Lysine Synthesis Research Articles

Design of metabolic regulatory structures for enhanced lysine synthesis flux using (log)linearized kinetic models

The problem of finding the optimal regulatory structures was formulated as a mixed-integer linear programming problem for lysine synthetic pathway using (log)linear models obtained from nonlinear kinetic models developed previously by us. Optimal structures were obtained from a set of postulated regulatory structures. This method of metabolic design allowed the identification of the type and the strength of the necessary regulations, the activities of the corresponding enzymes and the intermediate metabolite levels in the lysine pathway. The calculated results indicate that >20% increase of the internal lysine flux can be obtained when only the inhibitory regulation was allowed, and eight optimal structures with one regulatory loop were adopted. When the regulation due to enzyme activation was allowed, the internal lysine flux can be increased by >70%. Changes of the participating precursor and cofactor concentrations may not improve the lysine flux significantly in this system.

Protein and amino acid requirements of adults: current controversies.

Protein intakes vary widely but costs and benefits of such variation is a long standing unresolved issue. The wide range of reported values for the minimum protein intake for N equilibrium in adults, i.e. 0.39 to 1.09 g/kg is best explained by an Adaptive Metabolic Demands model in which metabolic demands include amino acid oxidation at a rate varying with habitual protein intake and which changes slowly with dietary change. Thus within the reported data the true minimum requirement intake, the lowest values in the range at intakes approaching the Obligatory Nitrogen Loss, allows only fully adapted subjects to achieve N equilibrium. The higher values reflect incomplete adaptation. (13)C-1 leucine tracer balance studies of this model show (a) a fall with age in apparent protein requirements, (b) better than predicted efficiency of wheat protein utilization, and (c) controversially, lower lysine requirements than other workers, consistent with new evidence of de novo synthesis of lysine from urea salvaged by large bowel microflora. The main implication of the requirements model for athletes on high protein diets is increased exercise induced amino acid oxidation and risk of loss of body N when such high intakes are not maintained.

Metabolic fluxes and l-lysine synthesis by Corynebacterium glutamicum in relation to cellular total reducing activity

The total reducing activity (TRA) of cells was used to estimate the physiological activity of Corynebacterium glutamicum under conditions of l-lysine synthesis. This was estimated as the rate of reduction of 2,3,5- triphenyltetrazolium chloride by intact cells. TRA of cells was linearly correlated with the intracellular concentrations of RNA and the bacterial growth rate. It was concluded that this activity reflected the rate of energy generation in cells. A decrease in TRA of growing cells was related to an increase in bacterial lysine synthesis activity. Alteration in metabolic pathway functioning and an increase in the intracellular concentrations of lysine precursors favoured an increase in the rate of lysine synthesis by bacterial cells when cellular TRA was decreasing.

Lysine metabolism in higher plants.

The essential amino acid lysine is synthesised in higher plants via a pathway starting with aspartate, that also leads to the formation of threonine, methionine and isoleucine. Enzyme kinetic studies and the analysis of mutants and transgenic plants that overaccumulate lysine, have indicated that the major site of the regulation of lysine synthesis is at the enzyme dihydrodipicolinate synthase. Despite this tight regulation, there is strong evidence that lysine is also subject to catabolism in plants, specifically in the seed. The two enzymes involved in lysine breakdown, lysine 2-oxoglutarate reductase (also known as lysine a-ketoglutarate reductase) and saccharopine dehydrogenase exist as a single bifunctional protein, with the former activity being regulated by lysine availability, calcium and phosphorylation/ dephosphorylation.

