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Gene transcriptions/Boxes/AGCs

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This is a digital photograph of Arabidopsis thaliana. Credit: Alberto Salguero Quiles en Getafe (Madrid), España.

"The GCC box, also referred to as the AGC box (10), GCC element (11), or AGCCGCC sequence (13), is an ethylene-responsive element found in the promoters of a large number of [pathogenesis related] PR genes whose expression is up-regulated following pathogen attack."[1]

Consensus sequences

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Main resource: Consensus sequences

The AGC box has a consensus sequence as 3'-AGCCGCC-5' in the direction of transcription.[2]

AGC

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"AGC is a binding site for factors responding to pathogen attacks (Ohme-Takagi et al., 2000)".[3]

Inverse copies

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For "AGC, one copy in inverse orientation of the AGC box (AGCCGCC) [is] present as two copies (-1346 and -1314) in the ERE".[2]

Enhancers

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Main resources: Gene transcriptions/Enhancers and Enhancers

"Enhancer activity, ethylene responsiveness, and binding of nuclear proteins depend on the integrity of two copies of the AGC box, AGCCGCC, present in the promoters of several ethylene-responsive genes."[2]

"The GLB enhancer contains two copies of the sequence AGCCGCC, which is conserved in several genes showing expression patterns similar to the GLB gene, as well as a sequence identical at 6 of 7 bp."[4]

Glucanase promoters

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"One common motif, AGCCGCC (AGC box), has been found to be present in nearly all chitinase and glucanase promoters so far analyzed (Ohme-Takagi and Shinshi 1990; Hart et al. 1993)."[5]

DNA-binding proteins

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"cDNA clones have been identified representing 4 novel DNA-binding proteins, called ethylene-responsive element binding proteins (EREBPs), that specifically bind the ERE AGC box".[2]

Functional non-coding DNA

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Functional "non-coding DNA is involved in the regulation of gene expression and thus in the evolution of novelties and adaptation between species [...] Functional non-coding sequences fall into two main categories: protein binding sites such as transcription factor binding sites (TFBSs), enhancers [such as the AGC box], and silencers, which are involved in the control of gene expression, and sequences that control chromatin organization such as insulators and matrix attachment regions".[6]

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"Genes of PR-1 and -5 proteins have now been identified in the genomes of various species of organisms, including humans and nematodes. PR proteins may contribute to the innate immunity of plants as well as to that of other organisms."[7]

Ostreococcus

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File:Ostreococcus RCC143 2.jpg
This is a photomicrograph of Ostreococcus. Credit: Wenche Eikrem and Jahn Throndsen, University of Oslo.

"Ocean-dwelling phytoplankton from the genus Ostreococcus emerge at the primitive root of the green plant lineage, dating back nearly 1.5 billion years. Today, these microscopic, free-living creatures, among the smallest eukaryotes ever characterized, barely a micron in diameter, contribute to a significant share of the world’s total photosynthetic activity. These “picophytoplankton”also exhibit great diversity that contrasts sharply with the dearth of ecological niches available to them in aquatic ecosystems. This observation, known as the “paradox of the plankton,” has long puzzled biologists."[8]

"Plumbing the depths of molecular-level information of related species, genomics offers a novel glimpse into this paradox. The researchers compared the genomes of two Ostreococcus species, O. lucimarinus and O. tauri, and saw dramatic changes in genome structure and metabolic capabilities."[8]

“We found several striking features of genome organization. Overlapping genes conserved across the species may enable them to cross-regulate their expression, while species-specific chromosomes with horizontally transferred genes can account for changes in the cell surface to adapt to different ecological niches.”[8]

“This work builds on the community’s emerging understanding about how carbon fixation is carried out by picoplankton.”[9]

“From an applied perspective, we are learning some of the tricks nature has employed to ‘engineer’ an extremely small eukaryote to thrive in nature–which may well find applications in bioengineering. It was particularly interesting to see the predicted use of selenium-containing enzymes as one of the tricks to maintain such tiny cells. There are many mechanisms that can account for species formation in photosynthetic phytoplankton, and this is just one of the major pieces to this long-standing puzzle for biologists.”[9]

“Assimilation of atmospheric CO2 by marine phytoplankton is a global-scale process that is responsible for about half of the biosphere net primary production. This active absorption of hundreds of millions of tons of carbon per day is essential for maintaining the control of the planet’s climate by counteracting greenhouse effects due to human activities. Clearly, this storage capacity is affected by changes in the photosynthetic efficiency of the algae, which in turn is linked to the environmental conditions experienced by these organisms in their environment.”[10]

Nicotiana

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The osmotin-like protein (OLP) "has no intron and ... its promoter region contains two AGCCGCC sequences that are conserved in most basic PR-protein genes."[11]

The "AGCCGCC sequence(s) is a DNA element(s) responsive to ethylene. An EREBP2 protein, isolated as one of the proteins binding the AGCCGCC sequence of the tobacco rβ-1,3-glucanase gene, also was found to bind to the AGCCGCC sequence(s) of OLP gene. These results suggest that the ethylene-induced expression of OLP is regulated by trans-acting factor(s) common to basic PR-proteins."[11]

"AGCCGCC sequences were found at -46 to -52 and -161 to -167. There was no repeated sequence (-938 to -903)".[11]

"Expression of the osmotin gene is similar to that of the OLP gene. The osmotin gene also has several AGCCGCC sequences; a complete AGCCGCC (from -50 to -44), a slightly modified CGCCGCC (from -144 to -138), and an AGCCGCC sequence in reverse orientation (from -162 to -156)."[11]

Arabidopsis

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This is an image of the flowers of Arabidopsi thaliana, a specimen of about 15 cm, in the first week of March 2004. Credit: Alberto Salguero Quiles in Getafe (Madrid), Spain.

