scholarly journals Eukaryotic nirK Genes Encoding Copper-Containing Nitrite Reductase: Originating from the Protomitochondrion?

2009 ◽  
Vol 75 (9) ◽  
pp. 2652-2658 ◽  
Author(s):  
Sang-Wan Kim ◽  
Shinya Fushinobu ◽  
Shengmin Zhou ◽  
Takayoshi Wakagi ◽  
Hirofumi Shoun
Keyword(s):  
Recombinant Protein ◽  
Phylogenetic Tree ◽  
Fusarium Oxysporum ◽  
Phylogenetic Relationship ◽  
Nitrite Reductase ◽  
Nitrate Respiration ◽  
Orthologous Genes ◽  
Genes Encoding ◽  
Genome Analyses

ABSTRACT Although denitrification or nitrate respiration has been found among a few eukaryotes, its phylogenetic relationship with the bacterial system remains unclear because orthologous genes involved in the bacterial denitrification system were not identified in these eukaryotes. In this study, we isolated a gene from the denitrifying fungus Fusarium oxysporum that is homologous to the bacterial nirK gene responsible for encoding copper-containing nitrite reductase (NirK). Characterization of the gene and its recombinant protein showed that the fungal nirK gene is the first eukaryotic ortholog of the bacterial counterpart involved in denitrification. Additionally, recent genome analyses have revealed the occurrence of nirK homologs in many fungi and protozoa, although the denitrifying activity of these eukaryotes has never been examined. These eukaryotic homolog genes, together with the fungal nirK gene of F. oxysporum, are grouped in the same branch of the phylogenetic tree as the nirK genes of bacteria, archaea, and eukaryotes, implying that eukaryotic nirK and its homologs evolved from a single ancestor (possibly the protomitochondrion). These results show that the fungal denitrifying system has the same origin as its bacterial counterpart.

scholarly journals Expression of Pseudomonas aeruginosa nitrite reductase in Pseudomonas putida and characterization of the recombinant protein

1992 ◽  
Vol 285 (2) ◽  
pp. 661-666 ◽  
Author(s):  
M C Silvestrini ◽  
F Cutruzzolà ◽  
R D'Alessandro ◽  
M Brunori ◽  
N Fochesato ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Electron Transfer ◽  
Recombinant Protein ◽  
Pseudomonas Putida ◽  
Molecular Mass ◽  
Nitrite Reductase ◽  
Water Soluble ◽  
Binding Kinetics ◽  
Cytochrome C551

Nitrite reductase from Pseudomonas aeruginosa has been successfully expressed in Pseudomonas putida. The purified recombinant enzyme contains haem c but no haem d1. Nonetheless, like the holoenzyme from Ps. aeruginosa, it is a stable dimer (molecular mass 120 kDa), and electron transfer to oxidized azurin is biphasic and follows bimolecular kinetics (k1 = 1.5 x 10(5) and k2 = 2.2 x 10(4) M-1.s-1). Unlike the chemically produced apoenzyme, recombinant nitrite reductase containing only haem c is water-soluble, stable at neutral pH and can be quantitatively reconstituted with haem d1, yielding a holoenzyme with the same properties as that expressed by Ps. aeruginosa (namely optical and c.d. spectra, molecular mass, cytochrome c551 oxidase activity and CO-binding kinetics).

scholarly journals Among Multiple Phosphomannomutase Gene Orthologues, Only One Gene Encodes a Protein with Phosphoglucomutase and Phosphomannomutase Activities in Thermococcus kodakaraensis

2004 ◽  
Vol 186 (18) ◽  
pp. 6070-6076 ◽  
Author(s):  
Naeem Rashid ◽  
Tamotsu Kanai ◽  
Haruyuki Atomi ◽  
Tadayuki Imanaka
Keyword(s):  
Gene Expression ◽  
Recombinant Protein ◽  
Heterologous Gene Expression ◽  
Heterologous Gene ◽  
Expression And Purification ◽  
Purification And Characterization ◽  
Orthologous Genes ◽  
Hyperthermophilic Archaeon ◽  
In Cells

