Role of central metabolism in the osmoadaptation of the halophilic bacterium Chromohalobacter salexigens.

Bacterial osmoadaptation involves the cytoplasmic accumulation of compatible solutes to counteract extracellular osmolarity. The halophilic and highly halotolerant bacterium Chromohalobacter salexigens is able to grow up to 3 m NaCl in a minimal medium due to the de novo synthesis of ectoines. This is an osmoregulated pathway that burdens central metabolic routes by quantitatively drawing off TCA cycle intermediaries. Consequently, metabolism in C. salexigens has adapted to support this biosynthetic route. Metabolism of C. salexigens is more efficient at high salinity than at low salinity, as reflected by lower glucose consumption, lower metabolite overflow, and higher biomass yield. At low salinity, by-products (mainly gluconate, pyruvate, and acetate) accumulate extracellularly. Using [1-(13)C]-, [2-(13)C]-, [6-(13)C]-, and [U-(13)C6]glucose as carbon sources, we were able to determine the main central metabolic pathways involved in ectoines biosynthesis from glucose. C. salexigens uses the Entner-Doudoroff pathway rather than the standard glycolytic pathway for glucose catabolism, and anaplerotic activity is high to replenish the TCA cycle with the intermediaries withdrawn for ectoines biosynthesis. Metabolic flux ratios at low and high salinity were similar, revealing a certain metabolic rigidity, probably due to its specialization to support high biosynthetic fluxes and partially explaining why metabolic yields are so highly affected by salinity. This work represents an important contribution to the elucidation of specific metabolic adaptations in compatible solute-accumulating halophilic bacteria.

Acetate scavenging activity in Escherichia coli: interplay of acetyl-CoA synthetase and the PEP-glyoxylate cycle in chemostat cultures.

Impairment of acetate production in Escherichia coli is crucial for the performance of many biotechnological processes. Aerobic production of acetate (or acetate overflow) results from changes in the expression of central metabolism genes. Acetyl-CoA synthetase scavenges extracellular acetate in glucose-limited cultures. Once converted to acetyl-CoA, it can be catabolized by the tricarboxylic acid cycle or the glyoxylate pathway. In this work, we assessed the significance of these pathways on acetate overflow during glucose excess and limitation. Gene expression, enzyme activities, and metabolic fluxes were studied in E. coli knock-out mutants related to the glyoxylate pathway operon and its regulators. The relevance of post-translational regulation by AceK-mediated phosphorylation of isocitrate dehydrogenase for pathway functionality was underlined. In chemostat cultures performed at increasing dilution rates, acetate overflow occurs when growing over a threshold glucose uptake rate. This threshold was not affected in a glyoxylate-pathway-deficient strain (lacking isocitrate lyase, the first enzyme of the pathway), indicating that it is not relevant for acetate overflow. In carbon-limited chemostat cultures, gluconeogenesis (maeB, sfcA, and pck), the glyoxylate operon and, especially, acetyl-CoA synthetase are upregulated. A mutant in acs (encoding acetyl-CoA synthetase) produced acetate at all dilution rates. This work demonstrates that, in E. coli, acetate production occurs at all dilution rates and that overflow is the result of unbalanced synthesis and scavenging activities. The over-expression of acetyl-CoA synthetase by cAMP-CRP-dependent induction limits this phenomenon in cultures consuming glucose at low rate, ensuring the recycling of the acetyl-CoA and acetyl-phosphate pools, although establishing an energy-dissipating substrate cycle.

cAMP-CRP co-ordinates the expression of the protein acetylation pathway with central metabolism in Escherichia coli.

