uxaC, uxuA, anduxuB) encode proteins that are homologous to enzymes involved in galacturonate and glucuronate catabolism. The gene cluster also includes a potential regulatory gene, uxuR, the product of which resembles repressors of the GntR family. The apparent transcriptional start point of the cluster was determined by primer extension analysis and is located 349 bp from the initial ATG codon. The potential operator site is a perfect 12-bp inverted repeat located downstream from the promoter between nucleotides +170 and +181. Gel retardation assays indicated that UxuR binds specifically to this sequence and that this binding is efficiently prevented in vitro by MeGlcUAXyl3, the most likely molecular inducer.

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Characterization of the Noncanonical Regulatory and Transporter Genes in Atratumycin Biosynthesis and Production in a Heterologous Host

Marine Drugs ◽

10.3390/md17100560 ◽

2019 ◽

Vol 17 (10) ◽

pp. 560 ◽

Cited By ~ 5

Author(s):

Zhijie Yang ◽

Xin Wei ◽

Jianqiao He ◽

Changli Sun ◽

Jianhua Ju ◽

...

Keyword(s):

Gene Cluster ◽

Streptomyces Coelicolor ◽

Regulatory Gene ◽

Regulatory Protein ◽

Biosynthetic Gene Cluster ◽

Negative Regulator ◽

Over Expression ◽

Lead Compounds ◽

Mycobacteria Tuberculosis ◽

Abc Transporter Genes

Atratumycin is a cyclodepsipeptide with activity against Mycobacteria tuberculosis isolated from deep-sea derived Streptomyces atratus SCSIO ZH16NS-80S. Analysis of the atratumycin biosynthetic gene cluster (atr) revealed that its biosynthesis is regulated by multiple factors, including two LuxR regulatory genes (atr1 and atr2), two ABC transporter genes (atr29 and atr30) and one Streptomyces antibiotic regulatory gene (atr32). In this work, three regulatory and two transporter genes were unambiguously determined to provide positive, negative and self-protective roles during biosynthesis of atratumycin through bioinformatic analyses, gene inactivations and trans-complementation studies. Notably, an unusual Streptomyces antibiotic regulatory protein Atr32 was characterized as a negative regulator; the function of Atr32 is distinct from previous studies. Five over-expression mutant strains were constructed by rational application of the regulatory and transporter genes; the resulting strains produced significantly improved titers of atratumycin that were ca. 1.7–2.3 fold greater than wild-type (WT) producer. Furthermore, the atratumycin gene cluster was successfully expressed in Streptomyces coelicolor M1154, thus paving the way for the transfer and recombination of large DNA fragments. Overall, this finding sets the stage for understanding the unique biosynthesis of pharmaceutically important atratumycin and lays the foundation for generating anti-tuberculosis lead compounds possessing novel structures.

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Expression of qa-1F activator protein: identification of upstream binding sites in the qa gene cluster and localization of the DNA-binding domain.

Molecular and Cellular Biology ◽

10.1128/mcb.7.3.1256 ◽

1987 ◽

Vol 7 (3) ◽

pp. 1256-1266 ◽

Cited By ~ 60

Author(s):

J A Baum ◽

R Geever ◽

N H Giles

Keyword(s):

Dna Binding ◽

Gene Cluster ◽

Transcriptional Control ◽

Protein Identification ◽

Regulatory Gene ◽

Quinic Acid ◽

Binding Domain ◽

Dna Binding Domain ◽

Activator Protein

The qa-1F regulatory gene of Neurospora crassa encodes an activator protein required for quinic acid induction of transcription in the qa gene cluster. This activator protein was expressed in insect cell culture with a baculovirus expression vector. The activator binds to 13 sites in the gene cluster that are characterized by a conserved 16-base-pair sequence of partial dyad symmetry. One site is located between the divergently transcribed qa-1F and qa-1S regulatory genes, corroborating prior evidence that qa-1F is autoregulated and controls expression of the qa-1S repressor. Multiple upstream sites located at variable positions 5' to the qa structural genes appear to allow for greater transcriptional control by qa-1F. Full-length and truncated activator peptides were synthesized in vitro, and the DNA-binding domain was localized to the first 183 amino acids. A 28-amino acid sequence within this region shows striking homology to N-terminal sequences from other lower-eucaryotic activator proteins. A qa-1F(Ts) mutation is located within this putative DNA-binding domain.

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An Aspergillus flavus secondary metabolic gene cluster containing a hybrid PKS–NRPS is necessary for synthesis of the 2-pyridones, leporins

Fungal Genetics and Biology ◽

10.1016/j.fgb.2015.05.010 ◽

2015 ◽

Vol 81 ◽

pp. 88-97 ◽

Cited By ~ 35

Author(s):

Jeffrey W. Cary ◽

Valdet Uka ◽

Zheng Han ◽

Dieter Buyst ◽

Pamela Y. Harris-Coward ◽

...

