scholarly journals A shared cis-regulatory module activates transcription in the suspensor of plant embryos

2018 ◽  
Author(s):  
Kelli F. Henry ◽  
Anhthu Q. Bui ◽  
Tomokazu Kawashima ◽  
Robert B. Goldberg
Keyword(s):  
Gibberellic Acid ◽  
Dna Sequences ◽  
Regulatory Network ◽  
Upstream Region ◽  
Regulatory Motifs ◽  
Runner Bean ◽  
Regulatory Module ◽  
Hormone Biosynthesis ◽  
Scarlet Runner Bean ◽  
Plant Embryo

AbstractThe mechanisms controlling the transcription of gene sets in specific regions of a plant embryo shortly after fertilization remain unknown. Previously, we showed that G564 mRNA, encoding a protein of unknown function, accumulates to high levels in the giant suspensor of both Scarlet Runner Bean (SRB) and Common Bean embryos, and a cis-regulatory module containing three unique DNA sequences, designated as the 10-bp, Region 2, and Fifth motifs, is required for G564 suspensor-specific transcription [Henry, K. F. et al., Plant Mol. Biol. 88(3):207-217 (2015); Kawashima, T. et al., Proc. Natl. Acad. Sci USA 106(9):3627-3632 (2009)]. We tested the hypothesis that these motifs are also required for transcription of the SRB GA 20-oxidase gene, which encodes a gibberellic acid hormone biosynthesis enzyme and is co-expressed with G564 at a high level in giant bean suspensors. We used deletion and gain-of-function experiments in transgenic tobacco embryos to show that two GA 20-oxidase DNA regions are required for suspensor-specific transcription – one in the 5’ untranslated region (UTR) (+119 to +205) and another in the 5’ upstream region (−341 to −316). Mutagenesis of sequences in these two regions determined that the cis-regulatory motifs required for G564 suspensor transcription are also required for GA 20-oxidase transcription within the suspensor, although the motif arrangement differs. Our results demonstrate the flexibility of motif positioning within a cis-regulatory module that activates gene transcription within giant bean suspensors, and suggest that G564 and GA 20-oxidase comprise part of a suspensor gene regulatory network.SignificanceLittle is known about how genes are expressed in different plant embryo regions. We tested the hypothesis that shared cis-regulatory motifs control the transcription of genes specifically in the suspensor. We carried out functional studies with the Scarlet Runner Bean (SRB) GA 20-oxidase gene that encodes a gibberellic acid (GA) hormone biosynthesis enzyme, and is expressed specifically within the suspensor. We show that cis-regulatory motifs required for GA 20-oxidase transcription within the suspensor are the same as those required for suspensor-specific transcription of the SRB G564 gene, although motif number, spacing and order differ. These cis-elements constitute a control module that is required to activate genes in the SRB suspensor and may form part of a suspensor regulatory network.

scholarly journals A shared cis-regulatory module activates transcription in the suspensor of plant embryos

2018 ◽  
Vol 115 (25) ◽  
pp. E5824-E5833 ◽  
Author(s):  
Kelli F. Henry ◽  
Anhthu Q. Bui ◽  
Tomokazu Kawashima ◽  
Robert B. Goldberg
Keyword(s):  
Dna Sequences ◽  
Upstream Region ◽  
Regulatory Motifs ◽  
Gene Sets ◽  
Regulatory Module ◽  
Hormone Biosynthesis ◽  
Gene Regulatory ◽  
Scarlet Runner Bean ◽  
High Level ◽  
Plant Embryo

The mechanisms controlling the transcription of gene sets in specific regions of a plant embryo shortly after fertilization remain unknown. Previously, we showed that G564 mRNA, encoding a protein of unknown function, accumulates to high levels in the giant suspensor of both Scarlet Runner Bean (SRB) and Common Bean embryos, and a cis-regulatory module containing three unique DNA sequences, designated as the 10-bp, Region 2, and Fifth motifs, is required for G564 suspensor-specific transcription [Henry KF, et al. (2015) Plant Mol Biol 88:207–217; Kawashima T, et al. (2009) Proc Natl Acad Sci USA 106:3627–3632]. We tested the hypothesis that these motifs are also required for transcription of the SRB GA 20-oxidase gene, which encodes a gibberellic acid hormone biosynthesis enzyme and is coexpressed with G564 at a high level in giant bean suspensors. We used deletion and gain-of-function experiments in transgenic tobacco embryos to show that two GA 20-oxidase DNA regions are required for suspensor-specific transcription, one in the 5′ UTR (+119 to +205) and another in the 5′ upstream region (−341 to −316). Mutagenesis of sequences in these two regions determined that the cis-regulatory motifs required for G564 suspensor transcription are also required for GA 20-oxidase transcription within the suspensor, although the motif arrangement differs. Our results demonstrate the flexibility of motif positioning within a cis-regulatory module that activates gene transcription within giant bean suspensors and suggest that G564 and GA 20-oxidase comprise part of a suspensor gene regulatory network.

