Publications by authors named "Ahmed F Yousef"

26 Publications

  • Page 1 of 1

Effects of light spectrum on morpho-physiological traits of grafted tomato seedlings.

PLoS One 2021 7;16(5):e0250210. Epub 2021 May 7.

College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China.

It is already known that there are many factors responsible for the successful grafting process in plants, including light intensity. However, the influence of the spectrum of light-emitting diodes (LEDs) on this process has almost never been tested. During the pre-grafting process tomato seedlings grew for 30 days under 100 μmol m-2 s-1 of mixed LEDs (red 70%+ blue 30%). During the post-grafting period, seedlings grew for 20 days under the same light intensity but the lightening source was either red LED, mixed LEDs (red 70% + blue 30%), blue LED or white fluorescent lamps. This was done to determine which light source(s) could better improve seedling quality and increase grafting success. Our results showed that application of red and blue light mixture (R7:B3) caused significant increase in total leaf area, dry weight (total, shoot and root), total chlorophyll/carotenoid ratio, soluble protein and sugar content. Moreover, this light treatment maintained better photosynthetic performance i.e. more effective quantum yield of PSII photochemistry Y(II), better photochemical quenching (qP), and higher electron transport rate (ETR). This can be partially explained by the observed upregulation of gene expression levels of PsaA and PsbA and the parallel protein expression levels. This in turn could lead to better functioning of the photosynthetic apparatus of tomato seedlings and then to faster production of photoassimilate ready to be translocated to various tissues and organs, including those most in need, i.e., involved in the formation of the graft union.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0250210PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8104444PMC
May 2021

Efficient Degradation of 2-Mercaptobenzothiazole and Other Emerging Pollutants by Recombinant Bacterial Dye-Decolorizing Peroxidases.

Biomolecules 2021 Apr 29;11(5). Epub 2021 Apr 29.

Department of Chemistry, College of Arts and Sciences, Khalifa University of Science and Technology, Abu Dhabi P.O. Box 127788, United Arab Emirates.

In recent years, concerns are being raised about the potential harmful effects of emerging pollutants (EPs) on human and aquatic lives. Extensive research is being conducted on developing efficient remediation strategies to target this new class of toxic pollutants. Studies focused on biological (enzyme-based) methods have shown potential as greener and possibly more economical alternatives to other treatment approaches, such as chemical methods. The current study focused on the use of recombinantly produced novel bacterial peroxidases, namely dye-decolorizing peroxidases (DyPs), to study their effectiveness in degrading a number of diverse EPs. In this context, a sensitive bioanalytical Liquid chromatography-tandem mass spectrometry (LCMSMS)-based method was developed to simultaneously detect a mixture of 31 EPs and to examine their degradability by a panel of seven different recombinant bacterial DyPs (rDyPs). We show that up to 9 of the 31 tested EPs could be degraded by at least one of the DyPs tested. The results also indicated that not all rDyPs behaved similarly in their abilities to degrade EPs, as some rDyPs (such as DyP and DyP) showed a promising potential to degrade EPs while others (such as DyP) were almost ineffective. Additionally, the role of redox mediators for effective emerging pollutant degradation by rDyPs was also examined, which showed dramatic improvement in the DyP-mediated degradation of five different EPs. Detailed analysis of 2-mercaptobenzothiazole degradation by DyP showed that six distinct breakdown products were generated. The present study showed for the first time that recombinant bacterial DyPs can be used for wastewater remediation by degrading a range of different EPs.
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http://dx.doi.org/10.3390/biom11050656DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8146892PMC
April 2021

Photosynthetic apparatus performance of tomato seedlings grown under various combinations of LED illumination.

PLoS One 2021 15;16(4):e0249373. Epub 2021 Apr 15.

College of Horticulture, Fujian Agricultural and Forestry University, Fuzhou, China.

It is already known that the process of photosynthesis depends on the quality and intensity of light. However, the influence of the new light sources recently used in horticulture, known as Light Emitting Diodes (LEDs), on this process is not yet fully understood. Chlorophyll a fluorescence measurement has been widely used as a rapid, reliable, and noninvasive tool to study the efficiency of the photosystem II (PSII) and to evaluate plant responses to various environmental factors, including light intensity and quality. In this work, we tested the responses of the tomato photosynthetic apparatus to different light spectral qualities. Our results showed that the best performance of the photosynthetic apparatus was observed under a mixture of red and blue light (R7:B3) or a mixture of red, green and blue light (R3:G2:B5). This was demonstrated by the increase in the effective photochemical quantum yield of PSII (Y[II]), photochemical quenching (qP) and electron transport rate (ETR). On the other hand, the mixture of red and blue light with a high proportion of blue light led to an increase in non-photochemical quenching (NPQ). Our results can be used to improve the production of tomato plants under artificial light conditions. However, since we found that the responses of the photosynthetic apparatus of tomato plants to a particular light regime were cultivar-dependent and there was a weak correlation between the growth and photosynthetic parameters tested in this work, special attention should be paid in future research.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0249373PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8049771PMC
April 2021

Influence of Bagging on the Development and Quality of Fruits.

