scholarly journals Structural Analysis and Whole Genome Mapping of a New Type of Plant Virus Subviral RNA: Umbravirus-Like Associated RNAs

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 646
Author(s):  
Jingyuan Liu ◽  
Elizabeth Carino ◽  
Sayanta Bera ◽  
Feng Gao ◽  
Jared P. May ◽  
...  
Keyword(s):  
Genome Mapping ◽  
Structural Features ◽  
Full Length ◽  
Nonsense Mediated Decay ◽  
Reading Frame ◽  
Road Map ◽  
Shape Structure ◽  
New Type ◽  
Subviral Rna

We report the biological and structural characterization of umbravirus-like associated RNAs (ulaRNAs), a new category of coat-protein dependent subviral RNA replicons that infect plants. These RNAs encode an RNA-dependent RNA polymerase (RdRp) following a −1 ribosomal frameshift event, are 2.7–4.6 kb in length, and are related to umbraviruses, unlike similar RNA replicons that are related to tombusviruses. Three classes of ulaRNAs are proposed, with citrus yellow vein associated virus (CYVaV) placed in Class 2. With the exception of CYVaV, Class 2 and Class 3 ulaRNAs encode an additional open reading frame (ORF) with movement protein-like motifs made possible by additional sequences just past the RdRp termination codon. The full-length secondary structure of CYVaV was determined using Selective 2’ Hydroxyl Acylation analyzed by Primer Extension (SHAPE) structure probing and phylogenic comparisons, which was used as a template for determining the putative structures of the other Class 2 ulaRNAs, revealing a number of distinctive structural features. The ribosome recoding sites of nearly all ulaRNAs, which differ significantly from those of umbraviruses, may exist in two conformations and are highly efficient. The 3′ regions of Class 2 and Class 3 ulaRNAs have structural elements similar to those of nearly all umbraviruses, and all Class 2 ulaRNAs have a unique, conserved 3′ cap-independent translation enhancer. CYVaV replicates independently in protoplasts, demonstrating that the reported sequence is full-length. Additionally, CYVaV contains a sequence in its 3′ UTR that confers protection to nonsense mediated decay (NMD), thus likely obviating the need for umbravirus ORF3, a known suppressor of NMD. This initial characterization lays down a road map for future investigations into these novel virus-like RNAs.

scholarly journals Molecular Characterization of the Fragilysin Pathogenicity Islet of Enterotoxigenic Bacteroides fragilis

1998 ◽  
Vol 66 (4) ◽  
pp. 1735-1739 ◽  
Author(s):  
J. Scott Moncrief ◽  
A. Jane Duncan ◽  
Rhonda L. Wright ◽  
Lisa A. Barroso ◽  
Tracy D. Wilkins
Keyword(s):  
Bacteroides Fragilis ◽  
Fluid Secretion ◽  
Structural Features ◽  
Pcr Analysis ◽  
Binding Motif ◽  
Target Sequence ◽  
Intestinal Epithelial ◽  
Reading Frame ◽  
Toxigenic Strains

ABSTRACT Enterotoxigenic strains of Bacteroides fragilis produce an extracellular metalloprotease toxin (termed fragilysin) which is cytopathic to intestinal epithelial cells and induces fluid secretion and tissue damage in ligated intestinal loops. We report here that the fragilysin gene is contained within a small genetic element termed the fragilysin pathogenicity islet. The pathogenicity islet of B. fragilis VPI 13784 was defined as 6,033 bp in length and contained nearly perfect 12-bp direct repeats near its ends. Sequencing across the ends of the pathogenicity islet from two additional enterotoxigenic strains, along with PCR analysis of 20 additional enterotoxigenic strains, revealed that the islet is inserted at a specific site on the B. fragilis chromosome. The site of integration in three nontoxigenic strains contained a 17-bp GC-rich sequence which was not present in toxigenic strains and may represent a target sequence for chromosomal integration. In addition to the fragilysin gene, we identified an open reading frame encoding a predicted protein with a size and structural features similar to those of fragilysin. The deduced amino acid sequence was 28.5% identical and 56.3% similar to fragilysin and contained a nearly identical zinc-binding motif and methionine-turn region.

scholarly journals (86) Isolation and Molecular Characterization of Putative Ascorbate Peroxidase from Citrus

