Browse
Submit Data
Databases
API
Help

Dataset Information

28 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

In silico characterization of synthetic promoters designed from mirabilis mosaic virus and rice tungro bacilliform virus.

ABSTRACT: CaMV35S is the most extensively used promoter for ectopic gene expression in plant system. However, multiple use of this promoter possesses several limitation i.e. homologous based gene silencing and differential suitability in monocot and dicot plants. The strength of a promoter is defined by the presence of cis-acting elements and trans acting nucleic binding factors, thus its strength can be regulated by changing the architecture of these regulatory elements. In the present study, eight hybrid promoters were designed from two parareteroviruses, rice tungro bacilliform viruses (RTBV) and mirabilis mosaic virus (MMV). The eight hybrid promoters, along with parental promoters were characterized for the presence of functional cis-elements and transcription factor binding sites (TFBS), which were predicted using bioinformatics tools such as PLACE and Matinspector. Presence of mirabilis mosaic virus modules for specific functions and over-represented modules was determined using Model inspector. A broad range of cis-elements (85), TFBS (1471) was obtained. Presence of Dehydration responsive element binding factors, Apetala 2 (AP2), WRKY, DNA binding with one finger DOF (DOFF) motifs had shown the functional relevance of these designed promoters with abiotic stress inducibility. In addition to these stress regulating TFBS, the presence of some enhancer like motifs such as P$OCSE, P$TERE, P$TODS, P$ASRC had shown the functional relevance of these promoters as a strong candidate for enhanced expression of ectopic gene.

SUBMITTER: Gupta D

PROVIDER: S-EPMC7459046 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Comparative analysis of rice plants infected with Rice tungro bacilliform virus

2012-12-31 | GSE38150 | GEO

Complete Genome Sequence of Rice Tungro Bacilliform Virus Infecting Asian Rice (Oryza sativa) in Malaysia.

Project description:Rice tungro disease was discovered in Malaysia in the 1930s. The first and only genome of Rice tungro bacilliform virus (RTBV) isolated from rice in Malaysia was sequenced in 1999. After nearly two decades, here, we present the complete genome sequence of an RTBV isolate in rice from Seberang Perai, Malaysia.

| S-EPMC6522785 | biostudies-literature

Comparative analysis of rice plants infected with Rice tungro bacilliform virus

Project description:Rice tungro bacilliform virus (RTBV) is determinant of the rice tungro disease symptom. We compare the gene responses by RTBV infection between RTBV susceptive (TN1) and resistant cultivar (TW16). TN1 infected with RTBV shows the mild stunting and leaf yellowing, although TW16 shows only mild stunting at only early infection stage, and recovers the symptoms. Keywords: virus infection, disease response Comparison between RTBV and mock infected rice. Biological replicates: 3 control, 3 infected, independently grown and harvested. 1 samples derived from 5 plants grown under same conditons

2012-12-31 | E-GEOD-38150 | biostudies-arrayexpress

RNA-interference in rice against Rice tungro bacilliform virus results in its decreased accumulation in inoculated rice plants.

Project description:Rice tungro is a viral disease seriously affecting rice production in South and Southeast Asia. Tungro is caused by the simultaneous infection in rice of Rice tungro bacilliform virus (RTBV), a double-stranded DNA virus and Rice tungro spherical virus (RTSV), a single-stranded RNA virus. To apply the concept of RNA-interference (RNAi) for the control of RTBV infection, transgenic rice plants expressing DNA encoding ORF IV of RTBV, both in sense as well as in anti-sense orientation, resulting in the formation of double-stranded (ds) RNA, were raised. RNA blot analysis of two representative lines indicated specific degradation of the transgene transcripts and the accumulation of small molecular weight RNA, a hallmark for RNA-interference. In the two transgenic lines expressing ds-RNA, different resistance responses were observed against RTBV. In one of the above lines (RTBV-O-Ds1), there was an initial rapid buildup of RTBV levels following inoculation, comparable to that of untransformed controls, followed by a sharp reduction, resulting in approximately 50-fold lower viral titers, whereas the untransformed controls maintained high levels of the virus till 40 days post-inoculation (dpi). In RTBV-O-Ds2, RTBV DNA levels gradually rose from an initial low to almost 60% levels of the control by 40 dpi. Line RTBV-O-Ds1 showed symptoms of tungro similar to the untransformed control lines, whereas line RTBV-O-Ds2 showed extremely mild symptoms.

| S-EPMC2522301 | biostudies-other

Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome: implications for integration and evolution.