Plants (Basel) 2021 Feb 13;10(2). Epub 2021 Feb 13.

College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.

Fruit quality is certainly influenced by biotic and abiotic factors, and a main quality attribute is the external appearance of the fruit. Various possible agronomical approaches are able to regulate the fruit microenvironment and, consequently, improve fruit quality and market value. Among these, fruit bagging has recently become an integral part of fruits' domestic and export markets in countries such as Japan, China, Korea Australia and the USA because it is a safe and eco-friendly technique to protect fruits from multiple stresses, preserving or improving the overall quality. Despite increasing global importance, the development of suitable bagging materials and, above all, their use in the field is quite laborious, so that serious efforts are required to enhance and standardize bagging material according to the need of the crops/fruits. This review provides information about the effects of bagging technique on the fruit aspect and texture, which are the main determinants of consumer choice.
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http://dx.doi.org/10.3390/plants10020358DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7918571PMC
February 2021

A conceptual framework modeling of functional microbial communities in wastewater treatment electro-bioreactors.

Water Sci Technol 2020 Dec;82(12):3047-3061

Center for Membranes and Advanced Water Technology (CMAT), Department of Chemical Engineering, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates E-mail:

Understanding the microbial ecology of a system allows linking members of the community and their metabolic functions to the performance of the wastewater bioreactor. This study provided a comprehensive conceptual framework for microbial communities in wastewater treatment electro-bioreactors (EBRs). The model was based on data acquired from monitoring the effect of altering different bioreactor operational parameters, such as current density and hydraulic retention time, on the microbial communities of an EBR and its nutrient removal efficiency. The model was also based on the 16S rRNA gene high-throughput sequencing data analysis and bioreactor efficiency data. The collective data clearly demonstrated that applying various electric currents affected the microbial community composition and stability and the reactor efficiency in terms of chemical oxygen demand, N and P removals. Moreover, a schematic that recommends operating conditions that are tailored to the type of wastewater that needs to be treated based on the functional microbial communities enriched at specific operating conditions was suggested. In this study, a conceptual model as a simplified representation of the behavior of microbial communities in EBRs was developed. The proposed conceptual model can be used to predict how biological treatment of wastewater in EBRs can be improved by varying several operating conditions.
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http://dx.doi.org/10.2166/wst.2020.553DOI Listing
December 2020

Detection and quantification of SARS-CoV-2 RNA in wastewater and treated effluents: Surveillance of COVID-19 epidemic in the United Arab Emirates.

Sci Total Environ 2021 Apr 19;764:142929. Epub 2020 Oct 19.

Department of Chemistry, Khalifa University of Science and Technology, PO Box 127788, Abu Dhabi, United Arab Emirates. Electronic address:

Testing SARS-CoV-2 viral loads in wastewater has recently emerged as a method of tracking the prevalence of the virus and an early-warning tool for predicting outbreaks in the future. This study reports SARS-CoV-2 viral load in wastewater influents and treated effluents of 11 wastewater treatment plants (WWTPs), as well as untreated wastewater from 38 various locations, in the United Arab Emirates (UAE) in May and June 2020. Composite samples collected over twenty-four hours were thermally deactivated for safety, followed by viral concentration using ultrafiltration, RNA extraction using commercially available kits, and viral quantification using RT-qPCR. Furthermore, estimates of the prevalence of SARS-CoV-2 infection in different regions were simulated using Monte Carlo. Results showed that the viral load in wastewater influents from these WWTPs ranged from 7.50E+02 to over 3.40E+04 viral gene copies/L with some plants having no detectable viral RNA by RT-qPCR. The virus was also detected in 85% of untreated wastewater samples taken from different locations across the country, with viral loads in positive samples ranging between 2.86E+02 and over 2.90E+04 gene copies/L. It was also observed that the precautionary measures implemented by the UAE government correlated with a drop in the measured viral load in wastewater samples, which were in line with the reduction of COVID-19 cases reported in the population. Importantly, none of the 11 WWTPs' effluents tested positive during the entire sampling period, indicating that the treatment technologies used in the UAE are efficient in degrading SARS-CoV-2, and confirming the safety of treated re-used water in the country. SARS-CoV-2 wastewater testing has the potential to aid in monitoring or predicting an outbreak location and can shed light on the extent viral spread at the community level.
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http://dx.doi.org/10.1016/j.scitotenv.2020.142929DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7571379PMC
April 2021

The Transcriptional Repressor BS69 is a Conserved Target of the E1A Proteins from Several Human Adenovirus Species.