Lysine acetylation is a well-established post-translational modification widely conserved and distributed in bacteria. Although multiple regulatory roles have been proved, little is known about its regulation. Here, we present evidence that the transcription of the Gcn5-like acetyltransferase YfiQ of Escherichia coli (proposed name: PatZ) is regulated by cAMP-CRP and its implications on acetate metabolism regulation. The acetate scavenging acetyl-CoA synthetase (Acs) is regulated at the transcriptional and post-translational levels. Post-translational regulation depends on a protein acetyltransferase (yfiQ) and an NAD(+) -dependent deacetylase (cobB). We have studied their expression under different environmental conditions. cobB is constitutively expressed from a promoter located upstream nagK. The expression of yfiQ occurs from its own promoter; it is upregulated in the stationary phase and in the presence of non-PTS carbon sources and is positively regulated by cAMP-CRP. Two putative CRP binding sites are necessary for its full activity. Gene deletion revealed that cobB is essential for growth on acetate, yfiQ deletion restoring growth of the cobB mutant. The fine tuning of metabolic enzymes results from the integration of multiple mechanisms, and redundant systems may exist. Despite the existence of divergent catabolite repression systems, this may be a conserved strategy common to both Gram-positive and -negative bacteria.

A recyclable enzymatic biodiesel production process in ionic liquids.

Immobilized Candida antarctica lipase B suspended in ionic liquids containing long alkyl-chain cations showed excellent synthetic activity and operational stability for biodiesel production. The interest of this process lies in the possibility of recycling the biocatalyst and the easy separation of the biodiesel from the reaction mixture. The ionic liquids used, 1-hexadecyl-3-methylimidazolium triflimide ([C(16)MIM][NTf(2)]) and 1-octadecyl-3-methylimidazolium triflimide ([C(18)MIM][NTf(2)]), produced homogeneous systems at the start of the reaction and, at the end of the same, formed a three-phase system, allowing the selective extraction of the products using straightforward separation techniques, and the recycling of both the ionic liquid and the enzyme. These are very important advantages which may be found useful in environmentally friendly production conditions.

Ectoines in cell stress protection: uses and biotechnological production.

Microorganisms produce and accumulate compatible solutes aiming at protecting themselves from environmental stresses. Among them, the wide spread in nature ectoines are receiving increasing attention by the scientific community because of their multiple applications. In fact, increasing commercial demand has led to a multiplication of efforts in order to improve processes for their production. In this review, the importance of current and potential applications of ectoines as protecting agents for macromolecules, cells and tissues, together with their potential as therapeutic agents for certain diseases are analyzed and current theories for the understanding of the molecular basis of their biological activity are discussed. The genetic, biochemical and environmental determinants of ectoines biosynthesis by natural and engineered producers are described. The major limitations of current bioprocesses used for ectoines production are discussed, with emphasis on the different microorganisms, environments, molecular engineering and fermentation strategies used to optimize the production and recovery of ectoines. The combined application of both bioprocess and metabolic engineering strategies, allowing a deeper understanding of the main factors controlling the production process is also stated. Finally, this review aims to summarize and update the state of the art in ectoines uses and applications and industrial scale production using bacteria, emphasizing the importance of reactor design and operation strategies, together with the metabolic engineering aspects and the need for feedback between wet and in silico work to optimize bioproduction.

An insight into the role of phosphotransacetylase (pta) and the acetate/acetyl-CoA node in Escherichia coli.

BACKGROUND: Acetate metabolism in Escherichia coli plays an important role in the control of the central metabolism and in bioprocess performance. The main problems related to the use of E. coli as cellular factory are i) the deficient utilization of carbon source due to the excretion of acetate during aerobic growth, ii) the inhibition of cellular growth and protein production by acetate and iii) the need for cofactor recycling (namely redox coenzymes and free CoASH) to sustain balanced growth and cellular homeostasis. RESULTS: This work analyzes the effect of mutations in the acetate excretion/assimilation pathways, acetyl-CoA synthethase (acs) and phosphotransacetylase (pta), in E. coli BW25113 grown on glucose or acetate minimal media. Biomass and metabolite production, redox (NADH/NAD+) and energy (ATP) state, enzyme activities and gene expression profiles related to the central metabolism were analyzed. The knock-out of pta led to a more altered phenotype than that of acs. Deletion of pta reduced the ability to grow on acetate as carbon source and strongly affected the expression of several genes related to central metabolic pathways. CONCLUSION: Results showed that pta limits biomass yield in aerobic glucose cultures, due to acetate production (overflow metabolism) and its inefficient use during glucose starvation. Deletion of pta severely impaired growth on acetate minimal medium and under anaerobiosis due to decreased acetyl-coenzyme A synthethase, glyoxylate shunt and gluconeogenic activities, leading to lower growth rate. When acetate is used as carbon source, the joint expression of pta and acs is crucial for growth and substrate assimilation, while pta deletion severely impaired anaerobic growth. Finally, at an adaptive level, pta deficiency makes the strain more sensitive to environmental changes and de-regulates the central metabolism.