Keyword(s):

Gene Cluster ◽

Aspergillus Flavus ◽

Metabolic Gene

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Cell Type–Specific Chromatin Decondensation of a Metabolic Gene Cluster in Oats

The Plant Cell ◽

10.1105/tpc.109.072124 ◽

2009 ◽

Vol 21 (12) ◽

pp. 3926-3936 ◽

Cited By ~ 45

Author(s):

Eva Wegel ◽

Rachil Koumproglou ◽

Peter Shaw ◽

Anne Osbourn

Keyword(s):

Gene Cluster ◽

Cell Type ◽

Chromatin Decondensation ◽

Metabolic Gene ◽

Cell Type Specific

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Identification of the nik Gene Cluster of Brucella suis: Regulation and Contribution to Urease Activity

Journal of Bacteriology ◽

10.1128/jb.183.2.426-434.2001 ◽

2001 ◽

Vol 183 (2) ◽

pp. 426-434 ◽

Cited By ~ 45

Author(s):

Véronique Jubier-Maurin ◽

Agnès Rodrigue ◽

Safia Ouahrani-Bettache ◽

Marion Layssac ◽

Marie-Andrée Mandrand-Berthelot ◽

...

Keyword(s):

Gene Cluster ◽

Transport System ◽

Metal Ion ◽

Urease Activity ◽

Regulatory Gene ◽

Transport Systems ◽

Hydrogenase Activity ◽

E Coli ◽

Insertional Inactivation ◽

Brucella Suis

ABSTRACT Analysis of a Brucella suis 1330 gene fused to agfp reporter, and identified as being induced in J774 murine macrophage-like cells, allowed the isolation of a gene homologous to nikA, the first gene of the Escherichia coli operon encoding the specific transport system for nickel. DNA sequence analysis of the corresponding B. suis niklocus showed that it was highly similar to that of E. coliexcept for localization of the nikR regulatory gene, which lies upstream from the structural nikABCDE genes and in the opposite orientation. Protein sequence comparisons suggested that the deduced nikABCDE gene products belong to a periplasmic binding protein-dependent transport system. ThenikA promoter-gfp fusion was activated in vitro by low oxygen tension and metal ion deficiency and was repressed by NiCl2 excess. Insertional inactivation of nikAstrongly reduced the activity of the nickel metalloenzyme urease, which was restored by addition of a nickel excess. Moreover, thenikA mutant of B. suis was functionally complemented with the E. coli nik gene cluster, leading to the recovery of urease activity. Reciprocally, an E. colistrain harboring a deleted nik operon recovered hydrogenase activity by heterologous complementation with the B. suis nik locus. Taking into account these results, we propose that thenik locus of B. suis encodes a nickel transport system. The results further suggest that nickel could enter B. suis via other transport systems. Intracellular growth rates of the B. suis wild-type and nikA mutant strains in human monocytes were similar, indicating that nikA was not essential for this step of infection. We discuss a possible role of nickel transport in maintaining enzymatic activities which could be crucial for survival of the bacteria under the environmental conditions encountered within the host.

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Characterization of a Gene Cluster Involved in 4-Chlorocatechol Degradation by Pseudomonas reinekei MT1

Journal of Bacteriology ◽

10.1128/jb.00331-09 ◽

2009 ◽

Vol 191 (15) ◽

pp. 4905-4915 ◽

Cited By ~ 14

Author(s):

Beatriz Cámara ◽

Patricia Nikodem ◽

Piotr Bielecki ◽

Roberto Bobadilla ◽

Howard Junca ◽

...

Keyword(s):

Gene Cluster ◽

Regulatory Gene ◽

Genomic Region ◽

Genes Encoding ◽

Catechol 1,2 Dioxygenase ◽

Dienelactone Hydrolase ◽

Intradiol Cleavage ◽

Maleylacetate Reductase ◽

Muconate Cycloisomerase

ABSTRACT Pseudomonas reinekei MT1 has previously been reported to degrade 4- and 5-chlorosalicylate by a pathway with 4-chlorocatechol, 3-chloromuconate, 4-chloromuconolactone, and maleylacetate as intermediates, and a gene cluster channeling various salicylates into an intradiol cleavage route has been reported. We now report that during growth on 5-chlorosalicylate, besides a novel (chloro)catechol 1,2-dioxygenase, C12OccaA, a novel (chloro)muconate cycloisomerase, MCIccaB, which showed features not yet reported, was induced. This cycloisomerase, which was practically inactive with muconate, evolved for the turnover of 3-substituted muconates and transforms 3-chloromuconate into equal amounts of cis-dienelactone and protoanemonin, suggesting that it is a functional intermediate between chloromuconate cycloisomerases and muconate cycloisomerases. The corresponding genes, ccaA (C12OccaA) and ccaB (MCIccaB), were located in a 5.1-kb genomic region clustered with genes encoding trans-dienelactone hydrolase (ccaC) and maleylacetate reductase (ccaD) and a putative regulatory gene, ccaR, homologous to regulators of the IclR-type family. Thus, this region includes genes sufficient to enable MT1 to transform 4-chlorocatechol to 3-oxoadipate. Phylogenetic analysis showed that C12OccaA and MCIccaB are only distantly related to previously described catechol 1,2-dioxygenases and muconate cycloisomerases. Kinetic analysis indicated that MCIccaB and the previously identified C12OsalD, rather than C12OccaA, are crucial for 5-chlorosalicylate degradation. Thus, MT1 uses enzymes encoded by a completely novel gene cluster for degradation of chlorosalicylates, which, together with a gene cluster encoding enzymes for channeling salicylates into the ortho-cleavage pathway, form an effective pathway for 4- and 5-chlorosalicylate mineralization.

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