Viruses 2018 11 22;10(12). Epub 2018 Nov 22.

Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada.

Early region 1A (E1A) is the first viral protein produced upon human adenovirus (HAdV) infection. This multifunctional protein transcriptionally activates other HAdV early genes and reprograms gene expression in host cells to support productive infection. E1A functions by interacting with key cellular regulatory proteins through short linear motifs (SLiMs). In this study, the molecular determinants of interaction between E1A and BS69, a cellular repressor that negatively regulates E1A transactivation, were systematically defined by mutagenesis experiments. We found that a minimal sequence comprised of MPNLVPEV, which contains a conserved PXLXP motif and spans residues 112⁻119 in HAdV-C5 E1A, was necessary and sufficient in binding to the myeloid, Nervy, and DEAF-1 (MYND) domain of BS69. Our study also identified residues P113 and L115 as critical for this interaction. Furthermore, the HAdV-C5 and -A12 E1A proteins from species C and A bound BS69, but those of HAdV-B3, -E4, -D9, -F40, and -G52 from species B, E, D, F, and G, respectively, did not. In addition, BS69 functioned as a repressor of E1A-mediated transactivation, but only for HAdV-C5 and HAdV-A12 E1A. Thus, the PXLXP motif present in a subset of HAdV E1A proteins confers interaction with BS69, which serves as a negative regulator of E1A mediated transcriptional activation.
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http://dx.doi.org/10.3390/v10120662DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6315623PMC
November 2018

Impact of current density on the function and microbial community structure in electro-bioreactors.

J Hazard Mater 2019 04 6;368:877-884. Epub 2018 Sep 6.

Department of Chemistry, Khalifa University of Science and Technology, Main Campus, PO Box 127788, Abu Dhabi, United Arab Emirates. Electronic address:

The assessment of bacterial communities in wastewater electro-bioreactors has garnered attention to improve efficiency of wastewater treatment plant (WWTP) processes. This study evaluated the effects of applying different current densities on the function and microbial community structure of an electro-bioreactor by measuring nutrient removal efficiency and analyzing 16S rRNA gene high-throughput sequencing. The electro-bioreactors at current density of 3, 5 and 7 A/m resulted in an enrichment of operational taxonomic units belonging to distinct functional bacterial families such as (Nitrospiraceae: 8.5, 12.5 and 12.6% relative abundance, respectively) and (Rhodocyclaceae: 8.1, 8.8 and 9.7% relative abundance, respectively), leading to efficient N-removal (>98%) and P-removal (>98%) higher than the control bioreactor (9.6 and 5.0%, respectively). Applying different electric currents proved to affect microbial community composition in electro-bioreactors. The results reported here could prove to be valuable for process control, optimization and improving WWTPs design and operation.
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http://dx.doi.org/10.1016/j.jhazmat.2018.09.016DOI Listing
April 2019

Assessment of Microbial Community Structure and Function in Serially Passaged Wastewater Electro-Bioreactor Sludge: An Approach to Enhance Sludge Settleability.

Sci Rep 2018 05 3;8(1):7013. Epub 2018 May 3.

Department of Chemistry, Khalifa University of Science and Technology, Masdar City Campus, PO Box, 54224, Abu Dhabi, United Arab Emirates.

Several studies have been carried out to understand bulking phenomena and the importance of environmental factors on sludge settling characteristics. The main objective of this study was to carry out functional characterization of microbial community structure of wastewater electro-bioreactor sludge as it undergoes serial passaging in the presence or absence of a current density over 15 days. Illumina MiSeq sequencing and QIIME were used to assess sludge microbial community shifts over time. (α) and (β) diversity analysis were conducted to assess the microbial diversity in electro-bioreactors. A phylogeny-based weighted UniFrac distance analysis was used to compare between bacterial communities while BIO-ENV trend and Spearman's rank correlation analysis were performed to investigate how reactor operational parameters correlated with bacterial community diversity. Results showed that the removal efficiency of soluble chemical oxygen demand (sCOD) ranged from 91-97%, while phosphorous (PO-P) removal was approximately 99%. Phylogenetic analysis revealed stark differences in the development of sludge microbial communities in the control and treatment reactor. There was no mention of any studies aimed at characterizing functional microbial communities under electric field and the results communicated here are the first, to our knowledge, that address this gap in the literature.
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http://dx.doi.org/10.1038/s41598-018-25509-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5934391PMC
May 2018

Effect of hydraulic retention time on microbial community structure in wastewater treatment electro-bioreactors.

Microbiologyopen 2018 08 24;7(4):e00590. Epub 2018 Mar 24.

Department of Chemical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.