In Arabidopsis thaliana "an ethylene-inducible, GCC box DNA-binding protein interacts with an ocs element binding protein".[1]

"In yeast and mammalian systems, it is well established that transcriptional down-regulation by DNA-binding repressors involves core histone deacetylation, mediated by their interaction within a complex containing histone deacetylase (e.g. HDA1), as well as various proteins (e.g. SIN3, SAP18, SAP30, and RhAp46). [An] Arabidopsis thaliana gene related in sequence to SAP18, designated AtSAP18, functions in transcription regulation in plants subjected to salt stress."[12]

Evidence has been provided "that SAP18 and HDA1 function as transcriptional repressors. [Further] they associate with Ethylene-Responsive Element binding Factors (ERFs) to create a hormone-sensitive multimeric repressor complex under conditions of environmental stress."[12]

"At the molecular level, the actions of ethylene upon gene expression involve Ethylene Responsive element binding Factors (ERFs), which display GCC box-specific binding activities in Arabidopsis (Ohme-Takagi and Shinshi, 1995). ERFs contain a highly conserved DNA binding domain (the EFR domain) consisting of 58-59 amino acids (Ohme-Takagi and Shinshi, 1995), which binds with high affinity to the GCC box (Hao et al., 1998)."[12]

Peaches

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"An AGC box (AGCCGCC) was found [from peach (Prunus persica L. Batsch cv. Loring)] between 886 and 892 bp upstream of the translation start site which has been shown in other ethylene-responsive PR genes to be a binding site for ethylene-responsive binding factor proteins (ERF proteins) (Ohme-Takagi and Shinshi, 1995; Sato et al., 1996; Jia and Martin, 1999; Fujimoto et al., 2000)."[3]

"The peach ACO1 does have an AGC box that has been found to bind ethylene responsive elements in response to pathogen infections (Ohme-Takagi et al., 2000; Rushton et al., 2002). Only the apple ACO1 also contains this sequence. In addition, both PpACO1 and the apple ACO1 have a MADS box transcription factor binding site (CarG) (Tilly et al., 1998), but none of the other ACO genes do. "[3]

E2F4

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Structure of the E2F4 protein shown is based on PyMOL rendering of PDB 1cf7. Credit: Emw.

Gene ID: 1874 - "The protein encoded by this gene is a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cell cycle and action of tumor suppressor proteins and is also a target of the transforming proteins of small DNA tumor viruses. The E2F proteins contain several evolutionally conserved domains found in most members of the family. These domains include a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins (DP), a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain. This protein binds to all three of the tumor suppressor proteins pRB, p107 and p130, but with higher affinity to the last two. It plays an important role in the suppression of proliferation-associated genes, and its gene mutation and increased expression may be associated with human cancer."[13]

"The AGC triplet repeat in the coding region of the E2F-4 gene, a member of the family, has been reported to be mutated in colorectal cancers with a microsatellite instability (MSI) phenotype. We found a wider range variation of the repeat number in DNAs from tumors, the corresponding normal mucosa, and healthy individuals. A total of 5 repeat variants, ranging from 8 to 17 AGC repeats, was detected in 6 (9.7%) of the 62 healthy individuals and 8 (8.9%) of the 90 normal DNAs of the patients. The wild-type 13 repeat was present in all of these individuals. The variation of the AGC repeat number may be a polymorphism. Further, loss of heterozygosity (LOH) at the E2F-4 locus in the tumor tissues of 2 (25%) of the 8 informative cases was detected."[14]

Hypotheses

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Main resource: Hypotheses
  1. An AGC box occurs in the human genome.

