scholarly journals Function and Regulation of the Formate Dehydrogenase Genes of the Methanogenic Archaeon Methanococcus maripaludis

2003 ◽  
Vol 185 (8) ◽  
pp. 2548-2554 ◽  
Author(s):  
Gwendolyn E. Wood ◽  
Andrew K. Haydock ◽  
John A. Leigh
Keyword(s):  
Gene Expression ◽  
Gene Cluster ◽  
Double Mutant ◽  
Formate Dehydrogenase ◽  
Gene Clusters ◽  
Growth Defect ◽  
Methanococcus Maripaludis ◽  
Gene Sets ◽  
Dehydrogenase Gene ◽  
Duplication Events

ABSTRACT Methanococcus maripaludis is a mesophilic species of Archaea capable of producing methane from two substrates: hydrogen plus carbon dioxide and formate. To study the latter, we identified the formate dehydrogenase genes of M. maripaludis and found that the genome contains two gene clusters important for formate utilization. Phylogenetic analysis suggested that the two formate dehydrogenase gene sets arose from duplication events within the methanococcal lineage. The first gene cluster encodes homologs of formate dehydrogenase α (FdhA) and β (FdhB) subunits and a putative formate transporter (FdhC) as well as a carbonic anhydrase analog. The second gene cluster encodes only FdhA and FdhB homologs. Mutants lacking either fdhA gene exhibited a partial growth defect on formate, whereas a double mutant was completely unable to grow on formate as a sole methanogenic substrate. Investigation of fdh gene expression revealed that transcription of both gene clusters is controlled by the presence of H2 and not by the presence of formate.

scholarly journals Redundancy of Enzymes for Formaldehyde Detoxification in Pseudomonas putida

2009 ◽  
Vol 191 (10) ◽  
pp. 3367-3374 ◽  
Author(s):  
Amalia Roca ◽  
Jose J. Rodríguez-Herva ◽  
Juan L. Ramos
Keyword(s):  
Pseudomonas Putida ◽  
Double Mutant ◽  
Formate Dehydrogenase ◽  
Gene Clusters ◽  
Exponential Growth Phase ◽  
Gene Products ◽  
Reading Frame ◽  
Dehydrogenase Gene ◽  
Transcriptional Promoters ◽  
Sublethal Concentrations

ABSTRACT Pseudomonas putida KT2440 exhibits redundant formaldehyde dehydrogenases and formate dehydrogenases that contribute to the detoxification of formaldehyde, a highly toxic compound. Physical and transcriptional analyses showed that the open reading frame (ORF) PP0328, encoding one of the formaldehyde dehydrogenases, is self-sufficient, whereas the other functional formaldehyde dehydrogenase gene (ORF PP3970) forms an operon with another gene of unknown function. Two formate dehydrogenase gene clusters (PP0489 to PP0492 and PP2183 to PP2186) were identified, and genes in these clusters were found to form operons. All four transcriptional promoters were mapped by primer extension and revealed the presence of noncanonical promoters expressed at basal level in the exponential growth phase and at a higher level in the stationary phase regardless of the presence of extracellular formaldehyde or formate. These promoters were characterized by a 5′-AG-CCA-C/A-CT-3′ conserved region between −7 and −16. To determine the contribution of the different gene products to formaldehyde and formate mineralization, mutants with single and double mutations of formaldehyde dehydrogenases were generated, and the effect of the mutations on formaldehyde catabolism was tested by measuring 14CO2 evolution from 14C-labeled formaldehyde. The results showed that both enzymes contributed to formaldehyde catabolism. A double mutant lacking these two enzymes still evolved CO2 from formaldehyde, suggesting the presence of one or more still-unidentified formaldehyde dehydrogenases. Mutants with single and double mutations in the clusters for formate dehydrogenases were also generated, and all of them were able to metabolize [14C]formate to 14CO2, suggesting a redundancy of functions that was not limited to only the annotated genes. Single and double mutants deficient in formaldehyde dehydrogenases and formate dehydrogenases exhibited longer lag phases than did the parental strain when confronted with concentrations of formaldehyde close to the MICs. This suggests a role for the detoxification system in tolerance to sublethal concentrations of formaldehyde.

scholarly journals An Inflammatory Gene-Expression Fingerprint in Monocytes of Autoimmune Thyroid Disease Patients