The impact of hydraulic retention time (HRT) on the performance and microbial community structure of control and electro-bioreactors was investigated. Control bioreactors and electro-bioreactors were operated at HRT ranging between 6 and 75 hr. The total bacterial counts in addition to the removal efficiency of NH -N, sCOD, and PO -P was assessed in all the reactors tested. In addition, Illumina sequencing was performed to determine the microbial communities that developed in these reactors under each HRT condition. Phylogenetic analysis showed that Proteobacteria and Bacteroidetes were the dominant phyla in those reactors. In addition, Nitrospira sp. and Pseudomonas sp. were found to be present in electro-bioreactors with higher relative abundance than in control bioreactors. The results presented here are the first to determine what different microbial communities in wastewater electro-bioreactors due to the application of an electric current under different HRTs.
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http://dx.doi.org/10.1002/mbo3.590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6079174PMC
August 2018

Exploring the selective lactic acid production from food waste in uncontrolled pH mixed culture fermentations using different reactor configurations.

Bioresour Technol 2017 Aug 20;238:416-424. Epub 2017 Apr 20.

Department of Chemical and Environmental Engineering, Khalifa University of Science and Technology, Masdar Institute, Masdar City P.O. Box 54224, Abu Dhabi, United Arab Emirates.

Carboxylic acid production from food waste by mixed culture fermentation is an important future waste management option. Obstacles for its implementation are the need of pH control, and a broad fermentation product spectrum leading to increased product separation costs. To overcome these obstacles, the selective production of lactic acid (LA) from model food waste by uncontrolled pH fermentation was tested using different reactor configurations. Batch experiments, semi-continuously fed reactors and a percolation system reached LA concentrations of 32, 16 and 15gCOD/L, respectively, with selectivities of 93%, 84% and 75% on COD base, respectively. The semi-continuous reactor was dominated by Lactobacillales. Our techno-economic analysis suggests that LA production from food waste can be economically feasible, with LA recovery and low yields remaining as major obstacles. To solve both problems, we successfully applied in-situ product extraction using activated carbon.
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http://dx.doi.org/10.1016/j.biortech.2017.04.057DOI Listing
August 2017

Adenovirus small E1A employs the lysine acetylases p300/CBP and tumor suppressor Rb to repress select host genes and promote productive virus infection.

Cell Host Microbe 2014 Nov 12;16(5):663-76. Epub 2014 Nov 12.

Molecular Biology Institute, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA; Department of Microbiology, Immunology and Molecular Genetics, UCLA David Geffen School of Medicine, Los Angeles, CA 90095-1570, USA. Electronic address:

Oncogenic transformation by adenovirus small e1a depends on simultaneous interactions with the host lysine acetylases p300/CBP and the tumor suppressor RB. How these interactions influence cellular gene expression remains unclear. We find that e1a displaces RBs from E2F transcription factors and promotes p300 acetylation of RB1 K873/K874 to lock it into a repressing conformation that interacts with repressive chromatin-modifying enzymes. These repressing p300-e1a-RB1 complexes specifically interact with host genes that have unusually high p300 association within the gene body. The TGF-β, TNF-, and interleukin-signaling pathway components are enriched among such p300-targeted genes. The p300-e1a-RB1 complex condenses chromatin in a manner dependent on HDAC activity, p300 lysine acetylase activity, the p300 bromodomain, and RB K873/K874 and e1a K239 acetylation to repress host genes that would otherwise inhibit productive virus infection. Thus, adenovirus employs e1a to repress host genes that interfere with viral replication.
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http://dx.doi.org/10.1016/j.chom.2014.10.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4418520PMC
November 2014

Identification and characterization of multiple conserved nuclear localization signals within adenovirus E1A.

Virology 2014 Apr 13;454-455:206-14. Epub 2014 Mar 13.

Department of Microbiology & Immunology, Western University, London Regional Cancer Program, London, ON, Canada N6A 4L6; Department of Oncology, Western University, London Regional Cancer Program, London, ON, Canada N6A 4L6. Electronic address:

The human adenovirus 5 (HAdV-5) E1A protein has a well defined canonical nuclear localization signal (NLS) located at its C-terminus. We used a genetic assay in the yeast Saccharomyces cerevisiae to demonstrate that the canonical NLS is present and functional in the E1A proteins of each of the six HAdV species. This assay also detects a previously described non-canonical NLS within conserved region 3 and a novel active NLS within the N-terminal/conserved region 1 portion of HAdV-5 E1A. These activities were also present in the E1A proteins of each of the other five HAdV species. These results demonstrate that, despite substantial differences in primary sequence, HAdV E1A proteins are remarkably consistent in that they contain one canonical and two non-canonical NLSs. By utilizing independent mechanisms, these multiple NLSs ensure nuclear localization of E1A in the infected cell.
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http://dx.doi.org/10.1016/j.virol.2014.02.020DOI Listing
April 2014

The adenovirus 55 residue E1A protein is a transcriptional activator and binds the unliganded thyroid hormone receptor.

