The Experts below are selected from a list of 15297 Experts worldwide ranked by ideXlab platform

Ruiqin Zhong - One of the best experts on this subject based on the ideXlab platform.

  • Secondary wall NAC binding Element (SNBE), a key Cis-Acting Element required for target gene activation by secondary wall NAC master switches
    Plant signaling & behavior, 2011
    Co-Authors: Ryan L. Mccarthy, Ruiqin Zhong
    Abstract:

    The biosynthesis of secondary walls in vascular plants requires the coordinated regulation of a suite of biosynthetic genes, and this coordination has recently been shown to be executed by the secondary wall NAC (SWN)-mediated transcriptional network. In Arabidopsis, five SWNs, including SND1, NST1/2 and VND6/7, function as master transcriptional switches to activate their common targets and consequently the secondary wall biosynthetic program. A recent report by Zhong et al.1 revealed that SWNs bind to a common Cis-Acting Element, namely secondary wall NAC binding Element (SNBE), which is composed of an imperfect palindromic 19-bp consensus sequence, (T/A)NN(C/T)(T/C/G)TNNNNNNNA(A/C)GN(A/C/T) (A/T). Genome-wide analysis of direct targets of SWNs showed that SWNs directly activate the expression of not only many transcription factors but also a battery of genes involved in secondary wall biosynthesis, cell wall modification and programmed cell death, the promoters of which all contain multiple SNBE sites. The functional significance of the SNBE sites is further substantiated by our current in planta expression study demonstrating that representative SNBE sequences from several SWN direct target promoters are sufficient to drive the expression of the GUS reporter gene in secondary wall-forming cells. The identification of the SWN DNA binding Element (SNBE) and the SWN direct targets marks an important step forward toward the dissection of the transcriptional network regulating the biosynthesis of secondary walls, the most abundant biomass produced by land plants.

David A Brian - One of the best experts on this subject based on the ideXlab platform.

  • Stem-Loop IV in the 5′ Untranslated Region Is a Cis-Acting Element in Bovine Coronavirus Defective Interfering RNA Replication
    Journal of virology, 2005
    Co-Authors: Sharmila Raman, David A Brian
    Abstract:

    Higher-order structures in the 5' untranslated region (UTR) of plus-strand RNA viruses are known in many cases to function as Cis-Acting Elements in RNA translation, replication, or transcription. Here we describe evidence supporting the structure and a Cis-Acting function in defective interfering (DI) RNA replication of stem-loop III, the third of four predicted higher-order structures mapping within the 210-nucleotide (nt) 5' UTR of the 32-kb bovine coronavirus (BCoV) genome. Stem-loop III maps at nt 97 through 116, has a calculated free energy of -9.1 kcal/mol in the positive strand and -3.0 kcal/mol in the negative strand, and has associated with it beginning at nt 100 an open reading frame (ORF) potentially encoding an 8-amino-acid peptide. Stem-loop III is presumed to function in the positive strand, but its strand of action has not been established. Stem-loop III (i) shows phylogenetic conservation among group 2 coronaviruses and appears to have a homolog in coronavirus groups 1 and 3, (ii) has in all coronaviruses for which sequence is known a closely associated short, AUG-initiated intra-5' UTR ORF, (iii) is supported by enzyme structure-probing evidence in BCoV RNA, (iv) must maintain stem integrity for DI RNA replication in BCoV DI RNA, and (v) shows a positive correlation between maintenance of the short ORF and maximal DI RNA accumulation in BCoV DI RNA. These results indicate that stem-loop III in the BCoV 5' UTR is a Cis-Acting Element for DI RNA replication and that its associated intra-5' UTR ORF may function to enhance replication. It is postulated that these two Elements function similarly in the virus genome.

