scholarly journals Cyanate Assimilation by the Alkaliphilic Cyanide-Degrading Bacterium Pseudomonas pseudoalcaligenes CECT5344: Mutational Analysis of the cyn Gene Cluster

2019 ◽  
Vol 20 (12) ◽  
pp. 3008 ◽  
Author(s):  
Lara Paloma Sáez ◽  
Purificación Cabello ◽  
María Isabel Ibáñez ◽  
Víctor Manuel Luque-Almagro ◽  
María Dolores Roldán ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Mutational Analysis ◽  
Batch Reactor ◽  
Transcriptional Analysis ◽  
Transcriptional Unit ◽  
Pseudomonas Pseudoalcaligenes ◽  
Degrading Bacterium ◽  
Cyanide Degradation ◽  
Alkaliphilic Bacterium ◽  
Reactor Operating

The alkaliphilic bacterium Pseudomonas pseudoalcaligenes CECT5344 can grow with cyanate, cyanide, or cyanide-containing industrial residues as the sole nitrogen source, but the assimilation of cyanide and cyanate takes place through independent pathways. Therefore, cyanide degradation involves a chemical reaction between cyanide and oxaloacetate to form a nitrile that is hydrolyzed to ammonium by the nitrilase NitC, whereas cyanate assimilation requires a cyanase that catalyzes cyanate decomposition to ammonium and carbon dioxide. The P. pseudoalcaligenes CECT5344 cynFABDS gene cluster codes for the putative transcriptional regulator CynF, the ABC-type cyanate transporter CynABD, and the cyanase CynS. In this study, transcriptional analysis revealed that the structural cynABDS genes constitute a single transcriptional unit, which was induced by cyanate and repressed by ammonium. Mutational characterization of the cyn genes indicated that CynF was essential for cynABDS gene expression and that nitrate/nitrite transporters may be involved in cyanate uptake, in addition to the CynABD transport system. Biodegradation of hazardous jewelry wastewater containing high amounts of cyanide and metals was achieved in a batch reactor operating at an alkaline pH after chemical treatment with hydrogen peroxide to oxidize cyanide to cyanate.

Alkaline cyanide degradation by Pseudomonas pseudoalcaligenes CECT5344 in a batch reactor. Influence of pH

2010 ◽  
Vol 179 (1-3) ◽  
pp. 72-78 ◽  
Author(s):  
M.J. Huertas ◽  
L.P. Sáez ◽  
M.D. Roldán ◽  
V.M. Luque-Almagro ◽  
M. Martínez-Luque ◽  
...  
Keyword(s):  
Batch Reactor ◽  
Pseudomonas Pseudoalcaligenes ◽  
Cyanide Degradation ◽  
Influence Of Ph

scholarly journals Transcriptional Analysis of the hmw Gene Cluster of Mycoplasma pneumoniae

1999 ◽  
Vol 181 (16) ◽  
pp. 4978-4985 ◽  
Author(s):  
Robert H. Waldo ◽  
Phillip L. Popham ◽  
Cynthia E. Romero-Arroyo ◽  
Elizabeth A. Mothershed ◽  
Kyungok K. Lee ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Mycoplasma Pneumoniae ◽  
Open Reading Frames ◽  
Host Cells ◽  
Transcriptional Analysis ◽  
Transcriptional Unit ◽  
S1 Nuclease ◽  
Effect Analysis ◽  
Reverse Transcription Pcr ◽  
Reading Frames