J Gen Virol 2014 Jan 17;95(Pt 1):142-152. Epub 2013 Oct 17.

Departments of Oncology, Microbiology & Immunology, University of Western Ontario and London Regional Cancer Centre, London, Ontario N6A 4L6, Canada.

The early region 1A (E1A) of human adenovirus types 2 and 5 is differentially spliced to yield five distinct mRNAs that encode different proteins. The smallest E1A RNA transcript encodes a 55 residue (55R) protein that shares only 28 amino acid residues with the other E1A proteins. Even though it is the most abundant E1A transcript at late times post-infection, little is known about the functions of this E1A isoform. In this study, we show that the E1A 55R protein interacts with, and modulates the activity of the unliganded thyroid hormone receptor (TR). We demonstrate that E1A 55R contains a signature motif known as the CoRNR box that confers interaction with the unliganded TR; this motif was originally identified in cellular corepressors. Using a system reconstituted in the yeast Saccharomyces cerevisiae, which lack endogenous TR and TR coregulators, we show that E1A 55R nonetheless differs from cellular corepressors as it functions as a strong co-activator of TR-dependent transcription and that it possesses an intrinsic transcriptional activation domain. These data indicate that the E1A 55R protein functions as a transcriptional regulator.
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http://dx.doi.org/10.1099/vir.0.056838-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3917064PMC
January 2014

The C-terminal region of E1A: a molecular tool for cellular cartography.

Biochem Cell Biol 2012 Apr 31;90(2):153-63. Epub 2012 Jan 31.

Department of Microbiology, The University of Western Ontario, London Regional Cancer Program, London, ON N6A 4L6, Canada.

The adenovirus E1A proteins function via protein-protein interactions. By making many connections with the cellular protein network, individual modules of this virally encoded hub reprogram numerous aspects of cell function and behavior. Although many of these interactions have been thoroughly studied, those mediated by the C-terminal region of E1A are less well understood. This review focuses on how this region of E1A affects cell cycle progression, apoptosis, senescence, transformation, and conversion of cells to an epithelial state through interactions with CTBP1/2, DYRK1A/B, FOXK1/2, and importin-α. Furthermore, novel potential pathways that the C-terminus of E1A influences through these connections with the cellular interaction network are discussed.
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http://dx.doi.org/10.1139/o11-080DOI Listing
April 2012

Adenovirus E1A directly targets the E2F/DP-1 complex.

J Virol 2011 Sep 29;85(17):8841-51. Epub 2011 Jun 29.

Department of Pathology and Molecular Medicine, MG DeGroote Institute for Infectious Disease Research, McMaster University, MDCL 4077, 1280 Main Street West, Hamilton, ON, Canada L8S 4K1.

Deregulation of the cell cycle is of paramount importance during adenovirus infection. Adenovirus normally infects quiescent cells and must initiate the cell cycle in order to propagate itself. The pRb family of proteins controls entry into the cell cycle by interacting with and repressing transcriptional activation by the E2F transcription factors. The viral E1A proteins indirectly activate E2F-dependent transcription and cell cycle entry, in part, by interacting with pRb and family members to free the E2Fs. We report here that an E1A 13S isoform can unexpectedly activate E2F-responsive gene expression independently of binding to the pRb family of proteins. We demonstrate that E1A binds to E2F/DP-1 complexes through a direct interaction with DP-1. E1A appears to utilize this binding to recruit itself to E2F-regulated promoters, and this allows the E1A 13S protein, but not the E1A 12S protein, to activate transcription independently of interaction with pRb. Importantly, expression of E1A 13S, but not E1A 12S, led to significant enhancement of E2F4 occupancy of E2F sites of two E2F-regulated promoters. These observations identify a novel mechanism by which adenovirus deregulates the cell cycle and suggest that E1A 13S may selectively activate a subset of E2F-regulated cellular genes during infection.
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http://dx.doi.org/10.1128/JVI.00539-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3165805PMC
September 2011

Comparison of E1A CR3-dependent transcriptional activation across six different human adenovirus subgroups.

J Virol 2010 Dec 29;84(24):12771-81. Epub 2010 Sep 29.

Department of Microbiology and Immunology, The University of Western Ontario, A4-833 London Regional Cancer Program, 800 Commissioners Road E., London, ON N6A 4L6, Canada.

