• Molecules and Cells
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• v.46 no.12
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• pp.736-742
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• 2023

NifB, a radical S-adenosylmethionine (SAM) enzyme, is pivotal in the biosynthesis of the iron-molybdenum cofactor (FeMo-co), commonly referred to as the M-cluster. This cofactor, located within the active site of nitrogenase, is essential for the conversion of dinitrogen (N₂) to NH₃. Recognized as the most intricate metallocluster in nature, FeMo-co biosynthesis involves multiple proteins and a sequence of steps. Of particular significance, NifB directs the fusion of two [Fe₄S₄] clusters to assemble the 8Fe core, while also incorporating an interstitial carbide. Although NifB has been extensively studied, its molecular mechanisms remain elusive. In this review, we explore recent structural analyses of NifB and provide a comprehensive overview of the established catalytic mechanisms. We propose prospective directions for future research, emphasizing the relevance to biochemistry, agriculture, and environmental science. The goal of this review is to lay a solid foundation for future endeavors aimed at elucidating the atomic details of FeMo-co biosynthesis.

• Proceedings of the Zoological Society Korea Conference
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• 1995.10b
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• pp.120-120
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• 1995

The total size of the pF AR1, a genomic clone of Frankia FaCI, was estimated to be about 44Kb by summation of the individual fragment length generated by single or double restriction enzymes. Southern hybridization analyses with Azotobacter vinelandii nif-genes as probes and partial sequencing analyses of the subclones revealed that organization of the nif-gene in the FaCI strain was nifV, H, D, K, E, N, X, W, B. The organization of the structural genes for nitrogenase is the same in this Frankia strain as it is in most other nitrogen-fixing prokaryotes but the positioning of the nifV-like gene relative to the nifHDK cluster differs. A consensus nif-promoter-like sequence, found at 5' of nifH, was not detected upstream of the niJV-like gene. nifV-like gene contained a ORF of 1206 NT encoding 401 amino acids. The nucleotide sequence and deduced amino acid sequence of the gene exhibit homology value of 65% and 41% with that from A vinelandii, respectively. The putative Shine-Dargamo sequences were present preceding nitK, nifH, D, K, and nifE, and in nitK gene putative start codon GTG was detected instead of A TG. The nucleotide and amino acid sequence of niIK of FaCI showed 82% and 76% homolgy with those of Frankia HFPCc 13, respectively. Amino acid sequence of niIK showed 69% and 61% homology with those of A vinelandii, Klebsiella pnewnoniae, respectively, while that of nifE 73% and 71%, respecti vely.i vely.

• Journal of Life Science
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• v.22 no.8
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• pp.1009-1017
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• 2012

The orf282 gene of Rhodobacter sphaeroides is located between the ccoNOQP operon encoding $cbb_3$ terminal oxidase and the fnrL gene encoding an anaerobic activator, FnrL. Its function remains unknown. In an attempt to reveal the function of the orf282 gene, we disrupted the gene by deleting a portion of the orf282 gene and constructed an orf282-knockout mutant. Two FnrL binding sites were found to be located upstream of orf282, and it was demonstrated that orf282 is positively regulated by FnrL. The orf282 gene is not involved in the regulation of spectral complex formation. The $cbb_3$ oxidase activity detected in the orf282 mutant was comparable to that in the wild-type sample, indicating that the orf282 gene is not involved in the regulation of the ccoNOQP operon and the biosynthesis of the cbb3 cytochrome c oxidase. The elevated promoter activity of the nifH and nifA genes, which are the structural genes of nitrogenase and its regulator, respectively, in the orf282 mutant, suggests that the orf282 gene product acts as a negative effector for nifH and nifA expression.

• Korean Journal of Microbiology
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• v.22 no.4
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• pp.265-269
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• 1984

For the utilization as donor cells of conjugation, DAP-Auxotrophs were isolated from C. coli cells, carrying plasmid $p^{RD1}$ with(a) drug resistance makers from Pseudononas $(Km^r, \;Carb^r, \;Tc^r)$ and (b) the nif-gene group from Klebsiela. E. coli $p^{RD1}$ cells were treated with nitrosoguanidine for the mutagenesis and cephalexin for the isolation of DAP-Auxotrophs. The nature of auxotrophs was verified by suitable biochemical test and checking with 6-cyanopurine as a color indicator for the presence of nif-gene.

