Significantly enhancing production of trans-4-hydroxy-l-proline by integrated system engineering in Escherichia coli

Trans-4-hydroxy-l-proline is produced by trans-proline-4-hydroxylase with l-proline through glucose fermentation. Here, we designed a thorough “from A to Z” strategy to significantly improve trans-4-hydroxy-l-proline production. Through rare codon selected evolution, Escherichia coli M1 produced 18.2 g L−1l-proline. Metabolically engineered M6 with the deletion of putA, proP, putP, and aceA, and proB mutation focused carbon flux to l-proline and released its feedback inhibition. It produced 15.7 g L−1trans-4-hydroxy-l-proline with 10 g L−1l-proline retained. Furthermore, a tunable circuit based on quorum sensing attenuated l-proline hydroxylation flux, resulting in 43.2 g L−1trans-4-hydroxy-l-proline with 4.3 g L−1l-proline retained. Finally, rationally designed l-proline hydroxylase gave 54.8 g L−1trans-4-hydroxy-l-proline in 60 hours almost without l-proline remaining—the highest production to date. The de novo engineering carbon flux through rare codon selected evolution, dynamic precursor modulation, and metabolic engineering provides a good technological platform for efficient hydroxyl amino acid synthesis.

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Availability of intestinal microbial lysine for whole body lysine homeostasis in human subjects

AJP Endocrinology and Metabolism ◽

10.1152/ajpendo.1999.277.4.e597 ◽

1999 ◽

Vol 277 (4) ◽

pp. E597-E607 ◽

Cited By ~ 15

Author(s):

Cornelia C. Metges ◽

Antoine E. El-Khoury ◽

Lidewij Henneman ◽

Klaus J. Petzke ◽

Ian Grant ◽

...

Keyword(s):

De Novo ◽

Human Subjects ◽

Isotope Ratio Mass Spectrometry ◽

Acid Synthesis ◽

Whole Body ◽

Microbial Protein ◽

Amino Acid Synthesis ◽

Adequate Diet ◽

Appearance Rate ◽

Intravenous And Oral Administration

We have investigated whether there is a net contribution of lysine synthesized de novo by the gastrointestinal microflora to lysine homeostasis in six adults. On two separate occasions an adequate diet was given for a total of 11 days, and a 24-h (12-h fast, 12-h fed) tracer protocol was performed on the last day, in which lysine turnover, oxidation, and splanchnic uptake were measured on the basis of intravenous and oral administration ofl-[1-13C]lysine andl-[6,6-2H2]lysine, respectively. [15N2]urea or15NH4Cl was ingested daily over the last 6 days to label microbial protein. In addition, seven ileostomates were studied with15NH4Cl. [15N]lysine enrichment in fecal and ileal microbial protein, as precursor for microbial lysine absorption, and in plasma free lysine was measured by gas chromatography-combustion-isotope ratio mass spectrometry. Differences in plasma [13C]- and [2H2]lysine enrichments during the 12-h fed period were observed between the two15N tracer studies, although the reason is unclear, and possibly unrelated to the tracer form per se. In the normal adults, after15NH4Cl and [15N2]urea intake, respectively, lysine derived from fecal microbial protein accounted for 5 and 9% of the appearance rate of plasma lysine. With ileal microbial lysine enrichment, the contribution of microbial lysine to plasma lysine appearance was 44%. This amounts to a gross microbial lysine contribution to whole body plasma lysine turnover of between 11 and 130 mg ⋅ kg−1 ⋅ day−1, depending on the [15N]lysine precursor used. However, insofar as microbial amino acid synthesis is accompanied by microbial breakdown of endogenous amino acids or their oxidation by intestinal tissues, this may not reflect a net increase in lysine absorption. Thus we cannot reliably estimate the quantitative contribution of microbial lysine to host lysine homeostasis with the present paradigm. However, the results confirm the significant presence of lysine of microbial origin in the plasma free lysine pool.

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Proteasome Inhibition in Brassica napus Roots Increases Amino Acid Synthesis to Offset Reduced Proteolysis

Plant and Cell Physiology ◽

10.1093/pcp/pcaa047 ◽

2020 ◽

Vol 61 (6) ◽

pp. 1028-1040

Author(s):

Dan Pereksta ◽

Dillon King ◽

Fahmida Saki ◽

Amith Maroli ◽

Elizabeth Leonard ◽

...