2010 ◽  
Vol 95 (4) ◽  
pp. 1962-1971 ◽  
Author(s):  
Leonie van der Heul-Nieuwenhuijsen ◽  
Roos C. Padmos ◽  
Roosmarijn C. Drexhage ◽  
Harm de Wit ◽  
Arie Berghout ◽  
...  
Keyword(s):  
Gene Expression ◽  
Thyroid Disease ◽  
Autoimmune Thyroid Disease ◽  
Autoimmune Diabetes ◽  
Gene Clusters ◽  
Whole Genome Analysis ◽  
Autoimmune Thyroid ◽  
Latent Autoimmune Diabetes ◽  
Overlapping Gene ◽  
Gene Sets

Abstract Context: In monocytes of patients with autoimmune diabetes, we recently identified a gene expression fingerprint of two partly overlapping gene clusters, a PDE4B-associated cluster (consisting of 12 core proinflammatory cytokine/compound genes), a FABP5-associated cluster (three core genes), and a set of nine overlapping chemotaxis, adhesion, and cell assembly genes correlating to both PDE4B and FABP5. Objective: Our objective was to study whether a similar monocyte inflammatory fingerprint as found in autoimmune diabetes is present in autoimmune thyroid disease (AITD). Design and Patients: Quantitative PCR was used for analysis of 28 genes in monocytes of 67 AITD patients and 70 healthy controls. The tested 28 genes were the 24 genes previously found abnormally expressed in monocytes of autoimmune diabetes patients plus four extra genes found in whole-genome analysis of monocytes of AITD patients reported here. Results: Monocytes of 24% of AITD and 50% of latent autoimmune diabetes of adults (LADA) patients shared an inflammatory fingerprint consisting of the set of 24 genes of the PDE4B, FABP5, and overlapping gene sets. This study in addition revealed that FCAR, the gene for the Fcα receptor I, and PPBP, the gene for CXCL7, were part of this proinflammatory monocyte fingerprint. Conclusions: Our study provides an important tool to determine a shared, specific proinflammatory state of monocytes in AITD and LADA patients, enabling further research into the role of such proinflammatory cells in the failure to preserve tolerance in these conditions and of key fingerprint genes involved.

scholarly journals The nif Gene Operon of the Methanogenic Archaeon Methanococcus maripaludis

1998 ◽  
Vol 180 (6) ◽  
pp. 1504-1511 ◽  
Author(s):  
Peter S. Kessler ◽  
Carrine Blank ◽  
John A. Leigh
Keyword(s):  
Nitrogen Fixation ◽  
Gene Cluster ◽  
Sequence Similarity ◽  
Methanogenic Archaea ◽  
Gene Clusters ◽  
Northern Analysis ◽  
Insertion Mutagenesis ◽  
Fragmentation Pattern ◽  
Methanococcus Maripaludis ◽  
Regulation Of Expression

ABSTRACT Nitrogen fixation occurs in two domains, Archaea andBacteria. We have characterized a nif(nitrogen fixation) gene cluster in the methanogenic archaeonMethanococcus maripaludis. Sequence analysis revealed eight genes, six with sequence similarity to known nif genes and two with sequence similarity to glnB. The gene order,nifH, ORF105 (similar to glnB),ORF121 (similar to glnB), nifD,nifK, nifE, nifN, andnifX, was the same as that found in part in other diazotrophic methanogens and except for the presence of theglnB-like genes, also resembled the order found in many members of the Bacteria. Using transposon insertion mutagenesis, we determined that an 8-kb region required for nitrogen fixation corresponded to the nif gene cluster. Northern analysis revealed the presence of either a single 7.6-kbnif mRNA transcript or 10 smaller mRNA species containing portions of the large transcript. Polar effects of transposon insertions demonstrated that all of these mRNAs arose from a single promoter region, where transcription initiated 80 bp 5′ tonifH. Distinctive features of the nif gene cluster include the presence of the six primary nif genes in a single operon, the placement of the two glnB-like genes within the cluster, the apparent physical separation of the cluster from any other nif genes that might be in the genome, the fragmentation pattern of the mRNA, and the regulation of expression by a repression mechanism described previously. Our study and others with methanogenic archaea reporting multiple mRNAs arising from gene clusters with only a single putative promoter sequence suggest that mRNA processing following transcription may be a common occurrence in methanogens.