• KSBB Journal
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• v.20 no.6
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• pp.418-424
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• 2005

Photoheterotrophic evolution of molecular hydrogen by Rhodobacter sphaeroides is mediated by nitrogenase that is regulated transcriptionally and post-translationally by ammonium ion. Two PII-like proteins, GlnB and GlnK, play key roles in mediating inhibition and repression of nitrogenase in the presence of ammonium ion. glnB and glnK of R. sphaeroides were interrupted to abolish the ammonium ion effect controlling nitrogenase. Ammonium ion effect was still observed in mutant having an interruption in either glnB or glnK. However, the nitrogenase activity of glnB-glnK double mutant is not affected by ammonium ion. $H_2$ evolution was improved by increasing gene dosages of nitrogenase-coding genes, nifHDK in trans in glnB-glnK double mutant.

• Journal of Microbiology and Biotechnology
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• v.20 no.5
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• pp.862-870
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• 2010

Cyperus rotundus L. is a perennial herb that was found to be dominating an area in northeast Brazil previously contaminated with petroleum. In order to increase our knowledge of microorganism-plant interactions in phytoremediation, the bacterial community present in the rhizosphere and roots of C. rotundus was evaluated by culture-dependent and molecular approaches. PCR-DGGE analysis based on the 16S rRNA gene showed that the bacterial community in bulk soil, rhizosphere, and root samples had a high degree of similarity. A complex population of alkane-utilizing bacteria and a variable nitrogen-fixing population were observed via PCR-DGGE analysis of alkB and nifH genes, respectively. In addition, two clone libraries were generated from alkB fragments obtained by PCR of bulk and rhizosphere soil DNA samples. Statistical analyses of these libraries showed that the compositions of their respective populations were different in terms of alkB gene sequences. Using culturedependent techniques, 209 bacterial strains were isolated from the rhizosphere and rhizoplane/roots of C. rotundus. Dot-blot analysis showed that 17 strains contained both alkB and nifH gene sequences. Partial 16S rRNA gene sequencing revealed that these strains are affiliated with the genera Bosea, Cupriavidus, Enterobacter, Gordonia, Mycoplana, Pandoraea, Pseudomonas, Rhizobium, and Rhodococcus. These isolates can be considered to have great potential for the phytoremediation of soil with C. rotundus in this tropical soil area.

• Korean Journal of Soil Science and Fertilizer
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• v.23 no.1
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• pp.60-66
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• 1990

Soybean [Glycin max (L.)] cv. Jangbaekkong was inoculated with 5 cultivated- and 5 uncultivated upland soils, in Yeongnam area, as soil inoculum and NifTAL peat inoculum as standard for soil inoculum potentials by Bradyrhizobium japonicum. 120 Bradyrhizobium japonicum isolates out of the soil populations were scored of three colony morphologies, designed "Dry", "Wet", and "Dry/Wet", and symbiotic effectiveness between "Dry" and "Wet" was compared. The results obtained were summarized as follows: 1. Indigenous populations of B. japonicum were above $10^4cells/g$. soil at the cultivated upland soils but were a few at the uncultivated upland soils except a colluvivum, orchard previously, in Yeongnam area. 2. Inoculum potentials of the cultivated upland soils were higher than the NifTAL inoculum and generally, nodule mass compensated nodule number for symbiotic effectiveness of soil populations. 3. Colony morphologies of soil populations showed the different proportions of "Dry" and "Wet" so that "Dry" types were dominant at the cultivated upland soils while "Wet" types at the uncultivated upland soils. 4. "Dry" colony morphology significantly exhibited higher symbiotic effectiveness than "Wet" types in nodule fresh weight, shoot dry weight, and shoot dry weight/nodule fresh weight. Therefore, as long as soil inoculum potentials, the growth of soybean at the cultivated upland soils could presumedly be affected by soil populations of Bradyrhizobium japonicum of "Dry" colony morphology.

