scholarly journals Precise characterization of rDNA genes by intraspecies and inter-loci comparison of rDNA sequences and biochemical analysis of ribosomal RNA molecules in Agrobacterium tumefaciens

2005 ◽  
Vol 80 (1) ◽  
pp. 9-17 ◽  
Author(s):  
J-ney Bautista-Zapanta ◽  
Kazuo Yoshida ◽  
Katsunori Suzuki
Keyword(s):  
Agrobacterium Tumefaciens ◽  
Ribosomal Rna ◽  
Biochemical Analysis ◽  
Rdna Genes ◽  
Rna Molecules ◽  
Rdna Sequences ◽  
Precise Characterization

Characterization of SSU and LSU rRNA genes of threeTrypanosoma (Herpetosoma) grosiisolates maintained in Mongolian jirds

Parasitology ◽  
2004 ◽  
Vol 130 (2) ◽  
pp. 157-167 ◽  
Author(s):  
H. SATO ◽  
A. OSANAI ◽  
H. KAMIYA ◽  
Y. OBARA ◽  
W. JIANG ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Geographical Origin ◽  
Large Subunit ◽  
Meriones Unguiculatus ◽  
Rrna Genes ◽  
Systematic Revision ◽  
Rdna Sequences ◽  
Relationship Of ◽  
Rna Genes

Trypanosoma (Herpetosoma) grosi, which naturally parasitizesApodemusspp., can experimentally infect Mongolian jirds (Meriones unguiculatus). Three isolates fromA. agrarius,A. peninsulae, andA. speciosus(named SESUJI, HANTO, and AKHA isolates, respectively) of different geographical origin (AKHA from Japan, and the others from Vladivostok), exhibited different durations of parasitaemia in laboratory jirds (2 weeks for HANTO, and 3 weeks for the others). To assess the genetic background of theseT. grosiisolates, their small (SSU) and large subunit (LSU) ribosomal RNA genes (rDNA) were sequenced along with those of 2 otherHerpetosomaspecies from squirrels. The SSU rDNA sequences of these 3 species along with available sequences of 3 otherHerpetosomatrypanosomes (T. lewisi,T. musculiandT. microti)seemed to reflect well the phylogenetic relationship of their hosts. Three isolates ofT. grosiexhibited base changes at 2–6 positions of 2019-base 18S rDNA, at 5–29 positions of 1817/1818-base 28Sα rDNA, or 1–5 positions of 1557–1559-base 28Sβ rDNA, and none was separated from the other 2 isolates by rDNA nucleotide sequences. Since base changes ofHerpetosomatrypanosomes at the level of inter- and intra-species might occur frequently in specified rDNA regions, the molecular analysis on these regions of rodent trypanosomes could help species/strain differentiation and systematic revision ofHerpetosomatrypanosome species, which must be more abundant than presently known.

scholarly journals RIBOSOME PRECURSOR PARTICLES IN NUCLEOLI

1969 ◽  
Vol 42 (1) ◽  
pp. 272-283 ◽  
Author(s):  
Ming C. Liau ◽  
Robert P. Perry
Keyword(s):  
Ribosomal Rna ◽  
Actinomycin D ◽  
Large Subunit ◽  
Cesium Chloride ◽  
Detectable Amount ◽  
Progressive Decrease ◽  
Rna Molecules ◽  
Gradual Shift ◽  
Cytoplasmic Ribosomes

Ribonucleoprotein (RNP) particles containing the precursors of ribosomal RNA were extracted from L cell nucleoli and analyzed under conditions comparable to those used in the characterization of cytoplasmic ribosomes. Using nucleoli from cells suitably labeled with 3H-uridine, we detected three basic RNP components, sedimenting at approximately 62S, 78S, and 110S in sucrose gradients containing magnesium. A fourth particle, sedimenting at about 95S, appears to be a dimer of the 62S and 78S components. When centrifuged in gradients containing EDTA, the 62S, 78S, and 110S particles sediment at about 55S, 65S, and 80S, respectively. RNA was extracted from RNP particles which were prepared by two cycles of zonal centrifugation. The 62S particles yielded 32S RNA and a detectable amount of 28S RNA, the 78S structures, 32S RNA and possibly some 36S RNA, and the 110S particles, a mixture of 45S, 36S, and 32S RNA's. When cells were pulsed briefly and further incubated in the presence of actinomycin D, there was a gradual shift of radioactivity from heavier to lighter particles. This observation is consistent with the scheme of maturation: 110S → 78S → 62S. The principal buoyant densities in cesium chloride of the 110S, 78S, and 62S particles are 1.465, 1.490, and 1.545, respectively. These densities are all significantly lower than 1.570, which is characteristic of the mature large subunit of cytoplasmic ribosomes, suggesting that the precursor particles have a relatively higher ratio of protein to RNA, and that ribosome maturation involves, in addition to decrease in the size of the RNA molecules, a progressive decrease in the proportion of associated protein.