Time course of LPS-induced gene expression in a mouse model of genitourinary inflammation

2001 ◽  
Vol 5 (3) ◽  
pp. 147-160 ◽  
Author(s):  
MARCIA R. SABAN ◽  
HELEN HELLMICH ◽  
NGOC-BICH NGUYEN ◽  
JOHN WINSTON ◽  
TIMOTHY G. HAMMOND ◽  
...  
Keyword(s):  
Gene Expression ◽  
Growth Factor ◽  
Gene Cluster ◽  
Cdna Microarray ◽  
Time Course ◽  
Gene Clusters ◽  
Rnase Protection ◽  
Peak Expression ◽  
Interleukin Receptors ◽  
Significant Gene

In this study, self-organizing map (SOM) gene cluster techniques are applied to the analysis of cDNA microarray analysis of gene expression changes occurring in the early stages of genitourinary inflammation. We determined the time course of lipopolysaccharide (LPS)-induced gene expression in experimental cystitis. Mice were euthanized 0.5, 1, 4, and 24 h after LPS instillation into the urinary bladder, and gene expression was determined using four replicate Atlas mouse cDNA expression arrays containing 588 known genes at each time point. SOM gene cluster analysis, performed without preconditions, identified functionally significant gene clusters based on the kinetics of change in gene expression. Genes were classified as follows: 1) expressed at time 0; 2) early genes (peak expression between 0.5 and 1 h); and 3) late genes (peak expression between 4 and 24 h). One gene cluster maintained a constant level of expression during the entire time period studied. In contrast, LPS treatment downregulated the expression of some genes expressed at time 0, in a cluster including transcription factors, protooncogenes, apoptosis-related proteins (cysteine protease), intracellular kinases, and growth factors. Gene upregulation in response to LPS was observed as early as 0.5 h in a cluster including the interleukin-6 (IL-6) receptor, α- and β-nerve growth factor (α- and β-NGF), vascular endothelial growth factor receptor-1 (VEGF R1), C-C chemokine receptor, and P-selectin. Another tight cluster of genes with marked expression at 1 h after LPS and insignificant expression at all other time points studied included the protooncogenes c-Fos, Fos-B, Fra-2, Jun-B, Jun-D, and Egr-1. Almost all interleukin genes were upregulated as early as 1 h after stimulation with LPS. Nuclear factor-κB (NF-κB) pathway genes collected in a single cluster with a peak expression 4 h after LPS stimulation. In contrast, most of the interleukin receptors and chemokine receptors presented a late peak of expression 24 h after LPS coinciding with the peak of neutrophil infiltration into the bladder wall. Selected cDNA microarray observations were confirmed by RNase protection assay. In conclusion, the cDNA array experimental approach provided a global profile of gene expression changes in bladder tissue after stimulation with LPS. SOM techniques identified functionally significant gene clusters, providing a powerful technical basis for future analysis of mechanisms of bladder inflammation.

scholarly journals Formate Metabolism in Shewanella oneidensis Generates Proton Motive Force and Prevents Growth without an Electron Acceptor

2016 ◽  
Vol 198 (8) ◽  
pp. 1337-1346 ◽  
Author(s):  
Aunica L. Kane ◽  
Evan D. Brutinel ◽  
Heena Joo ◽  
Rebecca Maysonet ◽  
Chelsey M. VanDrisse ◽  
...  
Keyword(s):  
Formate Dehydrogenase ◽  
Carbon Sources ◽  
Shewanella Oneidensis ◽  
Gene Clusters ◽  
Proton Motive Force ◽  
Motive Force ◽  
Content Type ◽  
Formate Oxidation ◽  
Dehydrogenase Gene

