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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
Transcription has three steps in bacteria: first, RNA polymerase binds to a promoter site on DNA to form a closed complex; then, RNA polymerase starts transcription by opening the DNA duplex to form a transcription bubble. In the second stage, termed elongation, the transcription bubble moves along DNA, and the RNA chain is extended by adding nucleotides in the 5’ to 3’ direction. Finally, transcription stops, and the DNA duplex reforms when RNA polymerase dissociates at a terminator site. In bacteria, each gene or operon is flanked by a promoter and a terminator. The promoter is a specific nucleotide sequence site where the RNA polymerase binds to DNA and starts making RNA (mRNA). The terminator is a similar instruction in the DNA where the RNA polymerase stops transcribing mRNA and dissociates from the DNA. This mechanism is the purest form of gene expression regulation in bacteria. Essential components of transcription are sigma factors (σ), which are subunits of all bacterial RNA polymerases. They are responsible for determining the specificity of promoter DNA binding and efficiently control transcription initiation. In conclusion, the first step in bacterial gene expression and the step most often controlled is transcription. Regulatory factors usually determine whether a specific gene is transcribed by RNA polymerase or not under specific environmental conditions.
Plant Biotechnology
Published in Firdos Alam Khan, Biotechnology Fundamentals, 2020
The success of transgene expression is generally based on transcription of mRNA and then into translation leading to protein synthesis. Promoter is a sequence of nucleic acids where RNA polymerase (a complex enzyme synthesizing the mRNA transcript) attaches to the DNA template. The nature of the promoter defines (together with other expression-regulating elements) under which conditions and intensity a gene will be transcribed. The promoter of the 35S gene of cauliflower mosaic virus (CaMV) is used very frequently in plant genetic engineering. This promoter confers high-level expression of exogenous genes in most cell types from virtually all species tested. As it is often advantageous to express a transgene only in certain tissues or quantities or at certain times, several other promoters can also be used such as promoters inducing gene expression after wounding or during fruit ripening only. Methods of gene transfer currently employed result in the random integration of foreign DNA throughout the genome of the recipient cells. The site of insertion may have a strong influence on the expression levels of the exogenous gene, resulting in different expression levels of an introduced gene even if the same promoter/gene construct was used. The exact mechanism of this phenomenon is not yet fully understood (Figure 6.8).
Cellular and Molecular Basis of Human Biology
Published in Lawrence S. Chan, William C. Tang, Engineering-Medicine, 2019
The human genome is consisted of 20,000 different genes and nucleic acids composed of 3 billion base pairs (Green et al. 2015). For the basic components of nucleic acid, the nucleotides, there are only 4 distinct nitrogenous bases: adenosine (short for A), thymine (T), guanine (G), and cytosine (C) and each nucleotide also contains a phosphate group and a sugar deoxyribose. One interesting and important fact is that virtually all differentiated cells have the identical and entire genome. Yet some proteins are produced by certain cell types and not by other cell types. The key factor is transcriptional factors, which function to bind to promoter region of DNA in initiating mRNA transcription. The binding of transcriptional factors enables the binding of RNA polymerase to DNA for the transcription. Activation and inactivation of certain transcriptional factors during human development determine the ability and inability to express certain proteins, and by extension their phenotype expressions, respectively (Hillis et al. 2014). Another interesting and also essential fact is that reactivation of cell-specific transcriptional factors could change a cell’s phenotype. For example, transgenic introduction of neuron-specific transcription factors into fibroblasts turn these connective tissue protein-producing cells into functional neurons with characteristic neuronal synapses (Hillis et al. 2014).
