Mutational analysis of the Bradyrhizobium japonicum common nod genes and further nod box-linked genomic DNA regions

1989 ◽  
Vol 215 (3) ◽  
pp. 407-415 ◽  
Author(s):  
Michael Göttfert ◽  
Joseph W. Lamb ◽  
Regula Gasser ◽  
Jan Semenza ◽  
Hauke Hennecke
Keyword(s):  
Bradyrhizobium Japonicum ◽  
Genomic Dna ◽  
Mutational Analysis ◽  
Nod Genes ◽  
Common Nod Genes

scholarly journals Induction of Bradyrhizobium japonicum common nod genes by isoflavones isolated from Glycine max

1987 ◽  
Vol 84 (21) ◽  
pp. 7428-7432 ◽  
Author(s):  
R. M. Kosslak ◽  
R. Bookland ◽  
J. Barkei ◽  
H. E. Paaren ◽  
E. R. Appelbaum
Keyword(s):  
Glycine Max ◽  
Bradyrhizobium Japonicum ◽  
Nod Genes ◽  
Common Nod Genes

The complete denitrification pathway of the symbiotic, nitrogen-fixing bacterium Bradyrhizobium japonicum

2005 ◽  
Vol 33 (1) ◽  
pp. 141-144 ◽  
Author(s):  
E.J. Bedmar ◽  
E.F. Robles ◽  
M.J. Delgado
Keyword(s):  
Nitric Oxide ◽  
Nitrous Oxide ◽  
Bradyrhizobium Japonicum ◽  
Mutational Analysis ◽  
Control Level ◽  
Gene Clusters ◽  
Alternative Form ◽  
Nitrate Respiration ◽  
Regulatory Cascade ◽  
Denitrification Genes

Denitrification is an alternative form of respiration in which bacteria sequentially reduce nitrate or nitrite to nitrogen gas by the intermediates nitric oxide and nitrous oxide when oxygen concentrations are limiting. In Bradyrhizobium japonicum, the N2-fixing microsymbiont of soya beans, denitrification depends on the napEDABC, nirK, norCBQD, and nosRZDFYLX gene clusters encoding nitrate-, nitrite-, nitric oxide- and nitrous oxide-reductase respectively. Mutational analysis of the B. japonicum nap genes has demonstrated that the periplasmic nitrate reductase is the only enzyme responsible for nitrate respiration in this bacterium. Regulatory studies using transcriptional lacZ fusions to the nirK, norCBQD and nosRZDFYLX promoter region indicated that microaerobic induction of these promoters is dependent on the fixLJ and fixK2 genes whose products form the FixLJ–FixK2 regulatory cascade. Besides FixK2, another protein, nitrite and nitric oxide respiratory regulator, has been shown to be required for N-oxide regulation of the B. japonicum nirK and norCBQD genes. Thus nitrite and nitric oxide respiratory regulator adds to the FixLJ–FixK2 cascade an additional control level which integrates the N-oxide signal that is critical for maximal induction of the B. japonicum denitrification genes. However, the identity of the signalling molecule and the sensing mechanism remains unknown.

Mutational analysis of circulating tumor cells in breast cancer patients by targeted clonal sequencing.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 10516-10516 ◽  
Author(s):  
Xunhai Xu ◽  
Yufeng Shen ◽  
William Dewitt ◽  
Deep Pandya ◽  
Farideh Z. Bischoff ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Tumor Cells ◽  
Circulating Tumor Cells ◽  
Deep Sequencing ◽  
Genomic Dna ◽  
Mutational Analysis ◽  
Hot Spot ◽  
Surrogate Marker ◽  
Error Rates ◽  
Novel Mutations

10516 Background: The molecular signature of circulating tumor cells (CTCs) may serve as a surrogate marker for accurate description of the metastatic tumor of interest, especially in the setting of treatment response and selection. We present a method for mutational analysis of CTCs in metastatic breast cancer (MBC) patients by using an emulsion-formulated, semiconductor-based, targeted clonal sequencing platform. Methods: CTCs in MBC patients were enriched by a microfluidic OncoCEE device using antibodies against both epithelial and mesenchymal markers. Genomic DNA was extracted from enriched CTC samples. Emulsion-based multiplex-PCR targeted for various cancer genes was performed, after which semiconductor-based deep sequencing was completed. The read error rates were analyzed based on quality score and context of sequence including homopolymers. Statistical significance for each mutational analysis was assessed using a method based on beta-binomial distribution. Results: Of the 17 patients samples obtained, we were able to enrich CTC samples in 9 of them (CTC range 1-1063, median=12). Multiplex targeted sequencing was performed on DNA from the enriched CTC patient samples (purity range 0.3-6%). Greater than 3000-fold coverage was accomplished. Missense mutations at E545D on PIK3CA (p= 2.0e-07), F354L on STK11 (p=2.0e-04), and Q61R on NRAS (p=2.0e-07) were detected. Novel mutations of L540F and Q1033K within the hot spot regions of PIK3CA were observed (p=1.3e-04). Genomic DNA from WBCs from a healthy female was analyzed concurrently as a negative control, in which none of the mutations were observed. Conclusions: Mutational analysis of CTCs in MBC patients can be accomplished by deep sequencing. We developed a de novo protocol for clonal mutation analysis on CTCs in MBC and detected various significant and novel mutations. We anticipate reporting sequencing results on CTCs and matched WBCs, as negative controls, from 40 MBC patients. This will provide the foundation for the future studies in which we will compare the mutational profile between CTCs and primary/metastatic tumors. We intend to validate clonal mutational analysis of CTCs as a predictive blood-based biomarker in subsequent trials.

scholarly journals Complete Genome Sequence of Bradyrhizobium japonicum Podophage Paso