Manipulação de cereais para acúmulo de lisina em sementes

A lisina é um aminoácido essencial cuja via de biossíntese faz parte da via metabólica do ácido aspártico, pela qual são também sintetizados os aminoácidos treonina, metionina e isoleucina. Além disso, a lisina é o principal aminoácido limitante em todos os cereais e por cerca de 30 anos a via do ácido aspártico tem sido estudada em plantas, com o intuito de desvendar e caracterizar os principais pontos chave na regulação das vias de biossíntese desses aminoácidos. Duas etapas distintas, uma primeira originada a partir do desenvolvimento da cultura de tecidos (anos 70-80) e a segunda a partir do desenvolvimento de técnicas para a transformação de plantas (anos 90), permitiram que mutantes bioquímicos e plantas trangênicas fossem produzidos com alterações específicas em passos metabólicos chave, levando à superprodução e acúmulo de treonina em vários tecidos das plantas. Entretanto, a acumulação de lisina em sementes não foi obtida. Tal fato, associado a estudos bioquímicos da via de degradação da lisina em cereais e em leguminosas, indicou que a manipulação da degradação seria tão ou mais importante que a manipulação da biossíntese de lisina para o acúmulo deste aminoácido em sementes dos cereais . Em milho, o uso e estudo de outros mutantes tais como o opaco-2 e variedades QPM (Quality Protein Maize) contribuíram significativamente para a compreensão dos eventos regulatórios. As estratégias para a obtenção de materiais ricos em lisina e sua relevância à manipulação de outros aminoácidos são revisados.

Arabidopsis loss-of-function mutant in the lysine pathway points out complex regulation mechanisms

In plants, the amino acids lysine, threonine, methionine and isoleucine have L-aspartate-β-semialdehyde (ASA) as a common precursor in their biosynthesis pathways. How this ASA precursor is dispersed among the different pathways remains vague knowledge. The proportional balances of free and/or protein-bound lysine, threonine, isoleucine and methionine are a function of protein synthesis, secondary metabolism and plant physiology. Some control points determining the flux through the distinct pathways are known, but an adequate explanation of how the competing pathways share ASA in a fine-tuned amino acid biosynthesis network is yet not available. In this article we discuss the influence of lysine biosynthesis on the adjacent pathways of threonine and methionine. We report the finding of an Arabidopsis thaliana dihydrodipicolinate synthase T-DNA insertion mutant displaying lower lysine synthesis, and, as a result of this, a strongly enhanced synthesis of threonine. Consequences of these cross-pathway regulations are discussed.

A Genetics Laboratory Module Involving Selection and Identification of Lysine Synthesis Mutants in the Yeast Saccharomyces cerevisiae

A Genetics Laboratory Module Involving Selection and Identification of Lysine Synthesis Mutants in the Yeast Saccharomyces cerevisiae

Optical immune sensors for the monitoring protein substances in the air

The efficiency of work of optical immune sensors based on the photoluminescence (Ph) of porous silicon (PS) and the fibre optics in combination with the enhanced chemical luminescence was examined during the monitoring of biological pollutants, produced during microbial synthesis of lysine, in the air inside and in the vicinity of a biotechnological plant. It was shown that the sensitivity of the analysis performed by the fibre optics sensor (5–20 μg/l) was higher than the sensitivity of the analysis accomplished with the help of the sensor based on the Ph PS (100 μg/l). The sensitivities of the proposed sensors were comparable with the sensitivity of the enzyme-linked immunosorbent assay (ELISA) method. The Ph PS sensor is characterised by fast and straightforward analysis, absence of any label, simplicity in operation, low costs of basic material and PS availability.

A Genetics Laboratory Module Involving Selection and Identification of Lysine Synthesis Mutants in the Yeast Saccharomyces cerevisiae

We examined how the shift in learning environment from in-person to online classes, due to the COVID-19 pandemic, impacted three constructs of student engagement: behavioral engagement, including students’ frequency of participating in class discussions, meeting with instructors, and studying with peers outside of class; cognitive engagement, including students’ sense of belonging and self-efficacy; and emotional engagement, including students’ attitudes toward science, their perceived value of the course, and their stress. Seventy-three undergraduate STEM students from across the country completed five-point Likert-style surveys in these areas of student engagement, both prior to their science course transitioning online and at the end of the spring 2020 semester. We found that while overall behavioral engagement did not change, students participated less frequently in class discussions (P = 0.0063) but met with professors more often outside of class (P = 0.0358). We saw no significant change in cognitive engagement, indicating that while students’ sense of belonging and self-efficacy ideally increases over the course of the semester, in this case, it did not. Most alarmingly, we found a significant decrease in emotional engagement (P = 0.0075), with students reporting a drastic decline in positive attitudes toward science (P < 0.0001). Student’s reported stress levels remained unchanged and students reported a slight increase in their perceived value of the science course they were taking. These data shed light on how the transition to online learning had an overall negative impact on undergraduate student engagement in science courses.

