scholarly journals The Ether-Cleaving Methyltransferase System of the Strict Anaerobe Acetobacterium dehalogenans: Analysis and Expression of the Encoding Genes

2008 ◽  
Vol 191 (2) ◽  
pp. 588-599 ◽  
Author(s):  
Anke Schilhabel ◽  
Sandra Studenik ◽  
Martin Vödisch ◽  
Sandra Kreher ◽  
Bernhard Schlott ◽  
...  
Keyword(s):  
Amino Acid Sequence Identity ◽  
Protein Complexes ◽  
Gene Clusters ◽  
Single Copy ◽  
Anaerobic Microorganisms ◽  
Sequence Identity ◽  
Copy Gene ◽  
Genes Encoding ◽  
Encoding Genes ◽  
Genetic Context

ABSTRACT Anaerobic O-demethylases are inducible multicomponent enzymes which mediate the cleavage of the ether bond of phenyl methyl ethers and the transfer of the methyl group to tetrahydrofolate. The genes of all components (methyltransferases I and II, CP, and activating enzyme [AE]) of the vanillate- and veratrol-O-demethylases of Acetobacterium dehalogenans were sequenced and analyzed. In A. dehalogenans, the genes for methyltransferase I, CP, and methyltransferase II of both O-demethylases are clustered. The single-copy gene for AE is not included in the O-demethylase gene clusters. It was found that AE grouped with COG3894 proteins, the function of which was unknown so far. Genes encoding COG3894 proteins with 20 to 41% amino acid sequence identity with AE are present in numerous genomes of anaerobic microorganisms. Inspection of the domain structure and genetic context of these orthologs predicts that these are also reductive activases for corrinoid enzymes (RACEs), such as carbon monoxide dehydrogenase/acetyl coenzyme A synthases or anaerobic methyltransferases. The genes encoding the O-demethylase components were heterologously expressed with a C-terminal Strep-tag in Escherichia coli, and the recombinant proteins methyltransferase I, CP, and AE were characterized. Gel shift experiments showed that the AE comigrated with the CP. The formation of other protein complexes with the O-demethylase components was not observed under the conditions used. The results point to a strong interaction of the AE with the CP. This is the first report on the functional heterologous expression of acetogenic phenyl methyl ether-cleaving O-demethylases.

scholarly journals Enzyme Specificity of 2-Nitrotoluene 2,3-Dioxygenase from Pseudomonas sp. Strain JS42 Is Determined by the C-Terminal Region of the α Subunit of the Oxygenase Component

1998 ◽  
Vol 180 (5) ◽  
pp. 1194-1199 ◽  
Author(s):  
Juanito V. Parales ◽  
Rebecca E. Parales ◽  
Sol M. Resnick ◽  
David T. Gibson
Keyword(s):  
Amino Acid Sequence Identity ◽  
Large Subunit ◽  
Small Subunit ◽  
Terminal Region ◽  
Oxidation Products ◽  
Enzyme Specificity ◽  
Α Subunit ◽  
Sequence Identity ◽  
Wide Range ◽  
Genes Encoding

ABSTRACT Biotransformations with recombinant Escherichia coliexpressing the genes encoding 2-nitrotoluene 2,3-dioxygenase (2NTDO) from Pseudomonas sp. strain JS42 demonstrated that 2NTDO catalyzes the dihydroxylation and/or monohydroxylation of a wide range of aromatic compounds. Extremely high nucleotide and deduced amino acid sequence identity exists between the components from 2NTDO and the corresponding components from 2,4-dinitrotoluene dioxygenase (2,4-DNTDO) from Burkholderia sp. strain DNT (formerlyPseudomonas sp. strain DNT). However, comparisons of the substrates oxidized by these dioxygenases show that they differ in substrate specificity, regiospecificity, and the enantiomeric composition of their oxidation products. Hybrid dioxygenases were constructed with the genes encoding 2NTDO and 2,4-DNTDO. Biotransformation experiments with these hybrid dioxygenases showed that the C-terminal region of the large subunit of the oxygenase component (ISPα) was responsible for the enzyme specificity differences observed between 2NTDO and 2,4-DNTDO. The small subunit of the terminal oxygenase component (ISPβ) was shown to play no role in determining the specificities of these dioxygenases.

scholarly journals Transcriptional Activation of Quinoline Degradation Operons of Pseudomonas putida 86 by the AraC/XylS-Type Regulator OxoS and Cross-Regulation of the PqorM Promoter by XylS

2005 ◽  
Vol 71 (12) ◽  
pp. 8618-8626 ◽  
Author(s):  
Birgit Carl ◽  
Susanne Fetzner
Keyword(s):  
Pseudomonas Putida ◽  
Gene Product ◽  
Transcriptional Activation ◽  
Amino Acid Sequence Identity ◽  
Open Reading Frames ◽  
Tol Plasmid ◽  
Sequence Identity ◽  
Genes Encoding ◽  
Reading Frames ◽  
Half Site