ABSTRACT Four orthologous genes (TK1108, TK1404, TK1777, and TK2185) that can be annotated as phosphomannomutase (PMM) genes (COG1109) have been identified in the genome of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. We previously found that TK1777 actually encodes a phosphopentomutase. In order to determine which of the remaining three orthologues encodes a phosphoglucomutase (PGM), we examined the PGM activity in T. kodakaraensis cells and identified the gene responsible for this activity. Heterologous gene expression and purification and characterization of the recombinant protein indicated that TK1108 encoded a protein with high levels of PGM activity (690 U mg−1), along with high levels of PMM activity (401 U mg−1). Similar analyses of the remaining two orthologues revealed that their protein products exhibited neither PGM nor PMM activity. PGM activity and transcription of TK1108 in T. kodakaraensis were found to be higher in cells grown on starch than in cells grown on pyruvate. Our results clearly indicate that, among the four PMM gene orthologues in T. kodakaraensis, only one gene, TK1108, actually encodes a protein with PGM and PMM activities.

scholarly journals Genomic characterization of a polyvalent hydrocarbonoclastic bacterium Pseudomonas sp. strain BUN14

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mouna Mahjoubi ◽  
Habibu Aliyu ◽  
Mohamed Neifar ◽  
Simone Cappello ◽  
Habib Chouchane ◽  
...  
Keyword(s):  
Crude Oil ◽  
Gc Content ◽  
Promising Candidate ◽  
Genes Encoding ◽  
Genome Phylogeny ◽  
Genomic Characterization ◽  
Genome Analyses ◽  
Large Repertoire ◽  
Type Strains

AbstractBioremediation offers a viable alternative for the reduction of contaminants from the environment, particularly petroleum and its recalcitrant derivatives. In this study, the ability of a strain of Pseudomonas BUN14 to degrade crude oil, pristane and dioxin compounds, and to produce biosurfactants, was investigated. BUN14 is a halotolerant strain isolated from polluted sediment recovered from the refinery harbor on the Bizerte coast, north Tunisia and capable of producing surfactants. The strain BUN14 was assembled into 22 contigs of 4,898,053 bp with a mean GC content of 62.4%. Whole genome phylogeny and comparative genome analyses showed that strain BUN14 could be affiliated with two validly described Pseudomonas Type Strains, P. kunmingensis DSM 25974T and P. chloritidismutans AW-1T. The current study, however, revealed that the two Type Strains are probably conspecific and, given the priority of the latter, we proposed that P. kunmingensis DSM 25974 is a heteronym of P. chloritidismutans AW-1T. Using GC-FID analysis, we determined that BUN14 was able to use a range of hydrocarbons (crude oil, pristane, dibenzofuran, dibenzothiophene, naphthalene) as a sole carbon source. Genome analysis of BUN14 revealed the presence of a large repertoire of proteins (154) related to xenobiotic biodegradation and metabolism. Thus, 44 proteins were linked to the pathways for complete degradation of benzoate and naphthalene. The annotation of conserved functional domains led to the detection of putative genes encoding enzymes of the rhamnolipid biosynthesis pathway. Overall, the polyvalent hydrocarbon degradation capacity of BUN14 makes it a promising candidate for application in the bioremediation of polluted saline environments.

Isolation and characterization of the genes encoding antimicrobial neutrophil cationic peptides, defensins.

Ensho ◽  
1995 ◽  
Vol 15 (1) ◽  
pp. 33-41
Author(s):  
Isao Nagaoka ◽  
Noriko Ishihara ◽  
Akimasa Someya ◽  
Kazuhisa Iwabuchi ◽  
Shin Yomogida ◽  
...  
Keyword(s):  
Cationic Peptides ◽  
Isolation And Characterization ◽  
Genes Encoding

Molecular Cloning and Characterization of Nitrite Reductase Gene from Sugarbeet

2011 ◽  
Vol 37 (8) ◽  
pp. 1406-1414
Author(s):  
Xiao-Yan SHI ◽  
Yan-Da ZENG ◽  
Shi-Long LI ◽  
Yu-Bo WANG ◽  
Feng-Ming MA ◽  
...  
Keyword(s):  
Molecular Cloning ◽  
Nitrite Reductase ◽  
Nitrite Reductase Gene ◽  
Reductase Gene

Pathogenicity and race characterization of Fusarium oxysporum f. sp. phaseoli isolates from Spain and Greece

2002 ◽  
Vol 51 (5) ◽  
pp. 605-611 ◽  
Author(s):  
F. M. Alves-Santos ◽  
L. Cordeiro-Rodrigues ◽  
J. M. Sayagués ◽  
R. Martín-Domínguez ◽  
P. García-Benavides ◽  
...  
Keyword(s):  
Fusarium Oxysporum

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 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%).

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