Construction of deoxyriboaldolase-overexpressing Escherichia coli and its application to 2-deoxyribose 5-phosphate synthesis from glucose and acetaldehyde for 2'-deoxyribonucleoside production

In vitro and in vivo evaluation of the anti-infective potential of the essential oil extracted from the leaves of Plectranthus amboinicus (lour.) spreng against Klebsiella pneumoniae and elucidation of its mechanism of action through proteomics approach

ETHNOPHARMACOLOGICAL RELEVANCE

Members of Plectranthus genus such as Plectranthus amboinicus (Lour.) Spreng is a well-known folkloric medicine around the globe in treating several human ailments such as cardiovascular, respiratory, digestive, urinary tract, skin and infective diseases. Its therapeutic value is primarily attributed to its essential oil. Although several properties of Plectranthus amboinicus essential oil have been documented, its mechanism of action and safety has not been completely elucidated.

AIM OF THE STUDY

To investigate the anti-infective potential of Plectranthus amboinicus essential oil against Klebsiella pneumoniae using in vitro and in vivo bioassays and identify its mode of action. The study was conducted to scientifically validate the traditional usage of Plectranthus amboinicus oil and propose it as a complementary and alternative medication to combat Klebsiella pneumoniae infections due to emerging antibiotic resistance problem.

MATERIALS AND METHODS

Plectranthus amboinicus essential oil was extracted through steam distillation and was chemically characterized using Gas Chromatography Mass Spectrometry (GC-MS). The antibacterial activity was assessed using microbroth dilution assay, metabolic viability assay and growth curve analysis. The mode of action was elucidated by the proteomics approach using Nano-LC-MS/MS followed by in silico analysis. The results of proteomic analysis were further validated through several in vitro assays. The cytotoxic nature of the essential oil was also confirmed using adenocarcinomic human alveolar basal epithelial (A549) cells. Furthermore, the safety and in vivo anti-infective efficacy of Plectranthus amboinicus essential oil was evaluated through survival assay, CFU assay and histopathological analysis of vital organs using zebrafish as a model organism.

RESULTS

The chemical characterization of Plectranthus amboinicus essential oil revealed that it is predominantly composed of thymol. Thymol rich P. amboinicus essential oil demonstrated potent inhibitory effects on Klebsiella pneumoniae growth, achieving a significant reduction at a concentration of 400 μg/mL within 4 h of treatment The nano-LC-MS/MS approach unveiled that the essential oil exerted its impact by disrupting the antioxidant defense system and efflux pump system of the bacterium, resulting in elevated cellular oxidative stress and affect the biosynthesis of biofilm. The same was validated through several in vitro assays. Furthermore, the toxicity of Plectranthus amboinicus essential oil determined using A549 cells and zebrafish survival assay established a non-toxic concentration of 400 μg/mL and 12.5 μg/mL respectively. The results of anti-infective potential of the essential oil using Zebrafish as a model organism demonstrated significantly improved survival rates, reduced bacterial load, alleviated visible signs of inflammation and mitigated the adverse effects of infection on various organs, as evidenced by histopathological analysis ensuring its safety for potential therapeutic application.

CONCLUSION

The executed in vitro and in vivo assays established the effectiveness of essential oil in inhibiting bacterial growth by targeting key proteins associated with the bacterial antioxidant defense system and disrupted the integrity of the cell membrane, highlighting its critical role in addressing the challenge posed by antibiotic-resistant Klebsiella pneumoniae.

Gut microbial response to host metabolic phenotypes

A large number of studies have proved that biological metabolic phenotypes exist objectively and are gradually recognized by humans. Gut microbes affect the host's metabolic phenotype. They directly or indirectly participate in host metabolism, physiology and immunity through changes in population structure, metabolite differences, signal transduction and gene expression. Obtaining comprehensive information and specific identification factors associated with gut microbiota and host metabolic phenotypes has become the focus of research in the field of gut microbes, and it has become possible to find new and effective ways to prevent or treat host metabolic diseases. In the future, precise treatment of gut microbes will become one of the new therapeutic strategies. This article reviews the content of gut microbes and carbohydrate, amino acid, lipid and nucleic acid metabolic phenotypes, including metabolic intermediates, mechanisms of action, latest research findings and treatment strategies, which will help to understand the relationship between gut microbes and host metabolic phenotypes and the current research status.