ABSTRACT The quinoline-degradative gene cluster (oxoO, open reading frames 1 to 6 [ORF1 to -6], qorMSL, ORF7 to -9, oxoR) of Pseudomonas putida 86 consists of several overlapping operons controlled in response to quinoline by the master promoter PoxoO and internal promoters Porf3, PqorM, and PoxoR. ORF7 to -9, presumed to be important for maturation of the molybdenum hydroxylase quinoline 2-oxidoreductase, are also weakly transcribed independently of quinoline. Expression of the oxoS gene, located upstream of oxoO, is not influenced by the carbon source. OxoS shows 26% amino acid sequence identity to XylS, the transcriptional regulator of the meta pathway promoter Pm of TOL plasmid pWW0, and is required for quinoline-dependent transcription from PoxoO, Porf3, PqorM, and PoxoR. 5′ deletion analysis of PoxoO and PqorM suggested that a 5′-TGCPuCT-N3-GGGATA-3′ motif, which resembles the distal 5′-TGCA-N6-GGNTA-3′ half-site of the tandem XylS binding site, is essential for oxoS-dependent transcriptional activation. PqorM, which shows similarity to the tandem XylS recognition site of Pm, was cross-activated by the xylS gene product in response to benzoate. The distal half-site of PqorM is necessary, but probably not sufficient, for transcriptional activation by XylS. Despite conservation in PoxoO of a distal 5′-TGCA-N6-GGNTA-3′ sequence, cross-activation of PoxoO by XylS and benzoate was not observed. The oxoS gene product in the presence of quinoline weakly stimulated transcription from the Pm promoter. Involvement of an XylS-type protein in the regulation of genes encoding synthesis of a molybdenum hydroxylase is without precedent and may reflect the evolutionary origin of this pathway in the metabolism of aromatic compounds.

scholarly journals Functional genomics of a Spiroplasma associated with the carmine cochineals Dactylopius coccus and Dactylopius opuntiae

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Arturo Vera-Ponce León ◽  
Marian Dominguez-Mirazo ◽  
Rafael Bustamante-Brito ◽  
Víctor Higareda-Alvear ◽  
Mónica Rosenblueth ◽  
...  
Keyword(s):  
Virulence Factor ◽  
Single Copy ◽  
Reproductive Organs ◽  
Molecular Signaling ◽  
Adult Males ◽  
New Members ◽  
Type Iv ◽  
Genes Encoding ◽  
Phylogenomic Analyses ◽  
Encoding Genes

Abstract Background Spiroplasma is a widely distributed endosymbiont of insects, arthropods, and plants. In insects, Spiroplasma colonizes the gut, hemolymph, and reproductive organs of the host. Previous metagenomic surveys of the domesticated carmine cochineal Dactylopius coccus and the wild cochineal D. opuntiae reported sequences of Spiroplasma associated with these insects. However, there is no analysis of the genomic capabilities and the interaction of this Spiroplasma with Dactylopius. Results Here we present three Spiroplasma genomes independently recovered from metagenomes of adult males and females of D. coccus, from two different populations, as well as from adult females of D. opuntiae. Single-copy gene analysis showed that these genomes were > 92% complete. Phylogenomic analyses classified these genomes as new members of Spiroplasma ixodetis. Comparative genome analysis indicated that they exhibit fewer genes involved in amino acid and carbon catabolism compared to other spiroplasmas. Moreover, virulence factor-encoding genes (i.e., glpO, spaid and rip2) were found incomplete in these S. ixodetis genomes. We also detected an enrichment of genes encoding the type IV secretion system (T4SS) in S. ixodetis genomes of Dactylopius. A metratranscriptomic analysis of D. coccus showed that some of these T4SS genes (i.e., traG, virB4 and virD4) in addition to the superoxide dismutase sodA of S. ixodetis were overexpressed in the ovaries. Conclusion The symbiont S. ixodetis is a new member of the bacterial community of D. coccus and D. opuntiae. The recovery of incomplete virulence factor-encoding genes in S. ixodetis of Dactylopius suggests that this bacterium is a non-pathogenic symbiont. A high number of genes encoding the T4SS, in the S. ixodetis genomes and the overexpression of these genes in the ovary and hemolymph of the host suggest that S. ixodetis use the T4SS to interact with the Dactylopius cells. Moreover, the transcriptional differences of S. ixodetis among the gut, hemolymph and ovary tissues of D. coccus indicate that this bacterium can respond and adapt to the different conditions (e.g., oxidative stress) present within the host. All this evidence proposes that there is a strong interaction and molecular signaling in the symbiosis between S. ixodetis and the carmine cochineal Dactylopius.

scholarly journals Yeast virus propagation depends critically on free 60S ribosomal subunit concentration.