Project description:BackgroundPlant genomes contain various kinds of repetitive sequences such as transposable elements, microsatellites, tandem repeats and virus-like sequences. Most of them, with the exception of virus-like sequences, do not allow us to trace their origins nor to follow the process of their integration into the host genome. Recent discoveries of virus-like sequences in plant genomes led us to set the objective of elucidating the origin of the repetitive sequences. Endogenous rice tungro bacilliform virus (RTBV)-like sequences (ERTBVs) have been found throughout the rice genome. Here, we reconstructed putative virus structures from RTBV-like sequences in the rice genome and characterized to understand evolutionary implication, integration manner and involvements of endogenous virus segments in the corresponding disease response.ResultsWe have collected ERTBVs from the rice genomes. They contain rearranged structures and no intact ORFs. The identified ERTBV segments were shown to be phylogenetically divided into three clusters. For each phylogenetic cluster, we were able to make a consensus alignment for a circular virus-like structure carrying two complete ORFs. Comparisons of DNA and amino acid sequences suggested the closely relationship between ERTBV and RTBV. The Oryza AA-genome species vary in the ERTBV copy number. The species carrying low-copy-number of ERTBV segments have been reported to be extremely susceptible to RTBV. The DNA methylation state of the ERTBV sequences was correlated with their copy number in the genome.ConclusionsThese ERTBV segments are unlikely to have functional potential as a virus. However, these sequences facilitate to establish putative virus that provided information underlying virus integration and evolutionary relationship with existing virus. Comparison of ERTBV among the Oryza AA-genome species allowed us to speculate a possible role of endogenous virus segments against its related disease.

| S-EPMC526188 | biostudies-literature

An analysis of the sequence of an infectious clone of rice tungro bacilliform virus, a plant pararetrovirus.

Project description:The nucleotide sequence of an infectious clone of rice tungro bacilliform virus (RTBV) DNA has been determined. The circular genome has 8002 bp and one strand contains four open reading frames (ORFs). One ORF is potentially capable of encoding a protein of 24 kD (P24) and has no initiation (ATG) codon. The other three ORFs potentially encode proteins of 12 kD, 194 kD and 46 kD (P12, P194, P46) respectively. The functions of P24, P12 and P46 are unknown. Comparative analyses with retroviruses and Commelina yellow mottle virus suggest that the 194 kD putative product is a polyprotein that is proteolytically cleaved to yield the virion coat protein, a protease and replicase (reverse transcriptase and RNase H) characteristic of retroelements. The DNA sequence reveals other features which strongly support our belief that RTBV is a pararetrovirus. These include sequences at the mapped positions of two discontinuities in the virion DNA which are complementary to tRNA metinit and purine-rich, and may be the priming sites for minus- and plus-strand DNA synthesis respectively. As the positions of likely transcriptional signals suggest, a full-length viral transcript is observed by northern analysis. The predicted folding of the 645 bp 5'-region of this RNA resembles that of caulimoviruses. Comparisons with other reverse transcribing elements are discussed.

| S-EPMC328178 | biostudies-other

Characterization of the protease domain of Rice tungro bacilliform virus responsible for the processing of the capsid protein from the polyprotein.

