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Catabolite Regulation of the Main Metabolism
Published in Kazuyuki Shimizu, Metabolic Regulation and Metabolic Engineering for Biofuel and Biochemical Production, 2017
The living organisms on earth survive by manipulating the cell system in response to the change in growth environment by sensing signals of both external and internal states of the cell. The complex signaling networks interconvert signals or stimuli for the cell to function properly. The transfer of information in signal transduction pathways and cascades is designed to respond to the variety of growth environment. Metabolism is the core for energy generation (catabolism) and cell synthesis (anabolism). Metabolic network, defined as the set and topology of metabolic biochemical reactions within a cell, plays an essential role for the cell to survive, where it is under organized control. The set of enzymes changes dynamically in accordance with the change in growth environment and the cell’s state. The enzymes which form the metabolic pathways are subject to multiple levels of regulation, and it is important to deeply understand the overall regulation mechanism. Although huge amount of information is embedded in the genome, only a subset of the pathways among possible topological networks is active at certain point in time under certain growth condition.
Metabolic Engineering
Published in Jean F. Challacombe, Metabolic Pathway Engineering, 2021
Cultured microorganisms have been used to make industrial products since the 1940s [1, 2]. Some of the early applications included cheeses, breads, and alcoholic beverages, as reported in ancient texts from Babylon, Greece, Egypt, China, and India [3]. Other applications included using natural organisms to produce novel biochemical compounds for pharmaceutical uses, as biopolymers, and other industrial benefits [4, 5]. Cellular process engineering applications have been moving toward increasing complexity with respect to the types of cells and cellular functions employed, and toward a more directed engineering approach. The field of metabolic engineering has contributed to this complexity, made possible by recombinant DNA technology, which provides powerful genetic tools and a mechanism to insert specific segments of DNA into organisms. Traditional metabolic engineering uses recombinant DNA methods to introduce genetic changes into an organism’s DNA to restructure metabolic networks, with several goals: improving the pathways involved in the production of particular metabolites, adding pathway genes that enable the production of new metabolites, and improving cellular functions of interest [1, 2, 6–8]. Early metabolic engineering studies focused on increasing the yield of a naturally produced industrial bioproduct or enabling microorganisms to produce novel biochemical compounds [1, 6, 8]. This type of metabolic engineering focuses on improving the cellular activities of industrial organisms through the manipulation of enzymatic, transport, and regulatory functions of the cell. Introducing genes of interest and regulatory elements to improve a strain distinguishes metabolic engineering from the more traditional genetics methods that rely on indirect manipulations of evolutionary processes.
Omics to address the opportunities and challenges of nanotechnology in agriculture
Published in Critical Reviews in Environmental Science and Technology, 2021
Sanghamitra Majumdar, Arturo A. Keller
Metabolites are the end-product of cellular regulatory processes that reflect the ultimate response of an organism to any external stimulus (Figure 1). The plant metabolic pathway databases, curated from experimental literature by the Plant Metabolic Network (PMN 13.0, Carnegie Institution for Science), report 4,544 compounds involved in 1,123 pathways across 350 plant species (Schläpfer et al., 2017). Plants collectively produce a diverse array of ≥ 200,000 metabolites, which are broadly divided into two major categories, primary and secondary metabolites (Dixon, 2001). Primary metabolites, which include carbohydrates, amino acids, vitamins, organic acids, and fatty acids, are required for plant growth and development (Fiehn, 2002). Secondary metabolites are synthesized from the primary metabolites for adaptation and defense response in plants (Fiehn, 2002). The major classes of secondary metabolites are polyketides, terpenoids, steroids, phenylpropanoids, alkaloids, and glucosinolates, which have their own biogenetic pathways and thousands of products and pathway intermediates (Hounsome et al., 2008). Primary metabolites are universal and conserved in their structures throughout the plant kingdom, whereas the secondary metabolites are species-specific and differ in chemical complexity.
A critical review of bioleaching of rare earth elements: The mechanisms and effect of process parameters
Published in Critical Reviews in Environmental Science and Technology, 2021
Payam Rasoulnia, Robert Barthen, Aino-Maija Lakaniemi
Certain chemoorganoheterotrophic microorganisms can be utilized for bioleaching of non-sulfidic REE resources containing e.g., phosphates, carbonates, oxides, and silicates without the need to maintain low pH and to add sulfur and/or iron to the system. These microorganisms utilize organic carbon sources such as glucose for growth and production of a variety of metabolites including organic acids, exopolysaccharides, amino acids and proteins (Hopfe et al., 2017; Pollmann et al., 2018). The fungi Aspergillus and Penicillium spp. are the most widely used heterotrophic microorganisms for bioleaching of REEs and other valuable metals from a variety of primary and secondary sources (Barnett et al., 2018; Brisson et al., 2016; Keekan, Jalondhara, & Abhilash, 2017; Qu et al., 2015; Qu & Lian, 2013; Rasoulnia & Mousavi, 2016a). Several other fungi, bacteria and yeasts have been also considered for REE leaching from different sources (Tables 2–4). G. oxydans that has demonstrated good potential at recovering REEs e.g., from FCC materials (Reed, Fujita, Daubaras, Jiao, & Thompson, 2016; Thompson et al., 2018) has been suggested as an attractive candidate for genetic engineering in order to enhance organic acid production rate and REE leaching efficiencies, because of the availability of its genome sequence and a recently developed metabolic network model (Prust et al., 2005; Reed, Fujita, Daubaras, Jiao, et al., 2016; Wu, Wang, & Lu, 2014). Candida bombicola, a nonpathogenic yeast strain capable to produce biosurfactants such as sophorolipids, was recently identified as another potent microorganism for bioleaching of REEs from coal fly ash (Park & Liang, 2019). Phosphate solubilizing microorganisms (PSMs) are promising candidates for REE solubilization from REE-phosphates. However, their ability to solubilize metal phosphates seems to be dependent on the phosphate compound. While Shin et al. (2015) reported that Ca-phosphate solubilizing Acetobacter aceti was also able to solubilize REE-phosphates this was not observed for other bacteria such as Klebsiella pneumoniae and Klebsiella oxytoca (Corbett, Eksteen, Niu, Croue, & Watkin, 2017).