A Genetics Laboratory Module Involving Selection and Identification of Lysine Synthesis Mutants in the Yeast Saccharomyces cerevisiae

We have developed a laboratory exercise, currently being used with college sophomores, which uses the yeast Saccharomyces cerevisiae to convey the concepts of amino acid biosynthesis, mutation, and gene complementation. In brief, selective medium is used to isolate yeast cells carrying a mutation in the lysine biosynthesis pathway. A spontaneous mutation in any one of three separate genetic loci will allow for growth on selective media; however, the frequency of mutations isolated from each locus differs. Following isolation of a mutated strain, students use complementation analysis to identify which gene contains the mutation. Since the yeast genome has been mapped and sequenced, students with access to the Internet can then research and develop hypotheses to explain the differences in frequencies of mutant genes obtained.

Metabolic flux distributions in Corynebacterium glutamicum during growth and lysine overproduction

The two main contributions of this article are the solidification of Corynebacterium glutamicum biochemistry guided by bioreaction network analysis, and the determination of basal metabolic flux distributions during growth and lysine synthesis. Employed methodology makes use of stoichiometrically based mass balances to determine flux distributions in the C. glutamicum metabolic network. Presented are a brief description of the methodology, a thorough literature review of glutamic acid bacteria biochemistry, and specific results obtained through a combination of fermentation studies and analysis-directed intracellular assays. The latter include the findings of the lack of activity of glyoxylate shunt, and that phosphoenolpyruvate carboxylase (PPC) is the only anaplerotic reaction expressed in C. glutamicum cultivated on glucose minimal media. Network simplifications afforded by the above findings facilitated the determination of metabolic flux distributions under a variety of culture conditions and led to the following conclusions. Both the pentose phosphate pathway and PPC support significant fluxes during growth and lysine overproduction, and that flux partitioning at the glucosa-6-phosphate branch point does not appear to limit lysine synthesis.

Metabolic flux distributions inCorynebacterium glutamicum during growth and lysine overproduction

The two main contributions of this article are the solidification of Corynebacterium glutamicum biochemistry guided by bioreaction network analysis, and the determination of basal metabolic flux distributions during growth and lysine synthesis. Employed methodology makes use of stoichiometrically based mass balances to determine flux distributions in the C. glutamicum metabolic network. Presented are a brief description of the methodology, a thorough literature review of glutamic acid bacteria biochemistry, and specific results obtained through a combination of fermentation studies and analysis-directed intracellular assays. The latter include the findings of the lack of activity of glyoxylate shunt, and that phosphoenolpyruvate carboxylase (PPC) is the only anaplerotic reaction expressed in C. glutamicum cultivated on glucose minimal media. Network simplifications afforded by the above findings facilitated the determination of metabolic flux distributions under a variety of culture conditions and led to the following conclusions. Both the pentose phosphate pathway and PPC support significant fluxes during growth and lysine overproduction, and that flux partitioning at the glucosa-6-phosphate branch point does not appear to limit lysine synthesis. © 1993 John Wiley & Sons, Inc.

Metabolic control analysis for lysine synthesis using Corynebacterium glutamicum and experimental verification

Metabolic control analysis was carried out for the lysine biosynthetic pathway in Corynebacterium glutamicum ATCC 21253 using mechanism-based kinetic models developed for enzymatic reactions for this pathway. The rate-limiting steps during lysine production were determined with the aid of flux control coefficients, which indicated that the lysine synthesis flux is governed mainly by both aspartokinase and permease activity in the export system. Analyses indicated that an increase in the activity of aspartokinase would significantly alleviate its effect on the overall flux, and the limiting step is expected to shift to permease and other lysine synthetic enzymes. The influences of many participating precursors and cofactors on lysine synthesis flux were also investigated through the calculation of response coefficients for individual parameters. Although most parameters were not found to exert significant influences on lysine flux, extracellular lysine concentration was found to have a substantial effect on lysine production, and detailed analysis indicated that a decrease in the external lysine concentration will enhance the metabolite synthesis considerably and shift the control from export step to other steps. Although a decrease in external pH (pH 0) seems to increase lysine flux, consideration of the export carrier concentration in response to external pH confirmed the optimum pH 0 to be 7.0. Two types of recombinant strains overexpressing aspartokinase and dihydrodipicolinate synthase were constructed to verify the results obtained from metabolic sensitivity analysis.