  • stem loop iv in the 5 untranslated region is a Cis Acting Element in bovine coronavirus defective interfering rna replication
    Journal of Virology, 2003
    Co-Authors: Sharmila Raman, David A Brian
    Abstract:

    Higher-order structures in the 5' untranslated region (UTR) of plus-strand RNA viruses are known in many cases to function as Cis-Acting Elements in RNA translation, replication, or transcription. Here we describe evidence supporting the structure and a Cis-Acting function in defective interfering (DI) RNA replication of stem-loop III, the third of four predicted higher-order structures mapping within the 210-nucleotide (nt) 5' UTR of the 32-kb bovine coronavirus (BCoV) genome. Stem-loop III maps at nt 97 through 116, has a calculated free energy of -9.1 kcal/mol in the positive strand and -3.0 kcal/mol in the negative strand, and has associated with it beginning at nt 100 an open reading frame (ORF) potentially encoding an 8-amino-acid peptide. Stem-loop III is presumed to function in the positive strand, but its strand of action has not been established. Stem-loop III (i) shows phylogenetic conservation among group 2 coronaviruses and appears to have a homolog in coronavirus groups 1 and 3, (ii) has in all coronaviruses for which sequence is known a closely associated short, AUG-initiated intra-5' UTR ORF, (iii) is supported by enzyme structure-probing evidence in BCoV RNA, (iv) must maintain stem integrity for DI RNA replication in BCoV DI RNA, and (v) shows a positive correlation between maintenance of the short ORF and maximal DI RNA accumulation in BCoV DI RNA. These results indicate that stem-loop III in the BCoV 5' UTR is a Cis-Acting Element for DI RNA replication and that its associated intra-5' UTR ORF may function to enhance replication. It is postulated that these two Elements function similarly in the virus genome.

  • Stem-loop III in the 5' untranslated region is a Cis-Acting Element in bovine coronavirus defective interfering RNA replication.
    Journal of virology, 2003
    Co-Authors: Sharmila Raman, Peter Bouma, Gwyn D Williams, David A Brian
    Abstract:

    Higher-order structures in the 5' untranslated region (UTR) of plus-strand RNA viruses are known in many cases to function as Cis-Acting Elements in RNA translation, replication, or transcription. Here we describe evidence supporting the structure and a Cis-Acting function in defective interfering (DI) RNA replication of stem-loop III, the third of four predicted higher-order structures mapping within the 210-nucleotide (nt) 5' UTR of the 32-kb bovine coronavirus (BCoV) genome. Stem-loop III maps at nt 97 through 116, has a calculated free energy of -9.1 kcal/mol in the positive strand and -3.0 kcal/mol in the negative strand, and has associated with it beginning at nt 100 an open reading frame (ORF) potentially encoding an 8-amino-acid peptide. Stem-loop III is presumed to function in the positive strand, but its strand of action has not been established. Stem-loop III (i) shows phylogenetic conservation among group 2 coronaviruses and appears to have a homolog in coronavirus groups 1 and 3, (ii) has in all coronaviruses for which sequence is known a closely associated short, AUG-initiated intra-5' UTR ORF, (iii) is supported by enzyme structure-probing evidence in BCoV RNA, (iv) must maintain stem integrity for DI RNA replication in BCoV DI RNA, and (v) shows a positive correlation between maintenance of the short ORF and maximal DI RNA accumulation in BCoV DI RNA. These results indicate that stem-loop III in the BCoV 5' UTR is a Cis-Acting Element for DI RNA replication and that its associated intra-5' UTR ORF may function to enhance replication. It is postulated that these two Elements function similarly in the virus genome.

James B. Flanegan - One of the best experts on this subject based on the ideXlab platform.