Whole-cell bioreporters for evaluating petroleum hydrocarbon contamination
Published in Critical Reviews in Environmental Science and Technology, 2021
Bo Jiang, Yizhi Song, Zengjun Liu, Wei E. Huang, Guanghe Li, Songqiang Deng, Yi Xing, Dayi Zhang
Acute-toxicity WCBs (Figure 1a) are constructed with reporter gene fused in the downstream of a constitutively expressed promoter. The promoter is usually highly expressed in the absence of toxicity stress and results in a high basal level expression of the reporter gene (Gu, Mitchell, & Kim, 2004). Postexposure to any compound with acute toxicity, e.g., Hg2+ (Mi, Tao, Zhang, & Si, 2019), coagulants (Al-Anizi et al., 2014) and PAHs (Sazykin et al., 2015), the expression level of the promoter is suppressed due to the reduced metabolic activity or growth rate of the bioreporter cells (Gu et al., 2004). The declining signal intensity is then measured and calculated as the acute toxicity, providing a whole map of the acute toxicity of target toxins on microbial cells. Microtox kit is a well-known acute-toxicity WCB (Bulich & Isenberg, 1981; Chang, Taylor, & Leach, 1981), using the freeze-dried V. fischeri cells and measuring bioluminescence by directly adding environmental water samples and comparing to pure water as reference. Additionally, some acute-toxicity WCBs are developed to study the quantitative structure-activity relationship (QSAR) of chemicals, e.g., hydrocarbons (Bundy, Durham, Paton, & Campbell, 2000), PAHs (Lee, Villaume, Cullen, Kim, & Gu, 2003), organic solvents (Cho et al., 2009) and metabolites during tetracycline degradation process (Wang, Zhi, Zhou, He, & Zhang, 2018), which illustrate the relationships between chemical structures and induced biosensing signals (Bovee, Lommerse, Peijnenburg, Fernandes, & Nielen, 2008).
Synthesis of programmable biological central processing system
Published in Journal of the Chinese Institute of Engineers, 2021
Wei-Xian Li, Jiangfeng Cheng, Chun-Liang Lin, Chia-Feng Juang
The TF bound to upstream DNA initiates transcription of the RNA polymerase bound to the promoter region. The reaction processes of the biological logic gates are based on the TF bound to the DNA upstream sites. The synthesized protein is the result of the RNA polymerase binding to the DNA; it can be a TF for synthesizing biological gates (Lauria et al. 2004; Buchler, Gerland, and Hwa 2003). This can be implemented by choosing a gene for the first gate and encoding the protein that acts as a TF for the second gate.
Phytoremediation of petroleum-contaminated soil by Salicornia: from PSY activity to physiological and morphological communications
Published in Environmental Technology, 2019
Tayebe Abdollahzadeh, Ali Niazi, Ali Moghadam, Zohreh Heydarian, Reza Ghasemi-Fasaei, Elina Kaviani, Neda Pourdad
According to the presented results, the highest amount of carotenoids was observed in 0.2% petroleum-contaminated soil (Figure 6(g,h)) while it was in parallel with the expression increase of PSY (Figure 5). It means that both PSY expression and carotenoid content increased in 0.2% petroleum-contaminated soil. However, the induction of the PSY expression was significantly increased 1 h after 0.2% petroleum stress (Figure 5(a) and Table S5a). The expression level of PSY showed twice more increase than control at 10 h after stress (Figure 5(a)). Although the control at 10 h increased compared to the control at 1 h after 0.2% petroleum stress, as shown in Figure 5(a), the increase of PSY expression at 10 h after stress was more than in the control. This slight increase in control is related to the light-responsive cis-acting elements (Table 3). It means that PSY with these motifs is a light-responsive gene and is regulated with light. These motifs are short sequences of DNA within a gene promoter region that are able to bind specific transcription factors and regulate transcription of genes. A transcription activator protein binds to the responsive element and stimulates transcription under light conditions [46]. In addition, PSY showed a significant increase in expression in long-term stress in 0.2% petroleum contamination (Figure 5(b) and Table S5b). Overall the expression of PSY increased in both short-term and long-term stresses in 0.2% petroleum (Figure 5). Rapid induction of Oryza sativa PSY3 due to salt treatment can be considered as the cause of plant resistance in osmotic stress [23]. Moreover, expression analysis of OsPSY3 following ABA treatment showed a significant increase in the level of OsPSY3, which remained stable even 6 h after treatment [23]. Also, Haematococcus pluvialis Flotow exposed to nutrient stress showed a higher level of the PSY transcript, which reached a maximum level two days after stress [47]. In short-term stress, the PSY expression level in 2% petroleum significantly reduced compared with the control in the first few hours of stress and the gene expression level significantly dropped 10 h after stress compared with the control (Figure 5(a)). Furthermore, the PSY expression level dropped significantly in 2% petroleum under long-term stress (Figure 5(b)). Hence, a downward trend of PSY expression under short- and long-term stresses was indicated in 2% petroleum (Figure 5 and Table S5a and S5b).