See also

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References

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  1. ↑ 1.0 1.1 Michael Büttner and Karam B. Singh (May 27, 1997). "Arabidopsis thaliana ethylene-responsive element binding protein (AtEBP), an ethylene-inducible, GCC box DNA-binding protein interacts with an ocs element binding protein". Proceedings of the National Academy of Sciences of the United States of America 94 (11): 5961-6. http://www.pnas.org/content/94/11/5961.long. Retrieved 2014-05-02. 
  2. ↑ 2.0 2.1 2.2 2.3 Gerhard Leubner-Metzger, Luciana Petruzzelli, Rosa Waldvogel, Regina Vögeli-Lange, and Frederick Meins, Jr. (November 1998). "Ethylene-responsive element binding protein (EREBP) expression and the transcriptional regulation of class I β-1, 3-glucanase during tobacco seed germination". Plant Molecular Biology 38 (5): 785-95. doi:10.1023/A:1006040425383. http://link.springer.com/article/10.1023/A:1006040425383. Retrieved 2014-05-02. 
  3. ↑ 3.0 3.1 3.2 Hangsik Moon and Ann M. Callahan (2004). "Developmental regulation of peach ACC oxidase promoter–GUS fusions in transgenic tomato fruits". Journal of Experimental Botany 55 (402): 1519-28. doi:10.1093/jxb/erh162. http://jxb.oxfordjournals.org/content/55/402/1519.full. Retrieved 2014-05-07. 
  4. ↑ CM Hart, F. Nagy, and F. Meins Jr. (January 1993). "A 61 bp enhancer element of the tobacco beta-1,3-glucanase B gene interacts with one or more regulated nuclear proteins". Plant Molecular Biology 21 (1): 121-31. PMID 8425042. http://www.ncbi.nlm.nih.gov/pubmed/8425042?dopt=Abstract. Retrieved 2014-05-02. 
  5. ↑ Imre E. Somssich (1994). L. Nover. ed. Regulatory Elements Governing Pathogenesis-Related (PR) Gene Expression, In: Plant Promoters and Transcription Factors. 20. Berlin: Springer-Verlag. pp. 163-79. doi:10.1007/978-3-540-48037-2_7. http://link.springer.com/chapter/10.1007/978-3-540-48037-2_7. Retrieved 2014-05-07. 
  6. ↑ Gwenael Piganeau, Klaas Vandepoele, Sébastien Gourbière, Yves Van de Peer, and Hervé Moreau (September 2009). "Unraveling cis-Regulatory Elements in the Genome of the Smallest Photosynthetic Eukaryote: Phylogenetic Footprinting in Ostreococcus". Journal of Molecular Evolution 69 (3): 249-59. doi:10.1007/s00239-009-927I-0. http://link.springer.com/article/10.1007/s00239-009-9271-0. Retrieved 2014-05-02. 
  7. ↑ Sakihito Kitajima and Fumihiko Sato (1999). "Plant pathogenesis-related proteins: molecular mechanisms of gene expression and protein function". Journal of Biochemistry 125 (1): 1-8. http://jb.oxfordjournals.org/content/125/1/1.short. Retrieved 2016-01-07. 
  8. ↑ 8.0 8.1 8.2 Igor Grigoriev (April 30, 2007). Puzzling Plankton Yield Secrets to Role in Evolution/Global Photosynthesis. Washington, DC USA: Department of Energy. http://jgi.doe.gov/news_4_30_07/. Retrieved 2014-05-06. 
  9. ↑ 9.0 9.1 Brian Palenik (April 30, 2007). Puzzling Plankton Yield Secrets to Role in Evolution/Global Photosynthesis. Washington, DC USA: Department of Energy. http://jgi.doe.gov/news_4_30_07/. Retrieved 2014-05-06. 
  10. ↑ Hervé Moreau (April 30, 2007). Puzzling Plankton Yield Secrets to Role in Evolution/Global Photosynthesis. Washington, DC USA: Department of Energy. http://jgi.doe.gov/news_4_30_07/. Retrieved 2014-05-06. 
  11. ↑ 11.0 11.1 11.2 11.3 Fumihiko Sato, Sakihito Kitajima and Tomotsugu Koyama (1996). "Ethylene-Induced Gene Expression of Osmotin-Like Protein, a Neutral Isoform of Tobacco PR-5, is Mediated by the AGCCGCC eft-Sequence". Plant and Cell Physiology 37 (3): 249-55. http://pcp.oxfordjournals.org/content/37/3/249.abstract?ijkey=ae2c0781e0fec37c9540b9812e70402dfee2a1b9&keytype2=tf_ipsecsha. Retrieved 2014-05-07. 
  12. ↑ 12.0 12.1 12.2 Chun-Peng Song and David W. Galbraith (January 2006). "AtSAP18, an orthologue of human SAP18, is involved in the regulation of salt stress and mediates transcriptional repression in Arabidopsis". Plant Molecular Biology 60 (2): 241-57. doi:10.1007/s11103-005-3880-9. http://link.springer.com/article/10.1007/s11103-005-3880-9. Retrieved 2016-01-07. 
  13. ↑ RefSeqJuly2008 (25 December 2016). E2F4 E2F transcription factor 4 ( Homo sapiens (human) ). Bethesda, MD, USA: National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/gene/1874. Retrieved 2017-01-08. 
  14. ↑ X. Zhong, H. Hemmi, J. Koike, K. Tsujita, H. Shimatake (March 2000). "Various AGC repeat numbers in the coding region of the human transcription factor gene E2F-4". Human Mutation 15 (3): 296-7. doi:10.1002/(SICI)1098-1004(200003)15:3<296::AID-HUMU18>3.0.CO;2-X. PMID 10679953. https://www.ncbi.nlm.nih.gov/pubmed/10679953. Retrieved 2017-01-08. 

Further reading

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