ABSTRACT Mycoplasma pneumoniae adherence to host cells is a multifactorial process that requires the cytadhesin P1 and additional accessory proteins. The hmw gene cluster consists of the genes p30, hmw3, and hmw1, the products of which are known to be essential for cytadherence, therpsD gene, and six open reading frames of unknown function. Putative transcriptional terminators flank this locus, raising the possibility that these genes are expressed as a single transcriptional unit. However, S1 nuclease protection and primer extension experiments identified probable transcriptional start sites upstream of thep32, p21, p50, and rpsDgenes. Each was preceded at the appropriate spacing by the −10-like sequence TTAAAATT, but the −35 regions were not conserved. Analysis of the M. pneumoniae genome sequence indicated that this promoter-like sequence is found upstream of only a limited number of open reading frames, including the genes for P65 and P200, which are structurally related to HMW1 and HMW3. Promoter deletion studies demonstrated that the promoter-like region upstream ofp21 was necessary for the expression of p30 and an hmw3-cat fusion in M. pneumoniae, while deletion of the promoter-like region upstream of p32 had no apparent effect. Analysis by reverse transcription-PCR confirmed transcriptional linkage of all the open reading frames in thehmw gene cluster. Taken together, these findings suggest that the genes of this locus constitute an operon expressed from overlapping transcripts.

scholarly journals New Insights into the Genetic Organization of the FK228 Biosynthetic Gene Cluster inChromobacterium violaceumNo. 968

2010 ◽  
Vol 77 (4) ◽  
pp. 1508-1511 ◽  
Author(s):  
Vishwakanth Y. Potharla ◽  
Shane R. Wesener ◽  
Yi-Qiang Cheng
Keyword(s):  
Natural Product ◽  
Gene Cluster ◽  
Gene Deletion ◽  
Regulatory Gene ◽  
Biosynthetic Gene Cluster ◽  
Transcriptional Analysis ◽  
Biosynthetic Gene ◽  
Genetic Organization

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.

scholarly journals Identification and Characterization of Cotinine Hydroxylase CotA that Initiates biodegradation of Wastewater Micropollutant Cotinine in Nocardioides sp. Strain JQ2195

2021 ◽  
Author(s):  
Lingling Zhao ◽  
Zhenyang Zhao ◽  
Kaiyun Zhang ◽  
Xuan Zhang ◽  
Siqiong Xu ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Tobacco Consumption ◽  
Hydroxyl Group ◽  
Carbon And Nitrogen ◽  
Enzymatic Transformation ◽  
Degrading Bacterium ◽  
Hydroxylase Gene ◽  
Urine Cotinine ◽  
Genetic Mechanisms

Cotinine is a stable toxic contaminant, produced as a byproduct of smoking. It is of emerging concern due to its global distribution in aquatic environments. Microorganisms have the potential to degrade cotinine, however, the genetic mechanisms of this process are unknown. Nocardioides sp. strain JQ2195 is a pure culture strain that has been reported to degrade cotinine at micropollutant concentrations. This strain utilizes cotinine as its sole carbon and nitrogen source. In this study, a 50 kb gene cluster (designated as cot ) involved in cotinine degradation, was predicted based on genomic and transcriptomic analyses. A novel three-component cotinine hydroxylase gene (designated as cotA1A2A3 ), which initiated cotinine catabolism was identified and characterized. CotA from Shinella sp. HZN7 was heterologously expressed and purified, and shown to convert cotinine into 6-hydroxycotinine. H 2 18 O-labelling and ESI-MS analysis confirmed that the hydroxyl group incorporated into 6-hydroxycotinine was derived from water. This study provides new molecular insights into the microbial metabolism of heterocyclic chemical pollutants. IMPORTANCE In the human body, cotinine is the major metabolite of nicotine, and 10–15% of generated cotinine is excreted in urine. Cotinine is a structural analogue of nicotine and is much more stable than nicotine. Increased tobacco consumption has led to high environmental concentrations of cotinine, which may have detrimental effects on aquatic ecosystems and human health. Nocardioides sp. strain JQ2195 is a unique cotinine-degrading bacterium. However, the underlying genetic and biochemical foundations of cotinine degradation are still unknown. In this study, a 50 kb gene cluster (designated cot ) was identified by genomic and transcriptomic analyses as being involved in the degradation of cotinine. A novel three-component cotinine hydroxylase gene (designated cotA1A2A3 ) catalyzed cotinine to 6-hydroxy-cotinine. This study provides new molecular insights into the microbial degradation and enzymatic transformation of cotinine.