Synthetic Activity of Recombinant Whole Cell Biocatalysts Containing 2-Deoxy-D-ribose-5-phosphate Aldolase from Pectobacterium atrosepticum

In nature 2-deoxy-D-ribose-5-phosphate aldolase (DERA) catalyses the reversible formation of 2-deoxyribose 5-phosphate from D-glyceraldehyde 3-phosphate and acetaldehyde. In addition, this enzyme can use acetaldehyde as the sole substrate, resulting in a tandem aldol reaction, yielding 2,4,6-trideoxy-D-erythro-hexapyranose, which spontaneously cyclizes. This reaction is very useful for the synthesis of the side chain of statin-type drugs used to decrease cholesterol levels in blood. One of the main challenges in the use of DERA in industrial processes, where high substrate loads are needed to achieve the desired productivity, is its inactivation by high acetaldehyde concentration. In this work, the utility of different variants of Pectobacterium atrosepticum DERA (PaDERA) as whole cell biocatalysts to synthesize 2-deoxyribose 5-phosphate and 2,4,6-trideoxy-D-erythro-hexapyranose was analysed. Under optimized conditions, E. coli BL21 (PaDERA C-His AA C49M) whole cells yields 99 % of both products. Furthermore, this enzyme is able to tolerate 500 mM acetaldehyde in a whole-cell experiment which makes it suitable for industrial applications.

2-Deoxy-D-ribose-5-phosphate aldolase (DERA): applications and modifications

2-Deoxy-D-ribose-5-phosphate aldolase (DERA) is a class I aldolase that offers access to several building blocks for organic synthesis. It catalyzes the stereoselective C-C bond formation between acetaldehyde and numerous other aldehydes. However, the practical application of DERA as a biocatalyst is limited by its poor tolerance towards industrially relevant concentrations of aldehydes, in particular acetaldehyde. Therefore, the development of proper experimental conditions, including protein engineering and/or immobilization on appropriate supports, is required. The present review is aimed to provide a brief overview of DERA, its history, and progress made in understanding the functioning of the enzyme. Furthermore, the current understanding regarding aldehyde resistance of DERA and the various optimizations carried out to modify this property are discussed.

Biosynthesis of 2-deoxysugars using whole-cell catalyst expressing 2-deoxy-D-ribose 5-phosphate aldolase

2-Deoxy-D-ribose 5-phosphate aldolase (DERA) accepts a wide variety of aldehydes and is used in de novo synthesis of 2-deoxysugars, which have important applications in drug manufacturing. However, DERA has low preference for non-phosphorylated substrates. In this study, DERA from Klebsiella pneumoniae (KDERA) was mutated to increase its enzyme activity and substrate tolerance towards non-phosphorylated polyhydroxy aldehyde. Mutant KDERA(K12) (S238D/F200I/ΔY259) showed a 3.15-fold improvement in enzyme activity and a 1.54-fold increase in substrate tolerance towards D-glyceraldehyde compared with the wild type. Furthermore, a whole-cell transformation strategy using resting cells of the BL21(pKDERA12) strain, containing the expressed plasmid pKDERA12, resulted in increase in 2-deoxy-D-ribose yield from 0.41 mol/mol D-glyceraldehyde to 0.81 mol/mol D-glyceraldehyde and higher substrate tolerance from 0.5 to 3 M compared to in vitro assays. With further optimization of the transformation process, the BL21(pKDERA12) strain produced 2.14 M (287.06 g/L) 2-deoxy-D-robose (DR), with a yield of 0.71 mol/mol D-glyceraldehyde and average productivity of 0.13 mol/L·h (17.94 g/L·h). These results demonstrate the potential for large-scale production of 2-deoxy-D-ribose using the BL21(pKDERA12) strain. Furthermore, the BL21(pKDERA12) strain also exhibited the ability to efficiently produce 2-deoxy-D-altrose from D-erythrose, as well as 2-deoxy-L-xylose and 2-deoxy-L-ribose from L-glyceraldehyde.

The case for an early biological origin of DNA

All life generates deoxyribonucleotides, the building blocks of DNA, via ribonucleotide reductases (RNRs). The complexity of this reaction suggests it did not evolve until well after the advent of templated protein synthesis, which in turn suggests DNA evolved later than both RNA and templated protein synthesis. However, deoxyribonucleotides may have first been synthesised via an alternative, chemically simpler route—the reversal of the deoxyriboaldolase (DERA) step in deoxyribonucleotide salvage. In light of recent work demonstrating that this reaction can drive synthesis of deoxyribonucleosides, we consider what pressures early adoption of this pathway would have placed on cell metabolism. This in turn provides a rationale for the replacement of DERA-dependent DNA production by RNR-dependent production.