  • 3′-Terminal Sequence in Poliovirus Negative-Strand Templates Is the Primary Cis-Acting Element Required for VPgpUpU-Primed Positive-Strand Initiation
    Journal of virology, 2005
    Co-Authors: Nidhi Sharma, Brian J. O'donnell, James B. Flanegan
    Abstract:

    The 5' cloverleaf in poliovirus RNA has a direct role in regulating the stability, translation, and replication of viral RNA. In this study, we investigated the role of stem a in the 5' cloverleaf in regulating the stability and replication of poliovirus RNA in HeLa S10 translation-replication reactions. Our results showed that disrupting the duplex structure of stem a destabilized viral RNA and inhibited efficient negative-strand synthesis. Surprisingly, the duplex structure of stem a was not required for positive-strand synthesis. In contrast, altering the primary sequence at the 5'-terminal end of stem a had little or no effect on negative-strand synthesis but dramatically reduced positive-strand initiation and the formation of infectious virus. The inhibition of positive-strand synthesis observed in these reactions was most likely a consequence of nucleotide alterations in the conserved sequence at the 3' ends of negative-strand RNA templates. Previous studies suggested that VPgpUpU synthesized on the cre(2C) hairpin was required for positive-strand synthesis. Therefore, these results are consistent with a model in which preformed VPgpUpU serves as the primer for positive-strand initiation on the 3'AAUUUUGUC5' sequence at the 3' ends of negative-strand templates. Our results suggest that this sequence is the primary Cis-Acting Element that is required for efficient VPgpUpU-primed positive-strand initiation.

  • 3 terminal sequence in poliovirus negative strand templates is the primary Cis Acting Element required for vpgpupu primed positive strand initiation
    Journal of Virology, 2005
    Co-Authors: Nidhi Sharma, Brian J Odonnell, James B. Flanegan
    Abstract:

    The 5' cloverleaf in poliovirus RNA has a direct role in regulating the stability, translation, and replication of viral RNA. In this study, we investigated the role of stem a in the 5' cloverleaf in regulating the stability and replication of poliovirus RNA in HeLa S10 translation-replication reactions. Our results showed that disrupting the duplex structure of stem a destabilized viral RNA and inhibited efficient negative-strand synthesis. Surprisingly, the duplex structure of stem a was not required for positive-strand synthesis. In contrast, altering the primary sequence at the 5'-terminal end of stem a had little or no effect on negative-strand synthesis but dramatically reduced positive-strand initiation and the formation of infectious virus. The inhibition of positive-strand synthesis observed in these reactions was most likely a consequence of nucleotide alterations in the conserved sequence at the 3' ends of negative-strand RNA templates. Previous studies suggested that VPgpUpU synthesized on the cre(2C) hairpin was required for positive-strand synthesis. Therefore, these results are consistent with a model in which preformed VPgpUpU serves as the primer for positive-strand initiation on the 3'AAUUUUGUC5' sequence at the 3' ends of negative-strand templates. Our results suggest that this sequence is the primary Cis-Acting Element that is required for efficient VPgpUpU-primed positive-strand initiation.

Ryan L. Mccarthy - One of the best experts on this subject based on the ideXlab platform.

  • Secondary wall NAC binding Element (SNBE), a key Cis-Acting Element required for target gene activation by secondary wall NAC master switches
    Plant signaling & behavior, 2011
    Co-Authors: Ryan L. Mccarthy, Ruiqin Zhong
    Abstract:

    The biosynthesis of secondary walls in vascular plants requires the coordinated regulation of a suite of biosynthetic genes, and this coordination has recently been shown to be executed by the secondary wall NAC (SWN)-mediated transcriptional network. In Arabidopsis, five SWNs, including SND1, NST1/2 and VND6/7, function as master transcriptional switches to activate their common targets and consequently the secondary wall biosynthetic program. A recent report by Zhong et al.1 revealed that SWNs bind to a common Cis-Acting Element, namely secondary wall NAC binding Element (SNBE), which is composed of an imperfect palindromic 19-bp consensus sequence, (T/A)NN(C/T)(T/C/G)TNNNNNNNA(A/C)GN(A/C/T) (A/T). Genome-wide analysis of direct targets of SWNs showed that SWNs directly activate the expression of not only many transcription factors but also a battery of genes involved in secondary wall biosynthesis, cell wall modification and programmed cell death, the promoters of which all contain multiple SNBE sites. The functional significance of the SNBE sites is further substantiated by our current in planta expression study demonstrating that representative SNBE sequences from several SWN direct target promoters are sufficient to drive the expression of the GUS reporter gene in secondary wall-forming cells. The identification of the SWN DNA binding Element (SNBE) and the SWN direct targets marks an important step forward toward the dissection of the transcriptional network regulating the biosynthesis of secondary walls, the most abundant biomass produced by land plants.