The largest E1A isoform of human adenovirus (Ad) includes a C-4 zinc finger domain within conserved region 3 (CR3) that is largely responsible for activating transcription of the early viral genes. CR3 interacts with multiple cellular factors, but its mechanism of action is modeled primarily on the basis of the mechanism for the prototype E1A protein of human Ad type 5. We expanded this model to include a representative member from each of the six human Ad subgroups. All CR3 domains tested were capable of transactivation. However, there were dramatic differences in their levels of transcriptional activation. Despite these functional variations, the interactions of these representative CR3s with known cellular transcriptional regulators revealed only modest differences. Four common cellular targets of all representative CR3s were identified: the proteasome component human Sug1 (hSug1)/S8, the acetyltransferases p300/CREB binding protein (CBP), the mediator component mediator complex subunit 23 (MED23) protein, and TATA binding protein (TBP). The first three factors appear to be critical for CR3 function. RNA interference against human TBP showed no significant reduction in transactivation by any CR3 tested. These results indicate that the cellular factors previously shown to be important for transactivation by Ad5 CR3 are similarly bound by the E1A proteins of other types. This was confirmed experimentally using a transcriptional squelching assay, which demonstrated that the CR3 regions of each Ad type could compete with Ad5 CR3 for limiting factors. Interestingly, a mutant of Ad5 CR3 (V147L) was capable of squelching wild-type Ad5 CR3, despite its failure to bind TBP, MED23, p300/CBP-associated factor (pCAF), or p300/CBP, suggestive of the possibility that an additional as yet unidentified cellular factor is required for transactivation by E1A CR3.
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http://dx.doi.org/10.1128/JVI.01243-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3004344PMC
December 2010

Stigmasterol and cholesterol regulate the expression of elicitin genes in Phytophthora sojae.

J Chem Ecol 2009 Jul 9;35(7):824-32. Epub 2009 Jul 9.

School of Environment and Natural Resources, The Ohio State University, Columbus, OH, USA.

Sterol acquisition by soilborne plant pathogens of the genus Phytophthora is presumed to involve extracellular proteins belonging to class-I elicitins. However, little is known about the relationship between sterol availability and elicitin secretion. The objective of this study was to determine the expression of class-I elicitin genes in Phytophthora sojae when grown in a medium containing stigmasterol or cholesterol. P. sojae growth was stimulated by nanomolar concentrations of stigmasterol and cholesterol, which also resulted in the down-regulation of its elicitin genes over time when expression profiles were monitored using real time Reverse Transcription Polymerase Chain Reaction (RT-PCR). The down-regulation of elicitin genes in response to the two sterols also coincided with a reduction in the amount of elicitins detected in spent filtrates. Our study is the first to show the influence of sterols on elicitin gene expression in Phytophthora, which is important with respect to the ecology of elicitin secretion as sterol carrier proteins in the environment.
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http://dx.doi.org/10.1007/s10886-009-9653-1DOI Listing
July 2009

Identification of a second independent binding site for the pCAF acetyltransferase in adenovirus E1A.

Virology 2009 Aug 21;391(1):90-8. Epub 2009 Jun 21.

Department of Oncology, The University of Western Ontario, London Regional Cancer Centre, London, Ontario, Canada N6A 4L6.

The conserved region 3 (CR3) portion of the human adenovirus (HAdV) 5 E1A protein functions as a potent transcriptional activator that induces expression of viral early genes during infection. Expression of HAdV-5 CR3 in the yeast Saccharomyces cerevisiae inhibits growth, as do the corresponding regions of the HAdV-3, 4, 9, 12 and 40 E1A proteins, which represent the remaining five HAdV subgroups. Growth inhibition is alleviated by disruption of the SAGA transcriptional regulatory complex, suggesting that CR3 targets the yeast SAGA complex. In yeast, transcriptional activation by several, but not all, of the CR3 regions requires the Gcn5 acetyltransferase component of SAGA. The CR3 regions of HAdV-3, 5, 9 and 40, but not HAdV-4 and 12 interact with the pCAF acetyltransferase, a mammalian ortholog of yeast Gcn5. Disruption of the previously described N-terminal pCAF binding site abrogates binding by the HAdV-5 243R E1A protein, but not the larger 289R E1A protein, which is otherwise identical except for the presence of CR3. RNA interference directed against pCAF decreased HAdV-5 CR3 dependent transcriptional activation in mammalian cells. Our results identify a second independent binding site for pCAF in E1A and suggest that it contributes to CR3 dependent transcriptional activation.
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http://dx.doi.org/10.1016/j.virol.2009.05.024DOI Listing
August 2009

The adenoviral E1A protein displaces corepressors and relieves gene repression by unliganded thyroid hormone receptors in vivo.

Cell Res 2009 Jun;19(6):783-92

Section on Molecular Morphogenesis, Laboratory of Gene Regulation and Development, PCRM, NICHD, NIH, Bethesda, MD 20892, USA.