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

1999 ◽  
Vol 181 (12) ◽  
pp. 3695-3704 ◽  
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.

Characterization and analysis of an industrial strain of Streptomyces bingchenggensis by genome sequencing and gene microarray

Genome ◽  
2013 ◽  
Vol 56 (11) ◽  
pp. 677-689 ◽  
Author(s):  
Xiang-Jing Wang ◽  
Bo Zhang ◽  
Yi-Jun Yan ◽  
Jing An ◽  
Ji Zhang ◽  
...  
Keyword(s):  
Natural Products ◽  
Gene Cluster ◽  
Crop Protection ◽  
Gc Content ◽  
Gene Clusters ◽  
High Expression ◽  
Expression Level ◽  
Transcriptional Analysis ◽  
Streptomyces Bingchenggensis ◽  
High Expression Level

Streptomyces bingchenggensis is a soil bacterium that produces milbemycins, a family of macrolide antibiotics that are commercially important in crop protection and veterinary medicine. In addition, S. bingchenggensis produces many other natural products including the polyether nanchangmycin and novel cyclic pentapeptides. To identify the gene clusters involved in the biosynthesis of these compounds, and better clarify the biochemical pathways of these gene clusters, the whole genome of S. bingchenggensis was sequenced, and the transcriptome profile was subsequently investigated by microarray. In comparison with other sequenced genomes in Streptomyces, S. bingchenggensis has the largest linear chromosome consisting of 11 936 683 base pairs (bp), with an average GC content of 70.8%. The 10 023 predicted protein-coding sequences include at least 47 gene clusters correlated with the biosynthesis of known or predicted secondary metabolites. Transcriptional analysis demonstrated an extremely high expression level of the milbemycin gene cluster during the entire growth period and a moderately high expression level of the nanchangmycin gene cluster during the initial hours that subsequently decreased. However, other gene clusters appear to be silent. The genome-wide analysis of the secondary metabolite gene clusters in S. bingchenggensis, coupled with transcriptional analysis, will facilitate the rational development of high milbemycins-producing strains as well as the discovery of new natural products.

scholarly journals Transcriptional analysis of the gap-pgk-tpi-ppc gene cluster of Corynebacterium glutamicum.

1993 ◽  
Vol 175 (12) ◽  
pp. 3905-3908 ◽  
Author(s):  
J W Schwinde ◽  
N Thum-Schmitz ◽  
B J Eikmanns ◽  
H Sahm
Keyword(s):  
Corynebacterium Glutamicum ◽  
Gene Cluster ◽  
Transcriptional Analysis

scholarly journals Insight into Energy Conservation via Alternative Carbon Monoxide Metabolism inCarboxydothermus pertinaxRevealed by Comparative Genome Analysis

2018 ◽  
Vol 84 (14) ◽  
Author(s):  
Yuto Fukuyama ◽  
Kimiho Omae ◽  
Yasuko Yoneda ◽  
Takashi Yoshida ◽  
Yoshihiko Sako
Keyword(s):  
Carbon Monoxide ◽  
Co Oxidation ◽  
Gene Cluster ◽  
Genome Analysis ◽  
Transcriptional Analysis ◽  
Comparative Genome Analysis ◽  
Co Dehydrogenase ◽  
Comparative Genome ◽  
Content Type ◽  
Energy Converting