scholarly journals Comparative analysis of embryo proper and suspensor transcriptomes in plant embryos with different morphologies

2021 ◽  
Vol 118 (6) ◽  
pp. e2024704118
Author(s):  
Min Chen ◽  
Jer-Young Lin ◽  
Xiaomeng Wu ◽  
Nestor R. Apuya ◽  
Kelli F. Henry ◽  
...  
Keyword(s):  
Common Bean ◽  
Chromatin Immunoprecipitation ◽  
Regulatory Network ◽  
Metabolic Pathways ◽  
Golgi Body ◽  
Embryo Morphology ◽  
Runner Bean ◽  
Genes Encoding ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Scarlet Runner Bean

An important question is what genes govern the differentiation of plant embryos into suspensor and embryo proper regions following fertilization and division of the zygote. We compared embryo proper and suspensor transcriptomes of four plants that vary in embryo morphology within the suspensor region. We determined that genes encoding enzymes in several metabolic pathways leading to the formation of hormones, such as gibberellic acid, and other metabolites are up-regulated in giant scarlet runner bean and common bean suspensors. Genes involved in transport and Golgi body organization are up-regulated within the suspensors of these plants as well, strengthening the view that giant specialized suspensors serve as a hormone factory and a conduit for transferring substances to the developing embryo proper. By contrast, genes controlling transcriptional regulation, development, and cell division are up-regulated primarily within the embryo proper. Transcriptomes from less specialized soybean and Arabidopsis suspensors demonstrated that fewer genes encoding metabolic enzymes and hormones are up-regulated. Genes active in the embryo proper, however, are functionally similar to those active in scarlet runner bean and common bean embryo proper regions. We uncovered a set of suspensor- and embryo proper–specific transcription factors (TFs) that are shared by all embryos irrespective of morphology, suggesting that they are involved in early differentiation processes common to all plants. Chromatin immunoprecipitation sequencing (ChIP-Seq) experiments with scarlet runner bean and soybean WOX9, an up-regulated suspensor TF, gained entry into a regulatory network important for suspensor development irrespective of morphology.

scholarly journals Reconstruction of a global gene regulatory network for Streptomyces coelicolor: Curation, inference, and assessment

2021 ◽  
Author(s):  
Andrea Zorro-Aranda ◽  
Juan Miguel Escorcia-Rodriguez ◽  
Jose Kenyi Gonzalez-Kise ◽  
Julio Augusto Freyre-Gonzalez
Keyword(s):  
Gene Regulatory Network ◽  
Dna Sequences ◽  
Regulatory Network ◽  
Sequence Data ◽  
Antibiotic Production ◽  
Streptomyces Coelicolor ◽  
System Level ◽  
Upstream Region ◽  
Regulatory Interactions ◽  
Gene Regulatory

Streptomyces coelicolor A3(2) is a model microorganism for the study of Streptomycetes, antibiotic production, and secondary metabolism in general. However, little effort to globally study its transcription has been made even though S. coelicolor has an outstanding variety of regulators among bacteria. We manually curated 29 years of literature and databases to assemble a meta-curated experimentally-validated gene regulatory network (GRN) with 5386 genes and 9707 regulatory interactions (~41% of the total expected interactions). This provides the most extensive and up-to-date reconstruction available for the regulatory circuitry of this organism. We found a low level of direct experimental validation for the regulatory interactions reported in the literature and curated in this work. Only ~6% (533/9687) are supported by experiments confirming the binding of the transcription factor to the upstream region of the target gene, the so-called "strong" evidence. To tackle network incompleteness, we performed network inference using several methods (including two proposed here) for motif detection in DNA sequences and GRN inference from transcriptomics. Further, we contrasted the structural properties and functional architecture of the networks to assess the predictions' reliability, finding the inference from DNA sequence data to be the most trustworthy. Finally, we show two possible applications of the inferred and the curated network. The inferred one allowed us to identify putative novel transcription factors for the key Streptomyces antibiotic regulatory proteins (SARPs). The curated one allows us to study the conservation of the system-level components between S. coelicolor and Corynebacterium glutamicum. There we identified the basal machinery as the common signature between the two organisms. The curated networks were deposited in Abasy Atlas (https://abasy.ccg.unam.mx/) while the inferences are available as Supplementary Material.

scholarly journals PEAKS: identification of regulatory motifs by their position in DNA sequences

2006 ◽  
Vol 23 (2) ◽  
pp. 243-244 ◽  
Author(s):  
Nicolás Bellora ◽  
Domènec Farré ◽  
M. Mar Albà
Keyword(s):  
Dna Sequences ◽  
Regulatory Motifs

Characterization of Colletotrichum lindemuthianum Races in Zambia and Evaluation of the CIAT Phaseolus Core Collection for Resistance to Anthracnose