• Korean Journal of Environmental Agriculture
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• v.22 no.3
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• pp.203-209
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• 2003

In the course of screening for antifungal agents, a bacterial strain, DM3 was isolated from a mud sample collected at Daechon in Chungnam province and identified as Bacillus licheniformis based on API 50CHB test. It has antifungal activity against 12 plant pathogenic fungi in paper disc assay. At the 95% lethal dose of gamma radiation ($^{60}Co$, 10 kGy, $D_{10}=2.32\;kGy$), the antifungal activity deficient mutant (mDM3) against Colletotrichum gloeosporioides was induced From 2-D electrophoresis analysis, serine hydroxymethyltransferase (45.0 kDa), hypothetical protein(40.7 kDa), NifU protein homolog(15.4 kDa), and resolvase(12.5 kDa) homologous proteins were detected only in B. licheniformis DM3. Lysozyme(18.1 kDa) and alkyl hydroperoxide reductase(15.6 kDa) homologous proteins were expressed uniquely in B. licheniformis mDM3. Further studies are needed to reveal that these proteins from B. licheniformis DM3 could be closely related to the antifungal activity against plant pathogenic fungi.

• Korean Journal of Soil Science and Fertilizer
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• v.24 no.1
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• pp.61-68
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• 1991

Thirty Bradyrhizobium japonicum isolates (10 strains per each soil) from 1 uncultivated [Sangnam(Soil 1), Milyang]- and 2 cultivated [Dong(Soil 2)and Chinbuk(Soil 3), Changweon] upland soils in Yeongnam area were evaluated on their symbiotic effectiveness to soybean [Glycin max (L.)] cv. Korean Jangbaekkong and American Clark and examined on their serological diversity. The results obtained were summarized as follows : 1. On symbiotic effectiveness of B. japonicum with plant genotypes, isolates showed a relatively high value of nodule mass in Jangbaekkong cv. and of shoot dry weight and total nitrogen in Clark cv. demonstrating the order of Soil 1> Soil 2> Soil 3 isolates. 2. Among 30 B. japonicum isolates, YCK 141 showed the best effectiveness on mean nitrogen fixation of two cultivars. 3. Thirty indigenous B. japonicum showed 6 types of serological diversities in the immunoblot analysis which were present in various proportions at Soil 2(5) and Soil 3(5) except Soil 1 where all isolates fell into the YCK 117 serogroup. And their distribution order was serotype YCK 117( 12 strains) > USDA 1l0(5strains), USDA 123(5 strains) > YCK 150(4 strains) > YCK 141(3 strains) > YCK 226(1 strain). 4. Especially, 10 isolates from Soil 1, an uncultivated orchard, showed a very homologous pattern in not only effectiveness but serological distribution. It seemed to indicate that the isolates were typically affected by numerous physical and environmental factors of the soil.

• Journal of Species Research
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• v.9 no.3
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• pp.210-217
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• 2020

Microseira wollei (Farlow ex Gomont) G.B.McGregor and Sendall ex Kennis, a mat-forming filamentous harmful cyanobacterium, has historically been found in the United States. Microseira wollei produces neurotoxins and hepatotoxins which affect declining water quality. In the present research, we report of unrecorded M. wollei with morphology, TEM anatomy, molecular phylogeny on the Korean population. Based on 16S rRNA gene sequences, Korean population were different by 0.02% (2 bp) to the Japanese population, 1.2-1.3% to the Australian population, and 2.5-3.7% to the United States populations. nifH gene sequences were 8.4-8.7% different to Australian ones and 3.5-3.8% to other population, however molecular phylogenetic analysis of M. wollei living in Korea revealed monophyly with the geographical populations of U.S.A., Australia, and other geographical populations. Since the mat of M. wollei has been reported to be maintained for several years in other countries, it is necessary further investigate the seasonal and regional distribution of this species in Korea.