Keyword(s):

Amino Acid ◽

Brassica Napus ◽

De Novo ◽

Metabolic Response ◽

Sugar Metabolism ◽

Proteasome Inhibition ◽

Acid Synthesis ◽

Amino Acid Synthesis ◽

Amino Acid Depletion ◽

Metabolic Activities

Abstract Cellular homeostasis is maintained by the proteasomal degradation of regulatory and misfolded proteins, which sustains the amino acid pool. Although proteasomes alleviate stress by removing damaged proteins, mounting evidence indicates that severe stress caused by salt, metal(oids), and some pathogens can impair the proteasome. However, the consequences of proteasome inhibition in plants are not well understood and even less is known about how its malfunctioning alters metabolic activities. Lethality causes by proteasome inhibition in non-photosynthetic organisms stem from amino acid depletion, and we hypothesized that plants respond to proteasome inhibition by increasing amino acid biosynthesis. To address these questions, the short-term effects of proteasome inhibition were monitored for 3, 8 and 48 h in the roots of Brassica napus treated with the proteasome inhibitor MG132. Proteasome inhibition did not affect the pool of free amino acids after 48 h, which was attributed to elevated de novo amino acid synthesis; these observations coincided with increased levels of sulfite reductase and nitrate reductase activities at earlier time points. However, elevated amino acid synthesis failed to fully restore protein synthesis. In addition, transcriptome analysis points to perturbed abscisic acid signaling and decreased sugar metabolism after 8 h of proteasome inhibition. Proteasome inhibition increased the levels of alternative oxidase but decreased aconitase activity, most sugars and tricarboxylic acid metabolites in root tissue after 48 h. These metabolic responses occurred before we observed an accumulation of reactive oxygen species. We discuss how the metabolic response to proteasome inhibition and abiotic stress partially overlap in plants.

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During Oxidative Stress the Clp Proteins of Escherichia coli Ensure that Iron Pools Remain Sufficient To Reactivate Oxidized Metalloenzymes

Journal of Bacteriology ◽

10.1128/jb.00235-20 ◽

2020 ◽

Vol 202 (18) ◽

Author(s):

Ananya Sen ◽

Yidan Zhou ◽

James A. Imlay

Keyword(s):

Escherichia Coli ◽

Hydrogen Peroxide ◽

Acid Synthesis ◽

Growth Defect ◽

Natural Environments ◽

Intracellular Iron ◽

Amino Acid Synthesis ◽

Common Component ◽

Content Type ◽

Iron Pool

ABSTRACT Hydrogen peroxide (H2O2) is formed in natural environments by both biotic and abiotic processes. It easily enters the cytoplasms of microorganisms, where it can disrupt growth by inactivating iron-dependent enzymes. It also reacts with the intracellular iron pool, generating hydroxyl radicals that can lethally damage DNA. Therefore, virtually all bacteria possess H2O2-responsive transcription factors that control defensive regulons. These typically include catalases and peroxidases that scavenge H2O2. Another common component is the miniferritin Dps, which sequesters loose iron and thereby suppresses hydroxyl-radical formation. In this study, we determined that Escherichia coli also induces the ClpS and ClpA proteins of the ClpSAP protease complex. Mutants that lack this protease, plus its partner, ClpXP protease, cannot grow when H2O2 levels rise. The growth defect was traced to the inactivity of dehydratases in the pathway of branched-chain amino acid synthesis. These enzymes rely on a solvent-exposed [4Fe-4S] cluster that H2O2 degrades. In a typical cell the cluster is continuously repaired, but in the clpSA clpX mutant the repair process is defective. We determined that this disability is due to an excessively small iron pool, apparently due to the oversequestration of iron by Dps. Dps was previously identified as a substrate of both the ClpSAP and ClpXP proteases, and in their absence its levels are unusually high. The implication is that the stress response to H2O2 has evolved to strike a careful balance, diminishing iron pools enough to protect the DNA but keeping them substantial enough that critical iron-dependent enzymes can be repaired. IMPORTANCE Hydrogen peroxide mediates the toxicity of phagocytes, lactic acid bacteria, redox-cycling antibiotics, and photochemistry. The underlying mechanisms all involve its reaction with iron atoms, whether in enzymes or on the surface of DNA. Accordingly, when bacteria perceive toxic H2O2, they activate defensive tactics that are focused on iron metabolism. In this study, we identify a conundrum: DNA is best protected by the removal of iron from the cytoplasm, but this action impairs the ability of the cell to reactivate its iron-dependent enzymes. The actions of the Clp proteins appear to hedge against the oversequestration of iron by the miniferritin Dps. This buffering effect is important, because E. coli seeks not just to survive H2O2 but to grow in its presence.