Metabolic Control Analysis for Lysine Synthesis Using Corynebacterium glutamicum and Experimental Verification.

Metabolic Control Analysis for Lysine Synthesis Using Corynebacterium glutamicum and Experimental Verification.

A Prokaryotic Gene Cluster Involved in Synthesis of Lysine through the Amino Adipate Pathway: A Key to the Evolution of Amino Acid Biosynthesis

In previous studies we determined the nucleotide sequence of the gene cluster containing lys20, hacA (lys4A), hacB (lys4B), orfE, orfF, rimK, argC, and argB of Thermus thermophilus, an extremely thermophilic bacterium. In this study, we characterized the role of each gene in the cluster by gene disruption and examined auxotrophy in the disruptants. All disruptants except for the orfE disruption showed a lysine auxotrophic phenotype. This was surprising because this cluster consists of genes coding for unrelated proteins based on their names, which had been tentatively designated by homology analysis. Although the newly found pathway contains alpha-aminoadipic acid as a lysine biosynthetic intermediate, this pathway is not the same as the eukaryotic one. When each of the gene products was phylogenetically analyzed, we found that genes evolutionarily-related to the lysine biosynthetic genes in T. thermophilus were all present in a hyperthermophilic and anaerobic archaeon, Pyrococcus horikoshii, and formed a gene cluster in a manner similar to that in T. thermophilus. Furthermore, this gene cluster was analogous in part to the present leucine and arginine biosyntheses pathways. This lysine biosynthesis cluster is assumed to be one of the origins of lysine biosynthesis and could therefore become a key to the evolution of amino acid biosynthesis.

Growth requirements of pyruvate-decarboxylase-negative Saccharomyces cerevisiae

Pyruvate-decarboxylase (Pdc)-negative Saccharomyces cerevisiae has been reported to grow in batch cultures on glucose-containing complex media, but not on defined glucose-containing media. By a combination of batch and chemostat experiments it is demonstrated that even in complex media, Pdc − S. cerevisiae does not exhibit prolonged growth on glucose. Pdc − strains do grow in carbon-limited cultures on defined media containing glucose-acetate mixtures. The acetate requirement for glucose-limited growth, estimated experimentally by continuously decreasing the acetate feed to chemostat cultures, matched the theoretical acetyl-CoA requirement for lipid and lysine synthesis, consistent with the proposed role of pyruvate decarboxylase in the synthesis of cytosolic acetyl-CoA.

Detecting patterns of protein distribution and gene expression in silico.

Most biological information is contained within gene and genome sequences. However, current methods for analyzing these data are limited primarily to the prediction of coding regions and identification of sequence similarities. We have developed a computer algorithm, CoSMoS (for context sensitive motif searches), which adds context sensitivity to sequence motif searches. CoSMoS was challenged to identify genes encoding peroxisome-associated and oleate-induced genes in the yeast Saccharomyces cerevisiae. Specifically, we searched for genes capable of encoding proteins with a type 1 or type 2 peroxisomal targeting signal and for genes containing the oleate-response element, a cis-acting element common to fatty acid-regulated genes. CoSMoS successfully identified 7 of 8 known PTS-containing peroxisomal proteins and 13 of 14 known oleate-regulated genes. More importantly, CoSMoS identified an additional 18 candidate peroxisomal proteins and 300 candidate oleate-regulated genes. Preliminary localization studies suggest that these include at least 10 previously unknown peroxisomal proteins. Phenotypic studies of selected gene disruption mutants suggests that several of these new peroxisomal proteins play roles in growth on fatty acids, one is involved in peroxisome biogenesis and at least two are required for synthesis of lysine, a heretofore unrecognized role for peroxisomes. These results expand our understanding of peroxisome content and function, demonstrate the utility of CoSMoS for context-sensitive motif scanning, and point to the benefits of improved in silico genome analysis.