Electron Microscope Study of RNA's of Paramyxoviruses

1972 ◽  
Vol 30 ◽  
pp. 196-197
Author(s):  
Ruchama Baum ◽  
J.T. Seto
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
Electron Microscope Study ◽  
Sendai Virus ◽  
Sodium Dodecyl ◽  
Rna Molecules ◽  
Virus Particles ◽  
Molecular Weights ◽  
Length Measurements

The ribonucleic acid (RNA) of paramyxoviruses has been characterized by biochemical and physiochemical methods. However, paramyxovirus RNA molecules have not been studied by electron microscopy. The molecular weights of these single-stranded viral RNA molecules are not known as yet. Since electron microscopy has been found to be useful for the characterization of single-stranded RNA, this investigation was initiated to examine the morphology and length measurements of paramyxovirus RNA's.Sendai virus Z strain and Newcastle disease virus (NDV), Milano strain, were used. For these studies it was necessary to develop a method of extracting RNA molecules from purified virus particles. Highly purified Sendai virus was treated with pronase (300 μg/ml) at 37°C for 30 minutes and the RNA extracted by the sodium dodecyl sulfate (SDS)-phenol procedure.

Characterization of Antibacterial-Producing Endophytic Fungi of Syzygiumpolyanthum Leaves

2020 ◽  
Vol 20 (4) ◽  
pp. 448-454
Author(s):  
Rahmita Burhamzah ◽  
Gemini Alam ◽  
Herlina Rante
Keyword(s):  
Molecular Characterization ◽  
Endophytic Fungi ◽  
Morphological Characterization ◽  
Test Method ◽  
Analysis Method ◽  
Nitrogen Base ◽  
Rdna Genes ◽  
Antibacterial Screening ◽  
Planting Method

Background: Endophytic fungi live in plants’ tissue and can produce the same bioactive compounds as its host plant produces. Syzygiumpolyanthum leaves have known to be one of the antibacterial compound producers. Aim and Objective: This study aimed to characterize morphologically, microscopically, and molecularly the antibacterial-producing endophytic fungi of Syzygiumpolyanthum leaves. Methods: The isolation of endophytic fungi was done by fragment planting method on PDA medium. The antibacterial screening was performed using the antagonistic test as the first screening followed by the disc diffusion test method. The morphological characterization was based on isolate’s mycelia color, growth pattern, margin, and surface texture of the colony, while the microscopic characterization was based on its hyphae characteristics. The molecular characterization of the isolate was done by nitrogen base sequence analysis method on nucleotide constituent of ITS rDNA genes of the isolate. Results: The results found that isolate DF1 has antibacterial activity against E.coli, S.aureus, P.acne, and P.aeruginosa, with the greatest inhibition at 10% concentration of broth fermentation extract on S.aureus with a diameter of inhibition of 13.77 mm. Conclusion: Based on macroscopic, microscopic, and molecular characterization, DF1 isolate is similar to Ceriporialacerate.

scholarly journals Functional Characterization of the mazEF Toxin-Antitoxin System in the Pathogenic Bacterium Agrobacterium tumefaciens

2021 ◽  
Vol 9 (5) ◽  
pp. 1107
Author(s):  
Wonho Choi ◽  
Yoshihiro Yamaguchi ◽  
Ji-Young Park ◽  
Sang-Hyun Park ◽  
Hyeok-Won Lee ◽  
...  
Keyword(s):  
Agrobacterium Tumefaciens ◽  
Physiological Function ◽  
Functional Characterization ◽  
Site Directed Mutagenesis ◽  
In Vitro Assays ◽  
Cell Growth Inhibition ◽  
The Right