Efficient Production of 2-Deoxyribose 5-Phosphate from Glucose and Acetaldehyde by Coupling of the Alcoholic Fermentation System of Baker’s Yeast and Deoxyriboaldolase-ExpressingEscherichia coli

2-Deoxyribose 5-phosphate production through coupling of the alcoholic fermentation system of baker's yeast and deoxyriboaldolase-expressing Escherichia coli was investigated. In this process, baker's yeast generates fructose 1,6-diphosphate from glucose and inorganic phosphate, and then the E. coli convert the fructose 1,6-diphosphate into 2-deoxyribose 5-phosphate via D-glyceraldehyde 3-phosphate. Under the optimized conditions with toluene-treated yeast cells, 356 mM (121 g/l) fructose 1,6-diphosphate was produced from 1,111 mM glucose and 750 mM potassium phosphate buffer (pH 6.4) with a catalytic amount of AMP, and the reaction supernatant containing the fructose 1,6-diphosphate was used directly as substrate for 2-deoxyribose 5-phosphate production with the E. coli cells. With 178 mM enzymatically prepared fructose 1,6-diphosphate and 400 mM acetaldehyde as substrates, 246 mM (52.6 g/l) 2-deoxyribose 5-phosphate was produced. The molar yield of 2-deoxyribose 5-phosphate as to glucose through the total two step reaction was 22.1%. The 2-deoxyribose 5-phosphate produced was converted to 2-deoxyribose with a molar yield of 85% through endogenous or exogenous phosphatase activity.

Construction of microbial platform for an energy-requiring bioprocess: practical 2'-deoxyribonucleoside production involving a C-C coupling reaction with high energy substrates

BACKGROUND

Reproduction and sustainability are important for future society, and bioprocesses are one technology that can be used to realize these concepts. However, there is still limited variation in bioprocesses and there are several challenges, especially in the operation of energy-requiring bioprocesses. As an example of a microbial platform for an energy-requiring bioprocess, we established a process that efficiently and enzymatically synthesizes 2'-deoxyribonucleoside from glucose, acetaldehyde, and a nucleobase. This method consists of the coupling reactions of the reversible nucleoside degradation pathway and energy generation through the yeast glycolytic pathway.

RESULTS

Using E. coli that co-express deoxyriboaldolase and phosphopentomutase, a high amount of 2'-deoxyribonucleoside was produced with efficient energy transfer under phosphate-limiting reaction conditions. Keeping the nucleobase concentration low and the mixture at a low reaction temperature increased the yield of 2'-deoxyribonucleoside relative to the amount of added nucleobase, indicating that energy was efficiently generated from glucose via the yeast glycolytic pathway under these reaction conditions. Using a one-pot reaction in which small amounts of adenine, adenosine, and acetone-dried yeast were fed into the reaction, 75 mM of 2'-deoxyinosine, the deaminated product of 2'-deoxyadenosine, was produced from glucose (600 mM), acetaldehyde (250 mM), adenine (70 mM), and adenosine (20 mM) with a high yield relative to the total base moiety input (83%). Moreover, a variety of natural dNSs were further synthesized by introducing a base-exchange reaction into the process.

CONCLUSION

A critical common issue in energy-requiring bioprocess is fine control of phosphate concentration. We tried to resolve this problem, and provide the convenient recipe for establishment of energy-requiring bioprocesses. It is anticipated that the commercial demand for dNSs, which are primary metabolites that accumulate at very low levels in the metabolic pool, will grow. The development of an efficient production method for these compounds will have a great impact in both fields of applied microbiology and industry and will also serve as a good example of a microbial platform for energy-requiring bioprocesses.

Selection of a new whole cell biocatalyst for the synthesis of 2-deoxyribose 5-phosphate

2-deoxyribose 5-phosphate (DR5P) is a key intermediate in the biocatalyzed preparation of deoxyribonucleosides. Therefore, DR5P production by means of simpler, cleaner, and economic pathways becomes highly interesting. One strategy involves the use of bacterial whole cells containing DR5P aldolase as biocatalyst for the aldol addition between acetaldehyde and D: -glyceraldehyde 3-phosphate or glycolytic intermediates that in situ generate the acceptor substrate. In this work, diverse microorganisms capable of synthesizing DR5P were selected by screening several bacteria genera. In particular, Erwinia carotovora ATCC 33260 was identified as a new biocatalyst that afforded 14.1-mM DR5P starting from a cheap raw material like glucose.