1995 ◽  
Vol 15 (5) ◽  
pp. 2772-2781 ◽  
Author(s):  
Y Ohtake ◽  
R B Wickner
Keyword(s):  
Ribosomal Subunit ◽  
Killer Toxin ◽  
Single Copy ◽  
Single Copy Gene ◽  
Virus Propagation ◽  
Ribosomal Subunits ◽  
Double Stranded Rna ◽  
Copy Gene ◽  
Genes Encoding ◽  
Virus Sequence

Over 30 MAK (maintenance of killer) genes are necessary for propagation of the killer toxin-encoding M1 satellite double-stranded RNA of the L-A virus. Sequence analysis revealed that MAK7 is RPL4A, one of the two genes encoding ribosomal protein L4 of the 60S subunit. We further found that mutants with mutations in 18 MAK genes (including mak1 [top1], mak7 [rpl4A], mak8 [rpl3], mak11, and mak16) had decreased free 60S subunits. Mutants with another three mak mutations had half-mer polysomes, indicative of poor association of 60S and 40S subunits. The rest of the mak mutants, including the mak3 (N-acetyltransferase) mutant, showed a normal profile. The free 60S subunits, L-A copy number, and the amount of L-A coat protein in the mak1, mak7, mak11, and mak16 mutants were raised to the normal level by the respective normal single-copy gene. Our data suggest that most mak mutations affect M1 propagation by their effects on the supply of proteins from the L-A virus and that the translation of the non-poly(A) L-A mRNA depends critically on the amount of free 60S ribosomal subunits, probably because 60S association with the 40S subunit waiting at the initiator AUG is facilitated by the 3' poly(A).

scholarly journals The Dynein Gene Family in Chlamydomonas reinhardtii

Genetics ◽  
1996 ◽  
Vol 144 (2) ◽  
pp. 569-585 ◽  
Author(s):  
Mary E Porter ◽  
Julie A Knott ◽  
Steven H Myster ◽  
Samuel J Farlow
Keyword(s):  
Gene Family ◽  
Genetic Map ◽  
Single Copy ◽  
Amino Acid Sequences ◽  
Single Copy Gene ◽  
Heavy Chains ◽  
Length Polymorphisms ◽  
Copy Gene ◽  
Genes Encoding ◽  
Insight Into

Abstract To correlate dynein heavy chain (Dhc) genes with flagellar mutations and gain insight into the function of specific dynein isoforms, we placed eight members of the Dhc gene family on the genetic map of Chlamydomonas. Using a PCR-based strategy, we cloned 11 Dhc genes from Chlamydomonas. Comparisons with other Dhc genes indicate that two clones correspond to genes encoding the alpha and beta heavy chains of the outer dynein arm. Alignment of the predicted amino acid sequences spanning the nucleotide binding site indicates that the remaining nine clones can be subdivided into three groups that are likely to include representatives of the inner-arm Dhc isoforms. Gene-specific probes reveal that each clone represents a single-copy gene that is expressed as a transcript of the appropriate size (>13 kb) sufficient to encode a high molecular weight Dhc polypeptide. The expression of all nine genes is upregulated in response to deflagellation, suggesting a role in axoneme assembly or motility. Restriction fragment length polymorphisms between divergent C. reinhardtii strains have been used to place each Dhr gene on the genetic map of Chlamydomonas. These studies lay the groundwork for correlating defects in different Dhc genes with specific flagellar mutations.

Identification of a single-copy gene encoding a Type I chlorophyll a/b-binding polypeptide of photosystem I in Arabidopsis thaliana

1992 ◽  
Vol 84 (4) ◽  
pp. 561-567 ◽  
Author(s):  
Poul E. Jensen ◽  
Michael Kristensen ◽  
Tine Hoff ◽  
Jan Lehmbeck ◽  
Bjarne M. Stummann ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Chlorophyll A ◽  
Photosystem I ◽  
Single Copy ◽  
Type I ◽  
Single Copy Gene ◽  
Gene Encoding ◽  
Copy Gene

scholarly journals Protein complex formation in methionine chain-elongation and leucine biosynthesis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Li-Qun Chen ◽  
Shweta Chhajed ◽  
Tong Zhang ◽  
Joseph M. Collins ◽  
Qiuying Pang ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Complete Characterization ◽  
Bimolecular Fluorescence Complementation ◽  
Chain Elongation ◽  
Substrate Channeling ◽  
Leucine Biosynthesis ◽  
Protein Complex Formation ◽  
Genes Encoding ◽  
Isopropylmalate Dehydrogenase