ABSTRACTShewanella oneidensisstrain MR-1 is a facultative anaerobe that thrives in redox-stratified environments due to its ability to utilize a wide array of terminal electron acceptors. Conversely, the electron donors utilized byS. oneidensisare more limited and include products of primary fermentation such as lactate, pyruvate, formate, and hydrogen. Lactate, pyruvate, and hydrogen metabolisms inS. oneidensishave been described previously, but little is known about the role of formate oxidation in the ecophysiology of these bacteria. Formate is produced byS. oneidensisthrough pyruvate formate lyase during anaerobic growth on carbon sources that enter metabolism at or above the level of pyruvate, and the genome contains three gene clusters predicted to encode three complete formate dehydrogenase complexes. To determine the contribution of each complex to formate metabolism, strains lacking one, two, or all three annotated formate dehydrogenase gene clusters were generated and examined for growth rates and yields on a variety of carbon sources. Here, we report that formate oxidation contributes to both the growth rate and yield ofS. oneidensisthrough the generation of proton motive force. Exogenous formate also greatly accelerated growth onN-acetylglucosamine, a carbon source normally utilized very slowly byS. oneidensisunder anaerobic conditions. Surprisingly, deletion of all three formate dehydrogenase gene clusters enabled growth ofS. oneidensisusing pyruvate in the absence of a terminal electron acceptor, a mode of growth never before observed in these bacteria. Our results demonstrate that formate oxidation is a fundamental strategy under anaerobic conditions for energy conservation inS. oneidensis.IMPORTANCEShewanellaspecies have garnered interest in biotechnology applications for their ability to respire extracellular terminal electron acceptors, such as insoluble iron oxides and electrodes. While much effort has gone into studying the proteins for extracellular electron transport, how electrons generated through the oxidation of organic carbon sources enter this pathway remains understudied. Here, we quantify the role of formate oxidation in the anaerobic physiology ofShewanella oneidensis. Formate oxidation contributes to both the growth rate and yield on a variety of carbon sources through the generation of proton motive force. Advances in our understanding of the anaerobic metabolism ofS. oneidensisare important for our ability to utilize and engineer this organism for applications in bioenergy, biocatalysis, and bioremediation.

Blood neuroendocrine tumor gene cluster analysis to predict somatostatin analog response.

2016 ◽  
Vol 34 (4_suppl) ◽  
pp. 276-276 ◽  
Author(s):  
Mark S. Kidd ◽  
Ignat Drozdov ◽  
Irvin Mark Modlin
Keyword(s):  
Gene Expression ◽  
Gene Cluster ◽  
Somatostatin Analogs ◽  
Tumor Biology ◽  
Therapy Response ◽  
Disease Status ◽  
Gene Clusters ◽  
Expression Of Genes ◽  
Epigenetic Remodeling ◽  
Group 2

276 Background: Defining therapeutic efficacy in NETs is problematic. We have identified circulating NET transcripts that accurately reflect tumor tissue levels and are sensitive measures of tumor biology. We also identified gene clusters that define NET activity e.g., proliferation. We hypothesized that targeted treatment would alter cluster expression and these could predict treatment response. We evaluated this using somatostatin analogs since they effectively ameliorate symptoms and inhibit tumor growth. Methods: We prospectively evaluated GEP-NETs (n=35) [M:F 12:23; median age: 58 years, small intestine: n=29, pancreas n=3, rectum n=3]. Circulating NET gene expression was assessed (qRT-PCR, normalized gene expression) and imaging (CT/MRI: disease status–RECIST criteria) undertaken. Treatments included: sandostatin (n=32), octreotide (n=2) and pasireotide (n=1); median dose 20mg (range 20-60mg). Gene clusters e.g., proliferation (Ki67, NAP1L1, NOL3, TECPR2) were evaluated as predictive “neoplasia hallmarks” using 2-tailed non-parametric and ROC analyses. Cluster expression is expressed as mean±SEM. Results: Imagery identified25 (71%) patients with stable disease; 10 were progressing. Expression of genes associated with secretory regulation, the “secretome” was significantly down-regulated in the disease-stabilized versus progressive group (2±0.5 vs. 30±25, p<0.001). Individuals with disease progression on SSA therapy exhibited both a significantly elevated proliferation-associated gene cluster (65±15 vs. 16±1, p<0.001) and an epigenetic remodeling cluster (44±6 vs. 32±10, p<0.005). ROC analysis confirmed these accurately identified therapy response (AUC: 0.86-0.97, p<0.0001). Other gene clusters e.g., metabolism (10±1.2 vs. 15.4±3) and apoptosis (1.3±0.2 vs. 1.1±0.8) were not different. Conclusions: SSA therapy alters circulating transcript measurements. Disease stabilization is associated with downregulation of genes linked to tumor secretion while progression is associated with elevation in gene clusters that define tumor proliferation and epigenetic reprogramming. Blood transcript measurements provide an accurate tool to predict the efficacy of SSA therapy.