The human adenovirus type 5 early region 1A (E1A) is one of two oncogenes present in the adenovirus genome and functions by interfering with the activities of cellular regulatory proteins. The E1A gene is alternatively spliced to yield five products. Earlier studies have revealed that E1A can regulate the function of thyroid hormone (T3) receptors (TRs). However, analysis in yeast compared with transfection studies in mammalian cell cultures yields surprisingly different effects. Here, we have examined the effect of E1A on TR function by using the frog oocyte in vivo system, where the effects of E1A can be studied in the context of chromatin. We demonstrate that different isoforms of E1A have distinct effects on TR function. The two longest forms inhibit both the repression by unliganded TR and activation by T3-bound TR. We further show that E1A binds to unliganded TR to displace the endogenous corepressor nuclear receptor corepressor, thus relieving the repression by unliganded TR. On the other hand, in the presence of T3, E1A inhibits gene activation by T3-bound TR indirectly, through a mechanism that requires its binding domain for the general coactivator p300. Taken together, our results thus indicate that E1A affects TR function through distinct mechanisms that are dependent upon the presence or absence of T3.
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http://dx.doi.org/10.1038/cr.2009.55DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2692372PMC
June 2009

Requirements for E1A dependent transcription in the yeast Saccharomyces cerevisiae.

BMC Mol Biol 2009 Apr 17;10:32. Epub 2009 Apr 17.

Department of Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada.

Background: The human adenovirus type 5 early region 1A (E1A) gene encodes proteins that are potent regulators of transcription. E1A does not bind DNA directly, but is recruited to target promoters by the interaction with sequence specific DNA binding proteins. In mammalian systems, E1A has been shown to contain two regions that can independently induce transcription when fused to a heterologous DNA binding domain. When expressed in Saccharomyces cerevisiae, each of these regions of E1A also acts as a strong transcriptional activator. This allows yeast to be used as a model system to study mechanisms by which E1A stimulates transcription.

Results: Using 81 mutant yeast strains, we have evaluated the effect of deleting components of the ADA, COMPASS, CSR, INO80, ISW1, NuA3, NuA4, Mediator, PAF, RSC, SAGA, SAS, SLIK, SWI/SNF and SWR1 transcriptional regulatory complexes on E1A dependent transcription. In addition, we examined the role of histone H2B ubiquitylation by Rad6/Bre1 on transcriptional activation.

Conclusion: Our analysis indicates that the two activation domains of E1A function via distinct mechanisms, identify new factors regulating E1A dependent transcription and suggest that yeast can serve as a valid model system for at least some aspects of E1A function.
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http://dx.doi.org/10.1186/1471-2199-10-32DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674444PMC
April 2009

Intrinsic structural disorder in adenovirus E1A: a viral molecular hub linking multiple diverse processes.

J Virol 2008 Aug 2;82(15):7252-63. Epub 2008 Apr 2.

Department of Microbiology and Immunology, The University of Western Ontario, London Regional Cancer Program, London, Ontario, Canada N6A 4L6.

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http://dx.doi.org/10.1128/JVI.00104-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2493305PMC
August 2008

Coactivator requirements for p53-dependent transcription in the yeast Saccharomyces cerevisiae.

Int J Cancer 2008 Feb;122(4):942-6

Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada.

p53 is a sequence-specific DNA-binding transcription factor and key regulator of cell cycle arrest and apoptosis. p53 is mutated in most human cancers and these mutations generally impair its ability to activate transcription. When expressed in Saccharomyces cerevisiae, p53 acts as a strong transcriptional activator allowing yeast to be used as a model system to study the effects of p53 mutations on activity. However, little is known about the exact mechanisms by which p53 functions in yeast. Using 76 mutant yeast strains, we have evaluated the effect of deleting components of the ADA, COMPASS, INO80, ISW1, Mediator, RSC, SAGA, SAS, SLIK, SWI/SNF, and SWR1 transcriptional regulatory complexes on p53-dependent transcription. In addition, we examined the role of histone H2B ubiquitylation by Rad6/Bre1 on p53 activation. Overall, our analysis indicates that there are several remarkable similarities between p53-dependent transcription in yeast and mammalian cells, suggesting that yeast can serve as a valid model system for at least some aspects of p53 function.
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http://dx.doi.org/10.1002/ijc.23174DOI Listing
February 2008

Corepressor/coactivator paradox: potential constitutive coactivation by corepressor splice variants.

Nucl Recept Signal 2006 Oct 30;4:e022. Epub 2006 Oct 30.

Department of Medicine, Endocrine Division, Mount Sinai Hospital, University of Toronto Medical School, Toronto, ON, Canada.