AbstractDuring the past two decades, glucosinolate (GLS) metabolic pathways have been under extensive studies because of the importance of the specialized metabolites in plant defense against herbivores and pathogens. The studies have led to a nearly complete characterization of biosynthetic genes in the reference plant Arabidopsis thaliana. Before methionine incorporation into the core structure of aliphatic GLS, it undergoes chain-elongation through an iterative three-step process recruited from leucine biosynthesis. Although enzymes catalyzing each step of the reaction have been characterized, the regulatory mode is largely unknown. In this study, using three independent approaches, yeast two-hybrid (Y2H), coimmunoprecipitation (Co-IP) and bimolecular fluorescence complementation (BiFC), we uncovered the presence of protein complexes consisting of isopropylmalate isomerase (IPMI) and isopropylmalate dehydrogenase (IPMDH). In addition, simultaneous decreases in both IPMI and IPMDH activities in a leuc:ipmdh1 double mutants resulted in aggregated changes of GLS profiles compared to either leuc or ipmdh1 single mutants. Although the biological importance of the formation of IPMI and IPMDH protein complexes has not been documented in any organisms, these complexes may represent a new regulatory mechanism of substrate channeling in GLS and/or leucine biosynthesis. Since genes encoding the two enzymes are widely distributed in eukaryotic and prokaryotic genomes, such complexes may have universal significance in the regulation of leucine biosynthesis.

scholarly journals The assembled and annotated genome of the pigeon louse Columbicola columbae, a model ectoparasite

2021 ◽  
Vol 11 (2) ◽  
Author(s):  
James G Baldwin-Brown ◽  
Scott M Villa ◽  
Anna I Vickrey ◽  
Kevin P Johnson ◽  
Sarah E Bush ◽  
...  
Keyword(s):  
Low Cost ◽  
Single Copy ◽  
Odorant Receptors ◽  
Rna Seq ◽  
Pediculus Humanus ◽  
Final Assembly ◽  
Oxford Nanopore ◽  
Genes Encoding ◽  
Host Parasite ◽  
G Protein Coupled

Abstract The pigeon louse Columbicola columbae is a longstanding and important model for studies of ectoparasitism and host-parasite coevolution. However, a deeper understanding of its evolution and capacity for rapid adaptation is limited by a lack of genomic resources. Here, we present a high-quality draft assembly of the C. columbae genome, produced using a combination of Oxford Nanopore, Illumina, and Hi-C technologies. The final assembly is 208 Mb in length, with 12 chromosome-size scaffolds representing 98.1% of the assembly. For gene model prediction, we used a novel clustering method (wavy_choose) for Oxford Nanopore RNA-seq reads to feed into the MAKER annotation pipeline. High recovery of conserved single-copy orthologs (BUSCOs) suggests that our assembly and annotation are both highly complete and highly accurate. Consistent with the results of the only other assembled louse genome, Pediculus humanus, we find that C. columbae has a relatively low density of repetitive elements, the majority of which are DNA transposons. Also similar to P. humanus, we find a reduced number of genes encoding opsins, G protein-coupled receptors, odorant receptors, insulin signaling pathway components, and detoxification proteins in the C. columbae genome, relative to other insects. We propose that such losses might characterize the genomes of obligate, permanent ectoparasites with predictable habitats, limited foraging complexity, and simple dietary regimes. The sequencing and analysis for this genome were relatively low cost, and took advantage of a new clustering technique for Oxford Nanopore RNAseq reads that will be useful to future genome projects.

scholarly journals Molecular characterization of clinical carbapenem-resistant Enterobacterales from Qatar

2021 ◽  
Author(s):  
Fatma Ben Abid ◽  
Clement K. M. Tsui ◽  
Yohei Doi ◽  
Anand Deshmukh ◽  
Christi L. McElheny ◽  
...  
Keyword(s):  
Common Species ◽  
Clinical Samples ◽  
Whole Genome ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Genes Encoding ◽  
Encoding Genes ◽  
Sequence Types ◽  
Common Sequence

AbstractOne hundred forty-nine carbapenem-resistant Enterobacterales from clinical samples obtained between April 2014 and November 2017 were subjected to whole genome sequencing and multi-locus sequence typing. Klebsiella pneumoniae (81, 54.4%) and Escherichia coli (38, 25.5%) were the most common species. Genes encoding metallo-β-lactamases were detected in 68 (45.8%) isolates, and OXA-48-like enzymes in 60 (40.3%). blaNDM-1 (45; 30.2%) and blaOXA-48 (29; 19.5%) were the most frequent. KPC-encoding genes were identified in 5 (3.6%) isolates. Most common sequence types were E. coli ST410 (8; 21.1%) and ST38 (7; 18.4%), and K. pneumoniae ST147 (13; 16%) and ST231 (7; 8.6%).

Sign in / Sign up

Export Citation Format

Share Document