ABSTRACTCarboxydothermusspecies are some of the most studied thermophilic carboxydotrophs. Their varied carboxydotrophic growth properties suggest distinct strategies for energy conservation via carbon monoxide (CO) metabolism. In this study, we used comparative genome analysis of the genusCarboxydothermusto show variations in the CO dehydrogenase-energy-converting hydrogenase gene cluster, which is responsible for CO metabolism with H2production (hydrogenogenic CO metabolism). Indeed, the ability or inability to produce H2with CO oxidation is explained by the presence or absence of this gene cluster inCarboxydothermus hydrogenoformans,Carboxydothermus islandicus, andCarboxydothermus ferrireducens. Interestingly, despite its hydrogenogenic CO metabolism,Carboxydothermus pertinaxlacks the Ni-CO dehydrogenase catalytic subunit (CooS-I) and its transcriptional regulator-encoding genes in this gene cluster, probably due to inversion. Transcriptional analysis inC. pertinaxshowed that the Ni-CO dehydrogenase gene (cooS-II) and distantly encoded energy-converting-hydrogenase-related genes were remarkably upregulated with 100% CO. In addition, when thiosulfate was available as a terminal electron acceptor in 100% CO, the maximum cell density and maximum specific growth rate ofC. pertinaxwere 3.1-fold and 1.5-fold higher, respectively, than when thiosulfate was absent. The amount of H2produced was only 62% of the amount of CO consumed, less than expected according to hydrogenogenic CO oxidation (CO + H2O → CO2+ H2). Accordingly,C. pertinaxwould couple CO oxidation by Ni-CO dehydrogenase II with simultaneous reduction of not only H2O but also thiosulfate when grown in 100% CO.IMPORTANCEAnaerobic hydrogenogenic carboxydotrophs are thought to fill a vital niche by scavenging potentially toxic CO and producing H2as an available energy source for thermophilic microbes. This hydrogenogenic carboxydotrophy relies on a Ni-CO dehydrogenase-energy-converting hydrogenase gene cluster. This feature is thought to be common to these organisms. However, the hydrogenogenic carboxydotrophCarboxydothermus pertinaxlacks the gene for the Ni-CO dehydrogenase catalytic subunit encoded in the gene cluster. Here, we performed a comparative genome analysis of the genusCarboxydothermus, a transcriptional analysis, and a cultivation study in 100% CO to prove the hydrogenogenic CO metabolism. Results revealed thatC. pertinaxcould couple Ni-CO dehydrogenase II alternatively to the distal energy-converting hydrogenase. Furthermore,C. pertinaxrepresents an example of the functioning of Ni-CO dehydrogenase that does not always correspond to its genomic context, owing to the versatility of CO metabolism and the low redox potential of CO.

scholarly journals Characterization of the Biosynthesis Gene Cluster for the Pyrrole Polyether Antibiotic Calcimycin (A23187) inStreptomyces chartreusisNRRL 3882

2010 ◽  
Vol 55 (3) ◽  
pp. 974-982 ◽  
Author(s):  
Qiulin Wu ◽  
Jingdan Liang ◽  
Shuangjun Lin ◽  
Xiufen Zhou ◽  
Linquan Bai ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Mutational Analysis ◽  
Divalent Cations ◽  
Biological Effects ◽  
Biosynthetic Gene Cluster ◽  
Type I ◽  
Biosynthesis Gene Cluster ◽  
Biosynthesis Gene ◽  
Hydroxyanthranilic Acid

ABSTRACTThe pyrrole polyether antibiotic calcimycin (A23187) is a rare ionophore that is specific for divalent cations. It is widely used as a biochemical and pharmacological tool because of its multiple, unique biological effects. Here we report on the cloning, sequencing, and mutational analysis of the 64-kb biosynthetic gene cluster fromStreptomyces chartreusisNRRL 3882. Gene replacements confirmed the identity of the gene cluster, andin silicoanalysis of the DNA sequence revealed 27 potential genes, including 3 genes for the biosynthesis of the α-ketopyrrole moiety, 5 genes that encode modular type I polyketide synthases for the biosynthesis of the spiroketal ring, 4 genes for the biosynthesis of 3-hydroxyanthranilic acid, anN-methyltransferase tailoring gene, a resistance gene, a type II thioesterase gene, 3 regulatory genes, 4 genes with other functions, and 5 genes of unknown function. We propose a pathway for the biosynthesis of calcimycin and assign the genes to the biosynthesis steps. Our findings set the stage for producing much desired calcimycin derivatives using genetic modification instead of chemical synthesis.

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