John J. Finer - One of the best experts on this subject based on the ideXlab platform.

  • A novel Cis-Acting Element in the GmERF3 promoter contributes to inducible gene expression in soybean and tobacco after wounding
    Plant Cell Reports, 2016
    Co-Authors: Carlos M. Hernandez-garcia, John J. Finer
    Abstract:

    Key message Using in silico and functional analyses, we cloned and validated the expression profile of an inducible soybean promoter (GmERF3) along with its novel wound-induced and delayed expression (WIDE) Element. Abstract Promoters and their contributing promoter Elements are the main regulators of gene expression at the transcriptional level. Although the Ethylene Response Factor ( ERF ) gene family is one of the most well-studied stress-responsive gene families in plants, their promoter regions have received little attention. In this study, we investigated the expression patterns driven by the soybean ( Glycine max ) GmERF3 promoter and its Cis -Acting Elements in soybean and tobacco. Transcriptomic data revealed that the native GmERF3 gene was differentially expressed in organs and tissues of plants. In transgenic soybeans containing a 1.3 kb GmERF3 promoter fused to the green fluorescent protein ( gfp ) gene, organ- and tissue-specificity was observed in untreated plants while mechanical wounding led to induction of GFP expression. Further in silico and in planta analyses of the GmERF3 promoter sequence in soybean revealed different Cis -Acting Elements, including a novel Cis -Acting Element, which contributed to increased expression, 1–2 days after mechanical wounding. We have named this DNA motif the wound-induced and delayed expression Element (GGATTCAAGTTTAACC). A synthetic promoter containing a tetrameric repeat of this Element showed high but late wound-induced GFP expression in leaves of transgenic tobacco. Our study expands the toolbox of inducible promoters and promoter Elements for potential use in basic and applied research.

  • A novel Cis-Acting Element in the GmERF3 promoter contributes to inducible gene expression in soybean and tobacco after wounding.
    Plant cell reports, 2015
    Co-Authors: Carlos M. Hernandez-garcia, John J. Finer
    Abstract:

    Using in silico and functional analyses, we cloned and validated the expression profile of an inducible soybean promoter (GmERF3) along with its novel wound-induced and delayed expression (WIDE) Element. Promoters and their contributing promoter Elements are the main regulators of gene expression at the transcriptional level. Although the Ethylene Response Factor (ERF) gene family is one of the most well-studied stress-responsive gene families in plants, their promoter regions have received little attention. In this study, we investigated the expression patterns driven by the soybean (Glycine max) GmERF3 promoter and its Cis-Acting Elements in soybean and tobacco. Transcriptomic data revealed that the native GmERF3 gene was differentially expressed in organs and tissues of plants. In transgenic soybeans containing a 1.3 kb GmERF3 promoter fused to the green fluorescent protein (gfp) gene, organ- and tissue-specificity was observed in untreated plants while mechanical wounding led to induction of GFP expression. Further in silico and in planta analyses of the GmERF3 promoter sequence in soybean revealed different Cis-Acting Elements, including a novel Cis-Acting Element, which contributed to increased expression, 1–2 days after mechanical wounding. We have named this DNA motif the wound-induced and delayed expression Element (GGATTCAAGTTTAACC). A synthetic promoter containing a tetrameric repeat of this Element showed high but late wound-induced GFP expression in leaves of transgenic tobacco. Our study expands the toolbox of inducible promoters and promoter Elements for potential use in basic and applied research.