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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.
Introduction to the Biological System
Published in Ashutosh Kumar Dubey, Amartya Mukhopadhyay, Bikramjit Basu, Interdisciplinary Engineering Sciences, 2020
Ashutosh Kumar Dubey, Amartya Mukhopadhyay, Bikramjit Basu
It is important to mention how proteins are constantly synthesized inside a cell by a sequential process of transcription and translation. Transcription is a molecular biology process wherein the genetic information encoded in a part of DNA is transcribed into a newly formed mRNA by specific RNA polymerase enzyme and other transcription factors. In simple terms, one strand of DNA during transcription, is copied to produce a single stranded RNA, which is complementary to the template strand of DNA. In eukaryotic cells, such a process involves the splicing, which leads to the formation of a mature mRNA chain. Another complementary process, translation is defined as the transformation of mature mRNA to a ribosome. In prokaryotic cells, without any well-defined compartmentalized organelles/nucleus, the transcription and translation process can occur simultaneously in cytoplasmic space. In contrast, the transcription usually takes place inside the nucleus, while the translation occurs in the cytoplasmic space in eukaryotic cells (see Figure 8.3). Therefore, the transcription–translation process in eukaryotic cells requires the transportation of mRNA from nucleus to cytoplasm, where ribosomes get attached to it.
Structures
Published in Thomas M. Nordlund, Peter M. Hoffmann, Quantitative Understanding of Biosystems, 2019
Thomas M. Nordlund, Peter M. Hoffmann
Messenger RNA (mRNA) is single stranded and carries information about a protein sequence to the ribosomes, the protein synthesis factories in the cell. Every three nucleotides (a codon) correspond to one amino acid, as we noted earlier. In eukaryotic cells, a precursor mRNA (pre-mRNA) is first transcribed from DNA in the cell nucleus and is processed to mature mRNA by removal of introns—noncoding sections of the pre-mRNA. The mRNA is then transported from the nucleus to the cytoplasm, where it is bound to ribosomes, large complexes of RNA and protein (Chapter 6), and translated into its corresponding protein form with the help of tRNA. Prokaryotic cells have no nucleus and cytoplasm compartments and mRNA will bind to the ribosome while it is being transcribed from DNA.
Re-Analysis of Non-Small Cell Lung Cancer and Drug Resistance Microarray Datasets with Machine Learning
Published in Cybernetics and Systems, 2023
Çiğdem Erol, Tchare Adnaane Bawa, Yalçın Özkan
All genes obtained as a result of the analyzes and their distribution according to frequencies are shared in the findings section (Tables 2 and 3). It is thought that genes with high frequency in the same data set should also be considered as potential candidates. As a result; ELOVL7, HMGA2, SAT1, RRM1, IER3, SLC7A11, and U2AF1 genes were found in at least 2 different datasets. Pathways for 7 genes obtained as a result of our research and their links are given in parentheses; ELOVL7 (Synthesis of very long-chain fatty acyl-CoAs), HMGA2 (Formation of Senescence-Associated Heterochromatin Foci), SAT1 (Interconversion of polyamines, Arginine and Proline metabolism), RRM1 (Glutathione metabolism, Pyrimidine metabolism, Purine metabolism, Mitochondrial DNA Depletion Syndrome-3), IER3 (PI5P, PP2A, and IER3 Regulate PI3K/AKT Signaling, Gastrin_CCK2R_240212), SLC7A11 (Amino acid transport across the plasma membrane, Basigin interactions, Transport of inorganic cations/anions and amino acids/oligopeptides), U2AF1 (Transport of Mature mRNA derived from an Intron-Containing Transcript, pre-mRNA splicing, RNA Polymerase II Transcription Termination, mRNA 3′-end processing).
Existence and global exponential stability of almost periodic solutions of genetic regulatory networks with time-varying delays
Published in Journal of Experimental & Theoretical Artificial Intelligence, 2020
Lian Duan, Fengjun Di, Zengyun Wang
Many studies have revealed the fact that time delay is a common phenomenon in the processes of actual regulation, transcription, translation, diffusion, and translocation-especially in that of a eukaryotic cell. For instance, it has been proven in an important experiment on mice that there exists a time lag of about 15 min in the peaks between the mRNA molecules and the proteins of the gene hes1 (Hirata et al., 2002). For the gene her1 in zebra fish, it takes about 21 min from the initiation of transcription to the arrival of the mature mRNA molecule in the cytoplasm, and about 2.8 min from the initiation of translation to the emergence of a complete functional protein molecule (Lewis, 2003). In view of these facts, the discrete time-delay should be considered when modelling GRNs because each macromolecule takes the time to transfer from its place of synthesis to the location as described in Zhang, Tang, Wu, and Fang (2014); Wu (2011), and much research has been carried out on the stability analysis of delayed autonomous genetic regulatory networks have done in (Chen & Aihara, 2002; Koo, Ji, Won, & Park, 2012; Lakshmanan, Rihan, Rakkiyappan, & Park, 2014; Li, Chen, & Aihara, 2006; Li, Chen, Liu, & Zhao, 2016; Wang, Luo, Yang, & Cao, 2016; Wu, Liao, Feng, Guo, & Zhang, 2010) and the references therein.