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Target of Rapamycin Inhibition in Chlamydomonas reinhardtii Triggers de Novo Amino Acid Synthesis by Enhancing Nitrogen Assimilation

The Plant Cell ◽

10.1105/tpc.18.00159 ◽

2018 ◽

Vol 30 (10) ◽

pp. 2240.1-2254 ◽

Cited By ~ 19

Author(s):

Umarah Mubeen ◽

Jessica Jüppner ◽

Jessica Alpers ◽

Dirk K. Hincha ◽

Patrick Giavalisco

Keyword(s):

Amino Acid ◽

Chlamydomonas Reinhardtii ◽

Nitrogen Assimilation ◽

De Novo ◽

Acid Synthesis ◽

Target Of Rapamycin ◽

Amino Acid Synthesis

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Mechanism of De Novo Branched-Chain Amino Acid Synthesis as an Alternative Electron Sink in Hypoxic Aspergillus nidulans Cells

Applied and Environmental Microbiology ◽

10.1128/aem.02135-09 ◽

2010 ◽

Vol 76 (5) ◽

pp. 1507-1515 ◽

Cited By ~ 36

Author(s):

Motoyuki Shimizu ◽

Tatsuya Fujii ◽

Shunsuke Masuo ◽

Naoki Takaya

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Aspergillus Nidulans ◽

De Novo ◽

Acid Synthesis ◽

Branched Chain Amino Acids ◽

Amino Acid Synthesis ◽

Lactate Dehydrogenase Activity ◽

Branched Chain Amino Acid ◽

Branched Chain

ABSTRACT Although branched-chain amino acids are synthesized as building blocks of proteins, we found that the fungus Aspergillus nidulans excretes them into the culture medium under hypoxia. The transcription of predicted genes for synthesizing branched-chain amino acids was upregulated by hypoxia. A knockout strain of the gene encoding the large subunit of acetohydroxy acid synthase (AHAS), which catalyzes the initial reaction of the synthesis, required branched-chain amino acids for growth and excreted very little of them. Pyruvate, a substrate for AHAS, increased the amount of hypoxic excretion in the wild-type strain. These results indicated that the fungus responds to hypoxia by synthesizing branched-chain amino acids via a de novo mechanism. We also found that the small subunit of AHAS regulated hypoxic branched-chain amino acid production as well as cellular AHAS activity. The AHAS knockout resulted in higher ratios of NADH/NAD+ and NADPH/NADP+ under hypoxia, indicating that the branched-chain amino acid synthesis contributed to NAD+ and NADP+ regeneration. The production of branched-chain amino acids and the hypoxic induction of involved genes were partly repressed in the presence of glucose, where cells produced ethanol and lactate and increased levels of lactate dehydrogenase activity. These indicated that hypoxic branched-chain amino acid synthesis is a unique alternative mechanism that functions in the absence of glucose-to-ethanol/lactate fermentation and oxygen respiration.

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Anaerobic Cysteine Degradation and Potential Metabolic Coordination in Salmonella enterica and Escherichia coli

Journal of Bacteriology ◽

10.1128/jb.00117-17 ◽

2017 ◽

Vol 199 (16) ◽

Cited By ~ 9

Author(s):

Melissa Loddeke ◽

Barbara Schneider ◽

Tamiko Oguri ◽

Iti Mehta ◽

Zhenyu Xuan ◽

...

Keyword(s):

Escherichia Coli ◽

Amino Acid ◽

Salmonella Enterica ◽

Acid Synthesis ◽

Lower Growth ◽

Amino Acid Synthesis ◽

Content Type ◽

E Coli ◽

Sulfur Containing ◽

Sulfur Containing Compounds

ABSTRACT Salmonella enterica has two CyuR-activated enzymes that degrade cysteine, i.e., the aerobic CdsH and an unidentified anaerobic enzyme; Escherichia coli has only the latter. To identify the anaerobic enzyme, transcript profiling was performed for E. coli without cyuR and with overexpressed cyuR. Thirty-seven genes showed at least 5-fold changes in expression, and the cyuPA (formerly yhaOM) operon showed the greatest difference. Homology suggested that CyuP and CyuA represent a cysteine transporter and an iron-sulfur-containing cysteine desulfidase, respectively. E. coli and S. enterica ΔcyuA mutants grown with cysteine generated substantially less sulfide and had lower growth yields. Oxygen affected the CyuR-dependent genes reciprocally; cyuP-lacZ expression was greater anaerobically, whereas cdsH-lacZ expression was greater aerobically. In E. coli and S. enterica, anaerobic cyuP expression required cyuR and cysteine and was induced by l-cysteine, d-cysteine, and a few sulfur-containing compounds. Loss of either CyuA or RidA, both of which contribute to cysteine degradation to pyruvate, increased cyuP-lacZ expression, which suggests that CyuA modulates intracellular cysteine concentrations. Phylogenetic analysis showed that CyuA homologs are present in obligate and facultative anaerobes, confirming an anaerobic function, and in archaeal methanogens and bacterial acetogens, suggesting an ancient origin. Our results show that CyuA is the major anaerobic cysteine-catabolizing enzyme in both E. coli and S. enterica, and it is proposed that anaerobic cysteine catabolism can contribute to coordination of sulfur assimilation and amino acid synthesis. IMPORTANCE Sulfur-containing compounds such as cysteine and sulfide are essential and reactive metabolites. Exogenous sulfur-containing compounds can alter the thiol landscape and intracellular redox reactions and are known to affect several cellular processes, including swarming motility, antibiotic sensitivity, and biofilm formation. Cysteine inhibits several enzymes of amino acid synthesis; therefore, increasing cysteine concentrations could increase the levels of the inhibited enzymes. This inhibition implies that control of intracellular cysteine levels, which is the immediate product of sulfide assimilation, can affect several pathways and coordinate metabolism. For these and other reasons, cysteine and sulfide concentrations must be controlled, and this work shows that cysteine catabolism contributes to this control.