Cloning, expression, and characterization of a new deoxyribose 5-phosphate aldolase from Yersinia sp. EA015

A new deoC gene encoding deoxyribose 5-phosphate aldolase (DERA) was identified in Yersinia sp. EA015 isolated from soil. The DERA gene had an open reading frame (ORF) of 672 base pairs encoding 223 amino acids to yield a protein of molecular mass 24.8 kDa. The amino acid sequence was 94% identical to that of DERA from Yersinia intermedia ATCC 29909. DERA was over-expressed in Escherichia coli and purified using Ni-NTA affinity chromatography. The specific activity was 137 micromol/min/mg. The Michaelis constant (k(m) value) of DERA was 9.1 mM. DERA was optimally active at pH 6.0 and 50 degrees C. DERA was tolerant to a high concentration (300 mM) of acetaldehyde.

One-pot Microbial Synthesis of 2′-deoxyribonucleoside from Glucose, Acetaldehyde, and a Nucleobase

A one-pot enzymatic synthesis of 2'-deoxyribonucleoside from glucose, acetaldehyde, and a nucleobase was established. Glycolysis by baker's yeast (Saccharomyces cerevisiae) generated ATP which was used to produce D: -glyceraldehyde 3-phosphate production from glucose via fructose 1,6-diphosphate. The D: -glyceraldehyde 3-phosphate produced was transformed to 2'-deoxyribonucleoside via 2-deoxyribose 5-phosphate and then 2-deoxyribose 1-phosphate in the presence of acetaldehyde and a nucleobase by deoxyriboaldolase, phosphopentomutase expressed in Escherichia coli, and a commercial nucleoside phosphorylase. About 33 mM 2'-deoxyinosine was produced from 600 mM glucose, 333 mM acetaldehyde and 100 mM adenine in 24 h. 2'-Deoxyinosine was produced from adenine due to the adenosine deaminase activity of E. coli transformants.

Biochemical retrosynthesis of 2′-deoxyribonucleosides from glucose, acetaldehyde, and a nucleobase

2'-Deoxyribonucleosides are important as building blocks for the synthesis of antisense drugs, antiviral nucleosides, and 2'-deoxyribonucleotides for polymerase chain reaction. The microbial production of 2'-deoxyribonucleosides from simple materials, glucose, acetaldehyde, and a nucleobase, through the reverse reactions of 2'-deoxyribonucleoside degradation and the glycolytic pathway, was investigated. The glycolytic pathway of baker's yeast yielded fructose 1,6-diphosphate from glucose using the energy of adenosine 5'-triphosphate generated from adenosine 5'-monophosphate through alcoholic fermentation with the yeast. Fructose 1,6-diphosphate was further transformed to 2-deoxyribose 5-phosphate in the presence of acetaldehyde by deoxyriboaldolase-expressing Escherichia coli cells via D-glyceraldehyde 3-phosphate. E. coli transformants expressing phosphopentomutase and nucleoside phosphorylase produced 2'-deoxyribonucleosides from 2-deoxyribose 5-phosphate and a nucleobase via 2-deoxyribose 1-phosphate through the reverse reactions of 2'-deoxyribonucleoside degradation. Coupling of the glycolytic pathway and deoxyriboaldolase-catalyzing reaction efficiently supplied 2-deoxyribose 5-phosphate, which is a key intermediate for 2'-deoxyribonucleoside synthesis. 2'-Deoxyinosine (9.9 mM) was produced from glucose, acetaldehyde, and adenine through three-step reactions via fructose 1,6-diphosphate and then 2-deoxyribose 5-phosphate, the molar yield as to glucose being 17.8%.

Whole organism biocatalysis

The use of biocatalysts for the industrial synthesis of chemicals has been attracting much attention as an environment-friendly synthetic method. Microbial cells play a leading role in 'chemo-enzymatic synthesis' because of their great diversity. Several microbes with unique catalytic abilities have been found through intensive screening and put to practical use. Besides, advanced molecular biological techniques are powerful tools for developing more satisfactory biocatalysts.