The functional consequences of the interaction of transcriptional coregulators with the human thyroid hormone receptor (TR) in mammalian cells are complex. We have used the yeast, Saccharomyces cerevisiae, which lack endogenous nuclear receptors (NRs) and NR coregulators, as a model to decipher mechanisms regulating transcriptional activation by TR. In effect, this system allows the reconstitution of TR mediated transcription complexes by the expression of specific combinations of mammalian proteins in yeast. In this yeast system, human adenovirus 5 early region 1A (E1A), a natural N-CoR splice variant (N-CoR(I)) or an artificial N-CoR truncation (N-CoR(C)) coactivate unliganded TRs and these effects are inhibited by thyroid hormone (TH). E1A contains a short peptide sequence that resembles known corepressor-NR interaction motifs (CoRNR box motif, CBM), and this motif is required for TR binding and coactivation. N-CoR(I) and N-CoR(C) contain three CBMs, but only the C-terminal CBM1 is critical for coactivation. These observations in a yeast model system suggest that E1A and N-CoR(I) are naturally occurring TR coactivators that bind in the typical corepressor mode. These findings also raise the possibility that alternative splicing events which form corepressor proteins containing only C-terminal CBM motifs could represent a novel mechanism in mammalian cells for regulating constitutive transcriptional activation by TRs.
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http://dx.doi.org/10.1621/nrs.04022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1630687PMC
October 2006

Roles for APIS and the 20S proteasome in adenovirus E1A-dependent transcription.

EMBO J 2006 Jun 8;25(12):2710-22. Epub 2006 Jun 8.

Cancer Research UK Institute for Cancer Studies, The Medical School, The University of Birmingham, Edgbaston, Birmingham, UK.

We have determined distinct roles for different proteasome complexes in adenovirus (Ad) E1A-dependent transcription. We show that the 19S ATPase, S8, as a component of 19S ATPase proteins independent of 20S (APIS), binds specifically to the E1A transactivation domain, conserved region 3 (CR3). Recruitment of APIS to CR3 enhances the ability of E1A to stimulate transcription from viral early gene promoters during Ad infection of human cells. The ability of CR3 to stimulate transcription in yeast is similarly dependent on the functional integrity of yeast APIS components, Sug1 and Sug2. The 20S proteasome is also recruited to CR3 independently of APIS and the 26S proteasome. Chromatin immunoprecipitation reveals that E1A, S8 and the 20S proteasome are recruited to both Ad early region gene promoters and early region gene sequences during Ad infection, suggesting their requirement in both transcriptional initiation and elongation. We also demonstrate that E1A CR3 transactivation and degradation sequences functionally overlap and that proteasome inhibitors repress E1A transcription. Taken together, these data demonstrate distinct roles for APIS and the 20S proteasome in E1A-dependent transactivation.
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http://dx.doi.org/10.1038/sj.emboj.7601169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1500861PMC
June 2006

E1A and a nuclear receptor corepressor splice variant (N-CoRI) are thyroid hormone receptor coactivators that bind in the corepressor mode.

Proc Natl Acad Sci U S A 2005 May 22;102(18):6267-72. Epub 2005 Apr 22.

Department of Medicine, Endocrine Division, Mount Sinai Hospital, University of Toronto Medical School, Toronto, ON, Canada M5G 1X5.

Unliganded thyroid hormone (TH) receptors (TRs) and other nuclear receptors (NRs) repress transcription of hormone-activated genes by recruiting corepressors (CoRs), such as NR CoR (N-CoR) and SMRT. Unliganded TRs also activate transcription of TH-repressed genes. Some evidence suggests that these effects also involve TR/CoR contacts; however, the precise reasons that CoRs activate transcription in these contexts are obscure. Unraveling these mechanisms is complicated by the fact that it is difficult to decipher direct vs. indirect effects of TR-coregulator contacts in mammalian cells. In this study, we used yeast, Saccharomyces cerevisiae, which lack endogenous NRs and NR coregulators, to determine how unliganded TRs can activate transcription. We previously showed that adenovirus 5 early-region 1A coactivates unliganded TRs in yeast, and that these effects are blocked by TH. We show here that human adenovirus type 5 early region 1A (E1A) contains a short peptide (LDQLIEEVL amino acids 20-28) that resembles CoR-NR interaction motifs (CoRNR boxes), and that this motif is required for TR binding and coactivation. Although full-length N-CoR does not coactivate TR in yeast, a naturally occurring N-CoR variant (N-CoR(I)) and an artificial N-CoR truncation (N-CoR(C)) that retain CoRNR boxes but lack N-terminal repressor domains behave as potent and direct TH-repressed coactivators for unliganded TRs. We conclude that E1A and N-CoR(I) are naturally occurring TR coactivators that bind in the typical CoR mode and suggest that similar factors could mediate transcriptional activation by unliganded TRs in mammals.
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http://dx.doi.org/10.1073/pnas.0501491102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088377PMC
May 2005