Project description:BackgroundRice tungro bacilliform virus (RTBV) is a pararetrovirus, and a member of the family Caulimoviridae in the genus Badnavirus. RTBV has a long open reading frame that encodes a large polyprotein (P3). Pararetroviruses show similarities with retroviruses in molecular organization and replication. P3 contains a putative movement protein (MP), the capsid protein (CP), the aspartate protease (PR) and the reverse transcriptase (RT) with a ribonuclease H activity. PR is a member of the cluster of retroviral proteases and serves to proteolytically process P3. Previous work established the N- and C-terminal amino acid sequences of CP and RT, processing of RT by PR, and estimated the molecular mass of PR by western blot assays.ResultsA molecular mass of a protein that was associated with virions was determined by in-line HPLC electrospray ionization mass spectral analysis. Comparison with retroviral proteases amino acid sequences allowed the characterization of a putative protease domain in this protein. Structural modelling revealed strong resemblance with retroviral proteases, with overall folds surrounding the active site being well conserved. Expression in E. coli of putative domain was affected by the presence or absence of the active site in the construct. Analysis of processing of CP by PR, using pulse chase labelling experiments, demonstrated that the 37 kDa capsid protein was dependent on the presence of the protease in the constructs.ConclusionThe findings suggest the characterization of the RTBV protease domain. Sequence analysis, structural modelling, in vitro expression studies are evidence to consider the putative domain as being the protease domain. Analysis of expression of different peptides corresponding to various domains of P3 suggests a processing of CP by PR. This work clarifies the organization of the RTBV polyprotein, and its processing by the RTBV protease.

| S-EPMC1087892 | biostudies-literature

RF2a, a bZIP transcriptional activator of the phloem-specific rice tungro bacilliform virus promoter, functions in vascular development.

Project description:Rice tungro bacilliform virus (RTBV) replicates only in phloem cells in infected rice plants and its promoter drives strong phloem-specific reporter gene expression in transgenic rice plants. We isolated a cDNA encoding a basic leucine zipper (bZIP) protein, RF2a, which binds to the Box II cis element that is important for expression from the promoter. RF2a, which stimulates Box II-dependent transcription in a homologous in vitro transcription system, accumulates in nuclei of phloem and certain other cell types in shoots, but is found at only very low levels in roots. Transgenic antisense plants in which RF2a accumulation was suppressed had normal roots but stunted, twisted leaves with small, disorganized vascular bundles, an enlarged sclerenchyma and large air spaces. We propose that the RTBV promoter exploits a host transcription factor that is critical for leaf tissue differentiation and vascular development for its expression.

| S-EPMC1170157 | biostudies-other

Rice tungro bacilliform virus open reading frames II and III are translated from polycistronic pregenomic RNA by leaky scanning.

Project description:Posttranscriptional components of the gene expression mechanism of rice tungro bacilliform virus (RTBV) were studied in transiently transfected protoplasts. RTBV translates several open reading frames from a polycistronic mRNA by leaky scanning. This mechanism is supported by the particular sequence features of the corresponding genome region and does not require a virus-encoded transactivator.

| S-EPMC192159 | biostudies-other

Identification of resistance to <i>Sugarcane mosaic virus, Sugarcane streak mosaic virus</i>, and <i>Sugarcane bacilliform virus</i> in new elite sugarcane accessions in India.

Project description:Sugarcane mosaic and leaf fleck diseases are significant viral diseases affecting sugarcane crops in India. The use of resistant sugarcane varieties is considered the most economical and effective approach to manage viral diseases, especially in vegetatively propagated crops such as sugarcane. Sugarcane mosaic virus (SCMV) and Sugarcane streak mosaic virus (SCSMV) are the primary pathogens responsible for mosaic disease in sugarcane-growing regions of India. Sugarcane bacilliform virus (SCBV), causing leaf fleck disease, is also often found in mixed infections with mosaic symptoms. The study aimed to identify new sources of resistance by screening sugarcane germplasm for resistance to SCMV, SCSMV, and SCBV. The screening was carried out under high inoculum using the infector row method in both plant and ratoon crops. Out of 129 genotypes tested, only 8 were found to be free of mosaic viruses, indicating a rare occurrence of resistant sources. The study revealed that mosaic disease is widespread, with nearly 95% of tested varieties/genotypes being infected with mosaic viruses. SCMV, SCSMV, and SCBV were detected in 121 out of 129 genotypes using the RT-PCR and PCR assays. Based on their response to the viruses, the tested genotypes were categorized into different resistance grades: highly resistant (grade 1), resistant (grade 2), moderately resistant (grade 3), susceptible (grade 4), and highly susceptible (grade 5). The results of the study provide valuable information about elite resistance resources that can be used for the prevention and control of mosaic disease. These resistant genotypes could also serve as potential donors for mosaic and leaf fleck disease resistance in breeding programs.

| S-EPMC10623450 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data