HortScience ◽  
2006 ◽  
Vol 41 (4) ◽  
pp. 1021D-1021
Author(s):  
Madhurababu Kunta ◽  
H. Sonia del Rio ◽  
Eliezer Louzada
Keyword(s):  
Ascorbate Peroxidase ◽  
Normal Growth ◽  
Stress Conditions ◽  
Full Length ◽  
Homology Search ◽  
Reading Frame ◽  
Key Enzyme ◽  
Differential Display Reverse Transcription ◽  
Polymerase Chain

Reactive oxygen species (ROS) are continuously produced during the normal aerobic metabolism and also under environmental stress conditions. They are the major damaging factors to the photosynthetic machinery under stress conditions and need to be scavenged for the normal growth of the plant. Ascorbate peroxidase (APX) is the key enzyme in detoxifying H2O2, one of ROS from chloroplast and cytosol. A cDNA encoding a putative APXcit was isolated from mature `Dancy' tangerine (Citrus reticulata Blanco) juice vesicles using differential display reverse transcription-polymerase chain reaction (RT-PCR). Subsequently, full-length APXcit cDNA clone and genomic clone were obtained and sequenced. The full-length APXcit sequence is composed by 1082-bp nucleotides, including an open reading frame (ORF) of 753 bp, encoding a protein of 250 amino acids (27 kDa). The 5' un-translated region (UTR) of the APXcit gene consisted of 91 nucleotides and the 3' UTR consisted of 238 nucleotides. Homology search for APXcit at GenBank database showed high similarity to APX from several plant species.

scholarly journals Molecular characterization of AwSox2 from bivalve Anodonta woodiana: Elucidating its player in the immune response

2019 ◽  
Vol 26 (5) ◽  
pp. 381-397
Author(s):  
Xichao Xia ◽  
Cuiui Guan ◽  
Jiawei Chen ◽  
Maolin Qiu ◽  
Jinxu Qi ◽  
...  
Keyword(s):  
Structural Features ◽  
Immune Defense ◽  
Poly I:C ◽  
Control Group ◽  
Freshwater Bivalve ◽  
Reading Frame ◽  
Embryonal Stem Cell ◽  
Anodonta Woodiana ◽  
Hematoxylin And Eosin

Sox2 is an embryonal stem cell Ag essential for early embryonic development, tissue homeostasis and immune regulation. In the current study, one complete Sox2 cDNA sequence was cloned from freshwater bivalve Anodonta woodiana and named AwSox2. Histological changes of testis derived from Bisphenol A (BPA) treatment were analyzed by hematoxylin and eosin staining. Expressions of AwSox2 derived from BPA, LPS and polyinosinic:polycytidylic (Poly I:C) challenge were measured by quantitative real-time PCR. The full-length cDNA of AwSox2 contained an open reading frame of 927 nucleotides bearing the typical structural features of Sox2 family. Obvious degeneration, irregular arrangement of spermatids, and clotted dead and intertwined spermatids were observed in BPA-treated groups. Administration of BPA could result in a dose-dependent up-regulation of AwSox2 expression in the male gonadal tissue of A. woodiana. In addition, expression of AwSox2 was significantly induced by LPS and Poly I:C treatment in the hepatopancreas, gill and hemocytes, compared with that of control group. These results indicated that up-regulations of AwSOx2 are closely related to apoptosis of spermatogonial stem cells derived from BPA treatment as well as enhancement of immune defense against LPS and Poly I:C challenge in A. woodiana.

scholarly journals TranSuite: a software suite for accurate translation and characterization of transcripts

2020 ◽  
Author(s):  
Juan C. Entizne ◽  
Wenbin Guo ◽  
Cristiane P.G. Calixto ◽  
Mark Spensley ◽  
Nikoleta Tzioutziou ◽  
...  
Keyword(s):  
Protein Translation ◽  
Software Suite ◽  
Transcript Isoforms ◽  
Nonsense Mediated Decay ◽  
Reading Frame ◽  
Premature Termination Codons ◽  
Translation Start ◽  
Protein Variants ◽  
Selection Of