Agrobacterium tumefaciens is a pathogen of various plants which transfers its own DNA (T-DNA) to the host plants. It is used for producing genetically modified plants with this ability. To control T-DNA transfer to the right place, toxin-antitoxin (TA) systems of A. tumefaciens were used to control the target site of transfer without any unintentional targeting. Here, we describe a toxin-antitoxin system, Atu0939 (mazE-at) and Atu0940 (mazF-at), in the chromosome of Agrobacterium tumefaciens. The toxin in the TA system has 33.3% identity and 45.5% similarity with MazF in Escherichia coli. The expression of MazF-at caused cell growth inhibition, while cells with MazF-at co-expressed with MazE-at grew normally. In vivo and in vitro assays revealed that MazF-at inhibited protein synthesis by decreasing the cellular mRNA stability. Moreover, the catalytic residue of MazF-at was determined to be the 24th glutamic acid using site-directed mutagenesis. From the results, we concluded that MazF-at is a type II toxin-antitoxin system and a ribosome-independent endoribonuclease. Here, we characterized a TA system in A. tumefaciens whose understanding might help to find its physiological function and to develop further applications.

scholarly journals Correction: characterization of the virB operon from Agrobacterium tumefaciens Ti plasmid.

1990 ◽  
Vol 265 (8) ◽  
pp. 4768
Author(s):  
J E Ward ◽  
D E Akiyoshi ◽  
D Regier ◽  
A Datta ◽  
M P Gordon ◽  
...  
Keyword(s):  
Agrobacterium Tumefaciens ◽  
Ti Plasmid ◽  
Virb Operon

Highly precise characterization of the hydration state upon thermal denaturation of human serum albumin using a 65 GHz dielectric sensor

2020 ◽  
Vol 22 (35) ◽  
pp. 19468-19479 ◽  
Author(s):  
Keiichiro Shiraga ◽  
Mako Urabe ◽  
Takeshi Matsui ◽  
Shojiro Kikuchi ◽  
Yuichi Ogawa
Keyword(s):  
Human Serum Albumin ◽  
Serum Albumin ◽  
Human Serum ◽  
Thermal Denaturation ◽  
Hydration Water ◽  
Biological Functions ◽  
Dielectric Sensor ◽  
Hydration State ◽  
Precise Characterization

The biological functions of proteins depend on harmonization with hydration water surrounding them.

scholarly journals In Vitro Characterization of the Enzyme Properties of the Phospholipid N-Methyltransferase PmtA from Agrobacterium tumefaciens

2009 ◽  
Vol 191 (7) ◽  
pp. 2033-2041 ◽  
Author(s):  
Meriyem Aktas ◽  
Franz Narberhaus
Keyword(s):  
Agrobacterium Tumefaciens ◽  
In Vitro Assay ◽  
Enzyme Properties ◽  
Vitro Assay ◽  
Plant Infection ◽  
In Vitro Characterization ◽  
End Products ◽  
And Control

ABSTRACT Agrobacterium tumefaciens requires phosphatidylcholine (PC) in its membranes for plant infection. The phospholipid N-methyltransferase PmtA catalyzes all three transmethylation reactions of phosphatidylethanolamine (PE) to PC via the intermediates monomethylphosphatidylethanolamine (MMPE) and dimethylphosphatidylethanolamine (DMPE). The enzyme uses S-adenosylmethionine (SAM) as the methyl donor, converting it to S-adenosylhomocysteine (SAH). Little is known about the activity of bacterial Pmt enzymes, since PC biosynthesis in prokaryotes is rare. In this article, we present the purification and in vitro characterization of A. tumefaciens PmtA, which is a monomeric protein. It binds to PE, the intermediates MMPE and DMPE, the end product PC, and phosphatidylglycerol (PG) and phosphatidylinositol. Binding of the phospholipid substrates precedes binding of SAM. We used a coupled in vitro assay system to demonstrate the enzymatic activity of PmtA and to show that PmtA is inhibited by the end products PC and SAH and the antibiotic sinefungin. The presence of PG stimulates PmtA activity. Our study provides insights into the catalysis and control of a bacterial phospholipid N-methyltransferase.

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