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Expression in Escherichia coli, purification and characterization of two mammalian thioesterases involved in fatty acid synthesis

Biochemical Journal ◽

10.1042/bj2730787 ◽

1991 ◽

Vol 273 (3) ◽

pp. 787-790 ◽

Cited By ~ 36

Author(s):

J Naggert ◽

A Witkowski ◽

B Wessa ◽

S Smith

Keyword(s):

Escherichia Coli ◽

Fatty Acid ◽

Fatty Acid Synthesis ◽

Fatty Acid Synthase ◽

De Novo ◽

Acid Synthesis ◽

Temperature Sensitive ◽

Lambda Repressor ◽

Thioesterase Ii ◽

Chain Lengths

Thioesterase I, a constituent domain of the multifunctional fatty acid synthase, and thioesterase II, an independent monofunctional protein, catalyse the chain-terminating reaction in fatty acid synthesis de novo at long and medium chain lengths respectively. The enzymes have been cloned and expressed in Escherichia coli under the control of the temperature-sensitive lambda repressor. The recombinant proteins are full-length catalytically competent thioesterases with specificities indistinguishable from those of the natural enzymes.

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Physiological consequences of mutation for ALS-inhibitor resistance

Weed Science ◽

10.1017/s0043174500091967 ◽

1999 ◽

Vol 47 (4) ◽

pp. 383-392 ◽

Cited By ~ 39

Author(s):

Charlotte V. Eberlein ◽

Mary J. Guttieri ◽

Philip H. Berger ◽

John K. Fellman ◽

Carol A. Mallory-Smith ◽

...

Keyword(s):

Specific Activity ◽

Feedback Inhibition ◽

Sequence Data ◽

Single Point ◽

Acetolactate Synthase ◽

Acid Synthesis ◽

Single Point Mutation ◽

Resistance Allele ◽

Amino Acid Synthesis ◽

Lactuca Serriola

Biochemical and physiological effects of target site resistance to herbicides inhibiting acetolactate synthase (ALS) were evaluated using sulfonylurea-resistant (R) and -susceptible (S) near isonuclearLactuca sativa‘Bibb’ lines derived by backcrossing the resistance allele fromLactuca serriolaL. intoL. sativa.Sequence data suggest that resistance inL. sativais conferred by a single-point mutation that encodes a proline197to histidine substitution in Domain A of the ALS protein; this is the same substitution observed in RL. serriola. Kmapp(pyruvate) values for ALS isolated from R and SL. sativawere 7.3 and 11.1 mM, respectively, suggesting that the resistance allele did not alter the pyruvate binding domain on the ALS enzyme. Both R and S ALS had greater affinity for 2-oxobutyrate than for pyruvate at the second substrate site. Ratios of acetohydroxybutyrate: acetolactate produced by R ALS across a range of 2-oxobutyrate concentrations were similar to acetohydroxybutyrate: acetolactate ratios produced by S ALS. Specific activity of ALS from RL. sativawas 46% of the specific activity from SL. sativa, suggesting that the resistance allele has detrimental effects on enzyme function, expression, or stability. ALS activity from R plants was less sensitive to feedback inhibition by valine, leucine, and isoleucine than ALS from S plants. Valine, leucine, and isoleucine concentrations were about 1.5 times higher in R seed than in S seed on a per gram of seed basis, and concentrations of valine and leucine were 1.3 and 1.6 times higher, respectively, in R leaves than in S leaves. Findings suggest that the mutation for resistance results in altered regulation of branched-chain amino acid synthesis.

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