ABSTRACTProtein translation programs often select the longest open reading frame (ORF) in a transcript leading to numerous inaccurate and mis-annotated ORFs in databases. Unproductive transcript isoforms containing premature termination codons (PTCs) are potential substrates for nonsense-mediated decay (NMD). These transcripts often contain truncated ORFs but are incorrectly annotated due to selection of a long ORF beginning at an AUG downstream of the PTC despite the transcript containing the authentic translation start AUG. In gene expression and alternative splicing analyses, it is important to identify transcript isoforms which code for different protein variants and to distinguish these from potential NMD substrates. Here, we present TranSuite, a pipeline of bioinformatics tools that address these challenges by performing accurate translations, characterizing alternative ORFs and identifying NMD and other features of transcripts in newly assembled and existing transcriptomes. Directly comparing ORFs defined by TranSuite and TransDecoder for the Arabidopsis transcriptome AtRTD2 identified ORF mis-calling in over 16k (27%) of transcripts by TransDecoder.

scholarly journals Molecular cloning and characterization of glutamate decarboxylase cDNA from the giant-embryo Oryza sativa

2010 ◽  
Vol 62 (4) ◽  
pp. 873-879 ◽  
Author(s):  
Hui Xu ◽  
Pan Liao ◽  
Jianbo Xiao ◽  
Qianfei Zhang ◽  
Yanjun Dong ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Glutamate Decarboxylase ◽  
Structural Features ◽  
Full Length ◽  
Gamma Aminobutyric Acid ◽  
Full Length Cdna ◽  
Gaba Production ◽  
Calculated Molecular Weight ◽  
Giant Embryo

A full-length cDNA encoding glutamate decarboxylase (designated as OsGAD3), which catalyzes the conversion of glutamate to gamma-aminobutyric acid (GABA), was isolated from the GABA-rich giant-embryo Oryza sativa (Shangshi Jing 315). The full-length cDNA of OsGAD3 (SSJ315) has a 1479 bp open reading frame (ORF) encoding a protein of 492 amino acid residues. The deduced protein had an isoelectric point (pI) of 5.72 and a calculated molecular weight of 56.1 kD. Sequence comparison showed that OsGAD3 (SSJ315) matches the glutamate decarboxylases of other plant species reported previously. Analysis of the structural features of the C-terminal portions of plant GADs revealed that OsGAD3 (SSJ315) has the typical CaM-binding domain (CaMBD) in the C-terminal region as most other plant GADs. Evolution analysis showed that plant GADs are conserved in the process of evolution. The cloning and characterization of the OsGAD3 (SSJ315) gene will enable us to use OsGAD3 to enhance GABA production in O. sativa (SSJ315) by metabolic engineering in the near future.

Skeletal elements of crinoid echinoderms: High-resolution structural and microanalytical results

1983 ◽  
Vol 41 ◽  
pp. 194-195
Author(s):  
D. F. Blake ◽  
L. F. Allard ◽  
D. R. Peacor
Keyword(s):  
High Resolution ◽  
Marine Invertebrates ◽  
Sea Urchins ◽  
Structural Features ◽  
Sea Stars ◽  
High Resolution Tem ◽  
Relationship Of ◽  
The Relationship ◽  
Insight Into

Echinodermata is a phylum of marine invertebrates which has been extant since Cambrian time (c.a. 500 m.y. before the present). Modern examples of echinoderms include sea urchins, sea stars, and sea lilies (crinoids). The endoskeletons of echinoderms are composed of plates or ossicles (Fig. 1) which are with few exceptions, porous, single crystals of high-magnesian calcite. Despite their single crystal nature, fracture surfaces do not exhibit the near-perfect {10.4} cleavage characteristic of inorganic calcite. This paradoxical mix of biogenic and inorganic features has prompted much recent work on echinoderm skeletal crystallography. Furthermore, fossil echinoderm hard parts comprise a volumetrically significant portion of some marine limestones sequences. The ultrastructural and microchemical characterization of modern skeletal material should lend insight into: 1). The nature of the biogenic processes involved, for example, the relationship of Mg heterogeneity to morphological and structural features in modern echinoderm material, and 2). The nature of the diagenetic changes undergone by their ancient, fossilized counterparts. In this study, high resolution TEM (HRTEM), high voltage TEM (HVTEM), and STEM microanalysis are used to characterize tha ultrastructural and microchemical composition of skeletal elements of the modern crinoid Neocrinus blakei.