2021 ◽  
Vol 10 (5) ◽  
Author(s):  
Dylan McBee ◽  
Aravind Ravindran ◽  
Heather Newkirk ◽  
Ben Burrowes ◽  
Ry Young ◽  
...  
Keyword(s):  
Complete Genome Sequence ◽  
Genome Annotation ◽  
Bradyrhizobium Japonicum ◽  
Genomic Dna ◽  
Genomic Analysis ◽  
Symbiotic Relationship ◽  
Negative Bacterium ◽  
Leguminous Plants ◽  
Gram Negative ◽  
Content Type

ABSTRACT Bradyrhizobium japonicum is a nitrogen-fixing, Gram-negative bacterium that forms a symbiotic relationship with leguminous plants. This announcement describes the isolation and genome annotation of B. japonicum T7-like podophage Paso. Genomic analysis reveals genes that are associated with both the T5 and T7 modes of genomic DNA entry into the host.

Organization Pattern of Common nod Genes in Mesorhizobium ciceri Strain MC 18-7

2003 ◽  
Vol 12 (1) ◽  
pp. 57-59
Author(s):  
Vivek Chimote ◽  
L. R. Kashyap
Keyword(s):  
Nod Genes ◽  
Mesorhizobium Ciceri ◽  
Common Nod Genes

scholarly journals Rhizobium nodM and nodN genes are common nod genes: nodM encodes functions for efficiency of nod signal production and bacteroid maturation.

1992 ◽  
Vol 174 (23) ◽  
pp. 7555-7565 ◽  
Author(s):  
N Baev ◽  
M Schultze ◽  
I Barlier ◽  
D C Ha ◽  
H Virelizier ◽  
...  
Keyword(s):  
Nod Genes ◽  
Signal Production ◽  
Common Nod Genes

scholarly journals Mutational analysis of TAC3 and TACR3 genes in patients with idiopathic central pubertal disorders

2012 ◽  
Vol 56 (9) ◽  
pp. 646-652 ◽  
Author(s):  
Cintia Tusset ◽  
Sekoni D. Noel ◽  
Ericka B. Trarbach ◽  
Letícia F. G. Silveira ◽  
Alexander A. L. Jorge ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Rare Variants ◽  
Mutational Analysis ◽  
Pubertal Development ◽  
Hypogonadotropic Hypogonadism ◽  
Central Precocious Puberty ◽  
Control Group ◽  
Loss Of Function ◽  
Coding Region ◽  
Constitutional Delay

OBJECTIVE: To investigate the presence of variants in the TAC3 and TACR3 genes, which encode NKB and its receptor (NK3R), respectively, in a large cohort of patients with idiopathic central pubertal disorders. SUBJECTS AND METHODS: Two hundred and thirty seven patients were studied: 114 with central precocious puberty (CPP), 73 with normosmic isolated hypogonadotropic hypogonadism (IHH), and 50 with constitutional delay of growth and puberty (CDGP). The control group consisted of 150 Brazilian individuals with normal pubertal development. Genomic DNA was extracted from peripheral blood and the entire coding region of both TAC3 and TACR3 genes were amplified and automatically sequenced. RESULTS: We identified one variant (p.A63P) in NKB and four variants, p.G18D, p.L58L (c.172C>T), p.W275* and p.A449S in NK3R, which were absent in the control group. The p.A63P variant was identified in a girl with CPP, and p.A449S in a girl with CDGP. The known p.G18D, p.L58L, and p.W275* variants were identified in three unrelated males with normosmic IHH. CONCLUSION: Rare variants in the TAC3 and TACR3 genes were identified in patients with central pubertal disorders. Loss-of-function variants of TACR3 were associated with the normosmic IHH phenotype. Arq Bras Endocrinol Metab. 2012;56(9):646-52

Unusual localization of nod and nif genes in Rhizobium leguminosarum bv. viciae

1997 ◽  
Vol 43 (4) ◽  
pp. 399-402 ◽  
Author(s):  
Sylvie-Isabelle Mazurier ◽  
Gisele Laguerre
Keyword(s):  
Plasmid Dna ◽  
Genomic Dna ◽  
Rhizobium Leguminosarum ◽  
Large Plasmid ◽  
Nif Genes ◽  
Symbiotic Genes ◽  
Nod Genes ◽  
Symbiotic Plasmid ◽  
Wild Strains ◽  
Sym Plasmid

Genomic DNA from seven strains of Rhizobium leguminosarum bv. viciae isolated from nodules of field-grown lentils showed homology to nod and nif gene probes, whereas plasmid DNA did not hybridize with these probes. The results suggest that symbiotic genes could be located on the chromosome or perhaps on a very large plasmid that could not be resolved in Eckhardt gels. Each strain contained one plasmid that hybridized with a pSym isolated from a R. leguminosarum strain of the same field population. This finding led us to hypothesize that the nod and nif genes of the seven strains might have originated from a Sym plasmid and have been integrated into another replicon. The ability to nodulate vetch was confirmed for all of the seven strains. Thus, wild strains of R. leguminosarum bv. viciae that nodulate vetch carry nod and nif genes either on the chromosome or on an extrachromosomal replicon of size much larger than the pSyms hitherto described.Key words: Rhizobium leguminosarum, nod genes, nif genes, chromosome, symbiotic plasmid, megaplasmid.

Exopolysaccharide (EPS) synthesis in Bradyrhizobium japonicum : sequence, operon structure and mutational analysis of an exo gene cluster

1998 ◽  
Vol 259 (2) ◽  
pp. 161-171 ◽  
Author(s):  
B. U. Becker ◽  
K. Kosch ◽  
M. Parniske ◽  
P. Müller
Keyword(s):  
Gene Cluster ◽  
Bradyrhizobium Japonicum ◽  
Mutational Analysis ◽  
Operon Structure
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