The variation of dTDP-l-rhamnose pathway genes in Vibrio cholerae

Microbiology ◽  
2003 ◽  
Vol 149 (9) ◽  
pp. 2463-2474 ◽  
Author(s):  
Qun Li ◽  
Matthew Hobbs ◽  
Peter R. Reeves
Keyword(s):  
Gene Transfer ◽  
Vibrio Cholerae ◽  
Gene Cluster ◽  
Lateral Gene Transfer ◽  
Gene Clusters ◽  
Antigen Gene ◽  
Gene Probes ◽  
O Antigen ◽  
Gene Sets ◽  
K 12

The genetic variation in the dTDP-l-rhamnose pathway genes (rmlA, rmlB, rmlC and rmlD) in Vibrio cholerae was investigated. The genes are part of the O antigen gene cluster and the aim was to study lateral gene transfer of O antigen gene clusters. The rml genes of an O6 strain were cloned using an Escherichia coli K-12 strain designed for selecting cloned rml genes. Thirty-three strains carrying the known rhamnose-containing O antigens were probed with O6-based rml gene probes, and 19 were positive with from one to all four of the gene probes. Nine rml gene sets from this group were sequenced and found to be in the order rmlBADC, at the 5′ end of the gene clusters. A gradient in the level of variation was observed, with highly similar sequences at the 5′ end rmlB gene, but very divergent and strain-specific sequences at the 3′ end of the rml gene set. The change in level of similarity varied in position, but was always abrupt and coincided with a change in GC content, indicating that the 5′ and 3′ parts are of different origin, and that recombination within rml genes has occurred. The rml gene sets of two of the strains that did not hybridize with any O6 rml gene probes were also cloned and sequenced. Both gene sets were in the middle of the O antigen gene cluster and were very divergent from each other and all other rml gene sets. This supports the hypothesis that presence of rml genes at the end of the O antigen gene cluster facilitates lateral gene transfer of rml-containing O antigen gene clusters in V. cholerae. The sequence relationships make it possible to identify sites of recombination and to distinguish DNA that has long been in V. cholerae and DNA that probably came into the species with the O antigen gene cluster.

D-Mannitol production by resting state whole cell biotransformation ofD-fructose by heterologous mannitol and formate dehydrogenase gene expression inBacillus megaterium

2007 ◽  
Vol 2 (11) ◽  
pp. 1408-1416 ◽  
Author(s):  
Carsten Bäumchen ◽  
Andreas H. F. J. Roth ◽  
Rebekka Biedendieck ◽  
Marco Malten ◽  
Martin Follmann ◽  
...  
Keyword(s):  
Gene Expression ◽  
Resting State ◽  
Formate Dehydrogenase ◽  
Whole Cell ◽  
Dehydrogenase Gene ◽  
Mannitol Production ◽  
Whole Cell Biotransformation

Expression of the NADP+-Dependent Formate Dehydrogenase Gene from Pseudomonas Increases the Lysine Production in Corynebacterium glutamicum

2019 ◽  
Vol 35 (6) ◽  
pp. 21-29
Author(s):  
T.E. Leonova ◽  
T.E. Shustikova ◽  
T.V. Gerasimova ◽  
Т.А. Ivankova ◽  
K.V. Sidorenko Sidorenko ◽  
...  
Keyword(s):  
Corynebacterium Glutamicum ◽  
Formate Dehydrogenase ◽  
Ministry Of Education ◽  
Lysine Production ◽  
Simultaneous Formation ◽  
Resource Center ◽  
Formate Oxidation ◽  
Gene Coding ◽  
Dehydrogenase Gene ◽  
Lysine Synthesis

Thepsefdh_D221Q gene coding for a mutant formate dehydrogenase (PseFDG_D221Q) from Pseudomonas, which catalyzes the formate oxidation with the simultaneous formation of NADPH, has been expressed in the cells of lysine-producing Corynebacterium glutamicum strains. The psefdh_D221Q gene was introduced into С. glutamicum strains as part of an autonomous plasmid or was integrated into the chromosome with simultaneous inactivation of host formate dehydrogenase genes. It was shown that the С. glutamicum strains with NADP+ -dependent formate dehydrogenase have an increased level of L-lysine synthesis in the presence of formate, if their own formate dehydrogenase is inactivated. L-lysine, formate dehydrogenase, NADPH, Corynebacterium glutamicum The work was carried out using the equipment of the Multipurpose Scientific This work was carried out on the equipment of the Multipurpose Scientific Installation of «All-Russian Collection of Industrial Microorganisms», National Bio-Resource Center, NRC «Kurchatov Institute»- GosNIIgenetika. This work was financially supported by the Ministry of Education and Science of Russia (Unique Project Identifier - RFMEFI61017X0011).

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