Ultrastructural identification of three types of sensory setae on copepod antennae

1995 ◽  
Vol 53 ◽  
pp. 956-957
Author(s):  
T. M. Weatherby ◽  
P.H. Lenz
Keyword(s):  
Phase Locking ◽  
Membrane Surface ◽  
Reaction Times ◽  
High Sensitivity ◽  
Structural Features ◽  
Calanoid Copepods ◽  
Marine Food Webs ◽  
Dendritic Membrane ◽  
Ultrastructural Characterization

Crustaceans, as well as other arthropods, are covered with sensory setae and hairs, including mechanoand chemosensory sensillae with a ciliary origin. Calanoid copepods are small planktonic crustaceans forming a major link in marine food webs. In conjunction with behavioral and physiological studies of the antennae of calanoids, we undertook the ultrastructural characterization of sensory setae on the antennae of Pleuromamma xiphias.Distal mechanoreceptive setae exhibit exceptional behavioral and physiological performance characteristics: high sensitivity (<10 nm displacements), fast reaction times (<1 msec latency) and phase locking to high frequencies (1-2 kHz). Unusual structural features of the mechanoreceptors are likely to be related to their physiological sensitivity. These features include a large number (up to 3000) of microtubules in each sensory cell dendrite, arising from or anchored to electron dense rods associated with the ciliary basal body microtubule doublets. The microtubules are arranged in a regular array, with bridges between and within rows. These bundles of microtubules extend far into each mechanoreceptive seta and terminate in a staggered fashion along the dendritic membrane, contacting a large membrane surface area and providing a large potential site of mechanotransduction.

Quantitative nano-characterization of heterogeneous catalysts

1995 ◽  
Vol 53 ◽  
pp. 398-399
Author(s):  
P.A. Crozier ◽  
M. Pan
Keyword(s):  
Heterogeneous Catalysts ◽  
Low Dose ◽  
Imaging Techniques ◽  
Structural Features ◽  
Catalyst Characterization ◽  
New Developments ◽  
Double Phase ◽  
Phase Systems ◽  
Dose Imaging

Heterogeneous catalysts can be of varying complexity ranging from single or double phase systems to complicated mixtures of metals and oxides with additives to help promote chemical reactions, extend the life of the catalysts, prevent poisoning etc. Although catalysis occurs on the surface of most systems, detailed descriptions of the microstructure and chemistry of catalysts can be helpful for developing an understanding of the mechanism by which a catalyst facilitates a reaction. Recent years have seen continued development and improvement of various TEM, STEM and AEM techniques for yielding information on the structure and chemistry of catalysts on the nanometer scale. Here we review some quantitative approaches to catalyst characterization that have resulted from new developments in instrumentation.HREM has been used to examine structural features of catalysts often by employing profile imaging techniques to study atomic details on the surface. Digital recording techniques employing slow-scan CCD cameras have facilitated the use of low-dose imaging in zeolite structure analysis and electron crystallography. Fig. la shows a low-dose image from SSZ-33 zeolite revealing the presence of a stacking fault.

Coherent electron nanodiffraction from clean silver nano particles in a UHV STEM

1993 ◽  
Vol 51 ◽  
pp. 1058-1059
Author(s):  
J. Liu ◽  
M. Pan ◽  
G. E. Spinnler
Keyword(s):  
Supported Catalysts ◽  
Imaging Techniques ◽  
Nano Particles ◽  
Metal Particles ◽  
Shape Structure ◽  
Dynamical Simulations ◽  
Small Metal Particles ◽  
Extract Information

Small metal particles have peculiar chemical and physical properties as compared to bulk materials. They are especially important in catalysis since metal particles are common constituents of supported catalysts. The structural characterization of small particles is of primary importance for the understanding of structure-catalytic activity relationships. The shape and size of metal particles larger than approximately 5 nm in diameter can be determined by several imaging techniques. It is difficult, however, to deduce the shape of smaller metal particles. Coherent electron nanodiffraction (CEND) patterns from nano particles contain information about the particle size, shape, structure and defects etc. As part of an on-going program of STEM characterization of supported catalysts we report some preliminary results of CEND study of Ag nano particles, deposited in situ in a UHV STEM instrument, and compare the experimental results with full dynamical simulations in order to extract information about the shape of Ag nano particles.

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