Plant Disease ◽  
2021 ◽  
Author(s):  
Kelvin Kamfwa ◽  
Paul Gepts ◽  
Swivia Hamabwe ◽  
Zombe Kapata Nalupya ◽  
Chikoti Mukuma ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Common Bean ◽  
Core Collection ◽  
Durable Resistance ◽  
Colletotrichum Lindemuthianum ◽  
Sources Of Resistance ◽  
Runner Bean ◽  
Causal Pathogen ◽  
Scarlet Runner Bean

Colletotrichum lindemuthianum, the causal pathogen of common bean (Phaseolus vulgaris) anthracnose, is highly variable. Therefore, understanding its race structure and identification of new sources of resistance is necessary for the development of varieties with durable resistance. The objectives of this study were (i) to characterize isolates of C. lindemuthianum collected from three major bean-growing regions in Zambia, and (ii) evaluate the CIAT Phaseolus core collection for resistance to C. lindemuthianum races 37, 73, and 566, and a blend of 20 races. Isolates collected from three major bean-growing districts in Zambia, namely Mporokoso, Mpika, and Mbala, were characterized as race 37, 73, and 566, respectively. A subset of the CIAT core collection comprised of 885 accessions of common bean, 13 accessions of scarlet runner bean (P. coccineus), and 11 accessions of year bean (P. dumosus) were evaluated for resistance to races 37, 73 and 566, and a blend of 20 races in a greenhouse at University of Zambia, Lusaka, Zambia. A total of 72%, 66%, 48% and 9% of P. vulgaris accessions evaluated were highly resistant to races 37, 73, 566 and a blend of 20 races, respectively. Also, accessions of P. coccineus and P. dumosus, highly resistant to races 37, 73 and 566, were identified. Only eight of the 331 P. vulgaris accessions were highly resistant to all three individual races (37, 73, and 566) and to a blend of 20 races. These eight accessions constitute a valuable breeding resource for developing varieties with durable resistance to C. lindemuthianum.

scholarly journals POISONING FROM EATING ROOT OF SCARLET RUNNER BEAN.

The Lancet ◽  
1897 ◽  
Vol 149 (3834) ◽  
pp. 519-520
Author(s):  
J.S. Macpherson
Keyword(s):  
Runner Bean ◽  
Scarlet Runner Bean

Intercropping Corn with Lablab Bean, Velvet Bean, and Scarlet Runner Bean for Forage

Crop Science ◽  
2008 ◽  
Vol 48 (1) ◽  
pp. 371-379 ◽  
Author(s):  
Kevin L. Armstrong ◽  
Kenneth A. Albrecht ◽  
Joseph G. Lauer ◽  
Heathcliffe Riday
Keyword(s):  
Velvet Bean ◽  
Runner Bean ◽  
Scarlet Runner Bean

scholarly journals Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs

2010 ◽  
Vol 4 (3) ◽  
pp. 333-344 ◽  
Author(s):  
Michiel Wels ◽  
Lex Overmars ◽  
Christof Francke ◽  
Michiel Kleerebezem ◽  
Roland J. Siezen
Keyword(s):  
Gene Expression ◽  
Lactobacillus Plantarum ◽  
Regulatory Network ◽  
Regulatory Motifs

scholarly journals A short 5'-flanking region mediates glucose repression of amylase gene expression in Drosophila melanogaster.

Genetics ◽  
1993 ◽  
Vol 134 (2) ◽  
pp. 507-515 ◽  
Author(s):  
C Magoulas ◽  
L Bally-Cuif ◽  
A Loverre-Chyurlia ◽  
B Benkel ◽  
D Hickey
Keyword(s):  
Drosophila Melanogaster ◽  
Dna Sequences ◽  
Glucose Repression ◽  
Essential Elements ◽  
Site Directed Mutagenesis ◽  
Deletion Analysis ◽  
Upstream Region ◽  
Directed Mutagenesis ◽  
Amylase Gene ◽  
Recombinant Gene

Abstract Expression of the alpha-amylase gene is highly repressed by dietary glucose in Drosophila melanogaster larvae. Here, we show that glucose repression is controlled by DNA sequences that are located upstream of the transcribed region. Recombinant gene constructions, in which the amylase promoter sequences were fused with the transcribed region of the Adh gene, were expressed in transgenic Drosophila larvae. The expression of ADH from the recombinant gene was shown to be subject to glucose repression. The function of potential regulatory cis-acting elements within the glucose responsive upstream region was examined by deletion analysis and by site-directed mutagenesis, coupled with expression assays in transformed larvae. The upstream deletion analysis showed that essential elements, both for overall activity and for glucose repression of the amylase gene, are located within a 109-bp region upstream of the transcription start site. Site-directed mutagenesis of these upstream sequences showed that the TATA motif, at position -31, and a novel 36-bp element, at position -109, were necessary for full activity of the amylase promoter. None of the introduced mutations resulted in loss of glucose responsiveness. These results indicate that glucose repression, in Drosophila, is mediated by transcriptional mechanisms that involve multiple, functionally redundant DNA elements.

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