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Genetic Regulation of Principal Microorganisms (Yeast, Zymomonas mobilis, and Clostridium thermocellum) Producing Bioethanol/Biofuel
Published in Ayerim Y. Hernández Almanza, Nagamani Balagurusamy, Héctor Ruiz Leza, Cristóbal N. Aguilar, Bioethanol, 2023
Dania Sandoval-Nuñez, Teresa Romero-Gutiérrez, Melchor Arellano-Plaza, Anne Gschaedler, Lorena Amaya-Delgado
Gene regulation is a cellular process consisting of activating or deactivating genes, which can occur at any point in the transcription-translation process. Gene regulation occurs most frequently at the transcriptional level. The regulation of gene expression in yeast can take place in different stages (Figure 4.1). In the nucleus, the chromatin remodeling process regulates the availability of a gene for transcription. Once transcribed, the primary mRNA transcript, or pre-mRNA, undergoes RNA processing, which involves splicing and adding a 5’ cap and 3’ poly (A) tail to produce a mature mRNA in the nucleus. Mature mRNA is exported from the nucleus to the cytoplasm, where its lifespan varies. Outside the nucleus, localization factors can direct mature mRNAs to specific regions of the cytoplasm where they are translated into polypeptides. The resulting polypeptides can undergo posttranslational modifications, which can regulate protein folding, glycosylation, intracellular transport, and protein activation and degradation.
NAC in Abiotic Stresses
Published in Hasanuzzaman Mirza, Nahar Kamrun, Fujita Masayuki, Oku Hirosuke, Tofazzal M. Islam, Approaches for Enhancing Abiotic Stress Tolerance in Plants, 2019
Sami Ullah Jan, Muhammad Jamil, Muhammad Faraz Bhatti, Alvina Gul
According to Gray et al. (2009), a transcription factor can be defined as a protein which has the tendency to locate and attach to a conserved sequence of DNA in gene’s promoter through employing its DNA-binding domain (DBD) for mediating gene regulation. This role of mediating gene expressivity in a genome performed by TFs is accomplished with high specificity (Nakashima et al., 2009). The cell contains a variety of proteins which possess DNA-binding activity, but TFs are differentiated from these proteins in the way that TFs possess a characteristic structural motif called a DNA-binding domain, which other proteins do not possess, a site for attachment to DNA (Gray et al., 2009; Yamasaki et al., 2005).
Principles and Techniques for Deoxyribonucleic Acid (DNA) Manipulation
Published in Hajiya Mairo Inuwa, Ifeoma Maureen Ezeonu, Charles Oluwaseun Adetunji, Emmanuel Olufemi Ekundayo, Abubakar Gidado, Abdulrazak B. Ibrahim, Benjamin Ewa Ubi, Medical Biotechnology, Biopharmaceutics, Forensic Science and Bioinformatics, 2022
Nwadiuto (Diuto) Esiobu, Ifeoma M. Ezeonu, Francisca Nwaokorie
Gene regulation is the process of controlling the rate and manner in which a gene is expressed. A complex set of interactions between genes, RNA molecules, proteins (including transcription factors) and other components of the expression system determine when and where specific genes are activated. It also determines the amount of protein or RNA product produced. The amounts and types of mRNA molecules produced during transcription in a cell usually reflect the metabolic state of that cell.
Enhanced deep convolutional neural network for malarial parasite classification
Published in International Journal of Computers and Applications, 2022
M. Suriya, V. Chandran, M. G. Sumithra
Hommelsheim CM et al. in [4] have proposed transcription-activator-like effectors (TALEs) which are a promising technology and enabled higher-specific genomes to be edited. Such particular techniques for engineering and gene regulation are also being created using proteins that bind RNA, such as PUFs and PPRs. TALEs, PUFs, and PPRs, are mainly characterized by their repetitive DNA-/RNA-binding domains with single nucleotide-binding specificity. Today’s available kits enable scientists to assemble these repetitive domains in any combination they want when producing gene targeting and editing TALEs. PCR amplifications of such repetitive DNAs are extremely difficult; however, as they mostly fail, resulting in unwanted artifact products or deletions. The performance of the polymerase chain reaction is limited in its capability.
Xenobiotic metabolism and transport in Caenorhabditis elegans
Published in Journal of Toxicology and Environmental Health, Part B, 2021
Jessica H. Hartman, Samuel J. Widmayer, Christina M. Bergemann, Dillon E. King, Katherine S. Morton, Riccardo F. Romersi, Laura E. Jameson, Maxwell C. K. Leung, Erik C. Andersen, Stefan Taubert, Joel N. Meyer
To exert effects on gene regulation, NHRs (and other TFs) need to interact with co-regulators, which help activate and repress gene expression as necessary. An important co-regulator in eukaryotes is the Mediator complex, which is composed of 25–30 subunits, some of which serve as direct docking sites for TFs (Grants, Goh, and Taubert 2015). Notably, one such subunit, MDT-15, interacts physically with several of the above noted TFs, including NHR-8, NHR-49, NHR-86, and SKN-1 (see below) (Arda et al. 2010; Reece-Hoyes et al. 2013; Taubert et al. 2006). Accordingly, mdt-15 is required to induce numerous phase I, II, and III detoxification genes in worms exposed to xenobiotic molecules, and its mutation or deletion results in sensitivity to xenobiotics such as fluoranthene and RPW24 (Pukkila-Worley et al. 2014; Taubert et al. 2008). A model whereby MDT-15 binds NHRs that have been activated in direct or indirect fashion by the presence of a xenobiotic molecule and co-activates the expression of pertinent detoxification genes is thus plausible. As co-regulators might be rate-limiting for expression of inducible gene programs, it would be interesting to further investigate the role of MDT-15 in NHR driven detoxification responses.
Discovery of genetic risk factors for disease
Published in Journal of the Royal Society of New Zealand, 2018
Overlap in signals for GWAS ‘hits’ and effects on gene expression observed in our studies of endometriosis (Powell et al. 2016) and the studies of puberty (Day et al. 2017) may be due to the same causal variant, but might also result from coincidental signals located in the same region. Formal tests to distinguish between these possibilities have been developed (Zhu et al. 2016) and show the overlap in endometriosis signals and at least some of the signals for age at puberty result from the same causal SNP regulating expression of relevant genes (Powell et al. 2016; Zhu et al. 2016). Methods combining signals from GWAS and gene expression (Zhu et al. 2016) also identify novel genes that are not significant in the GWAS studies alone. Similar methods can also be used to combine results from GWAS, gene expression and epigenetic signals that will help understand the regulation of gene expression and the likely causal relationships between genetic effects on gene regulation and consequences for disease.