Development of a kinetic model for l-lysine biosynthesis in Corynebacterium glutamicum and its application to metabolic control analysis

A mathematical model describing intracellular lysine synthesis by Corynebacterium glutamicum in batch fermentation was developed. The model is based on material balance equations of the key metabolites, and includes mechanistically based, experimentally matched rate equations for individual enzymes. From the measurements of the levels of intra- and extracellular metabolites during cultivation, the kinetic parameters in the model were identified through the decomposition of the network of reactions. The model predictions and experimental observations were in reasonable agreement. Using the model developed, metabolic control analysis was carried out to identify the rate-limiting steps, by evaluating the control on the overall lysine synthesis flux exerted by individual enzymatic reactions, which suggested how the control on lysine synthesis changes from aspartokinase to lysine permease as fermentation proceeded and indicated that lysine production could be enhanced by improving aspartokinase activity of this strain through genetic manipulation.

The Arabidopsis thaliana dhdps gene encoding dihydrodipicolinate synthase, key enzyme of lysine biosynthesis, is expressed in a cell-specific manner.

Lysine synthesis in prokaryotes, some phycomycetes and higher plants starts with the condensation of L-aspartate-beta-semialdehyde (L-ASA) and pyruvate into dihydrodipicolinic acid. The enzyme that catalyses this step, dihydrodipicolinate synthase (DHDPS), is inhibited by the end-product lysine and is therefore thought to have a regulatory control on lysine synthesis. We have cloned and sequenced an Arabidopsis thaliana DNA fragment containing 900 bases upstream of the dhdps coding sequence. A transcriptional fusion of this fragment with the beta-glucuronidase reporter gene (uidA. Gus) was used to study the transcription properties of this promoter fragment (DS). No lysine-induced repression on transcription could be detected. Expression of DS-Gus activity in transformed Arabidopsis thaliana and Nicotiana tabacum was found to be cell type-specific. In the vegetative parts of the plant, GUS activity was located in meristems and young vasculature of roots, in vasculature of stem and leaves and in the meristems of young shoots. In flowers, high expression was found in the carpels, style, stigma, developing embryos, tapetum of young anthers and pollen. We demonstrated that the Arabidopsis DS promoter can direct its cell type-specific expression in a heterologous plant, Nicotiana tuabacum. The importance of transcriptional regulation of the dhdps gene, and in more general genes involved in amino acid biosynthesis, is discussed.

The α-aminoadipate pathway for lysine biosynthesis is widely distributed among Thermus strains

We previously reported that lysine is synthesized through the α-aminoadipate pathway in Thermus thermophilus HB27 (T. Kosuge and T. Hoshino, FEMS Microbiol. Lett., 169, 361–367, 1998), which was the first report demonstrating the synthesis of lysine through the α-aminoadipate pathway in Bacteria. LYS20 and LYS4, which respectively encode homocitrate synthase and homoaconitate hydratase have already been identified as the lysine biosynthetic genes in T. thermophilus HB27. In the present work, we examined eight other Thermus strains for the existence of genes belonging to the α-aminoadipate pathway. BamHI- or BglII-digested total DNAs from the eight strains were analyzed by Southern hybridization using LYS20 or LYS4 as a DNA probe. DNA fragments that hybridized with one or both of the genes were detected in seven of the Thermus strains but not in T. ruber. The sizes of the fragments that hybridized with the LYS20 and LYS4 probes were the same among T. thermophilus HB27, T. thermophilus HB8, “ T. caldophilus” GK24, and four “ T. flavus” strains. For example, a similar 4.3-kb fragment was detected in each of the above seven strains. In this fragment, four open reading frames were found downstream of the LYS4 gene in T. thermophilus HB27. Gene disruption experiments revealed that three open reading frames are involved in lysine biosynthesis in T. thermophilus HB27. These results strongly suggest that the lysine biosynthetic gene cluster for the α-aminoadipate pathway is widely distributed in the genus Thermus.