On the nature of ionic liquids and their effects on lipases that catalyze ester synthesis.

Free and immobilized lipases from Candida antarctica (CALA and CALB), Thermomyces lanuginosus (TLL) and Rhizomucor miehei (RML) were used as catalysts in the synthesis of butyl propionate by transesterification in reaction media consisting in nine different ionic liquids. Enzyme activities were clearly dependent on the nature of the ions, the results being improving as the alkyl chain length of the imidazolium cation increased, and as a function of the type of anion ([PF(6)], [BF(4)] or [ethylsulphate]). The best synthetic activity (655.5U/mg protein at 40 degrees C) was obtained when free CALB were assayed in the water-miscible IL cocosalkyl pentaethoxy methyl ammonium methosulfate ([CPMA][MS]), and was clearly related with the water content of the medium. The synthetic activity of free CALB in [CPMA][MS] was enhanced with the increase in temperature, while practically no effect was obtained for TLL. The ability of free CALB to synthesize aliphatic esters of different alkyl chain lengths, using different alkyl vinyl esters and 1-alkanols as substrates, was also studied in [CPMA][MS], the best results (4500U/mg protein) being obtained for the synthesis of hexyl butyrate.

Production of L-carnitine by secondary metabolism of bacteria.

The increasing commercial demand for L-carnitine has led to a multiplication of efforts to improve its production with bacteria. The use of different cell environments, such as growing, resting, permeabilized, dried, osmotically stressed, freely suspended and immobilized cells, to maintain enzymes sufficiently active for L-carnitine production is discussed in the text. The different cell states of enterobacteria, such as Escherichia coli and Proteus sp., which can be used to produce L-carnitine from crotonobetaine or D-carnitine as substrate, are analyzed. Moreover, the combined application of both bioprocess and metabolic engineering has allowed a deeper understanding of the main factors controlling the production process, such as energy depletion and the alteration of the acetyl-CoA/CoA ratio which are coupled to the end of the biotransformation. Furthermore, the profiles of key central metabolic activities such as the TCA cycle, the glyoxylate shunt and the acetate metabolism are seen to be closely interrelated and affect the biotransformation efficiency. Although genetically modified strains have been obtained, new strain improvement strategies are still needed, especially in Escherichia coli as a model organism for molecular biology studies. This review aims to summarize and update the state of the art in L-carnitine production using E. coli and Proteus sp, emphasizing the importance of proper reactor design and operation strategies, together with metabolic engineering aspects and the need for feed-back between wet and in silico work to optimize this biotransformation.

Role of wet experiment design in data generation: from in vivo to in silico and back.

A thorough understanding of the in vivo kinetics of microorganisms requires the analysis of different data sets and therefore needs support from different sources of genome, transcriptome, proteome and metabolome data, as well as to generate new data in the laboratory to depict cell phenotypes in different scenarios. The value of dynamic metabolic data depends on the adequate design of wet experiments. In this paper a schematic representation of wet dynamic experiments to generate data is discussed. As a case study, the linking of the central metabolism with the carnitine secondary metabolism in E. coli is presented. The feed-back between the data generated and in silico modeling helps our understanding of the Escherichia coli expressed phenotype and permits new wet experiments to be designed to generate data concerning metabolic optimization.

Plasmid maintenance and physiology of a genetically engineered Escherichia coli strain during continuous L-carnitine production.

The effect of immobilization on cell physiology and how this determines cell metabolic performance is an important concern for developing bioprocess. This is particularly true for genetically modified microorganisms and their genetic stability. For this reason the stability and physiological state of plasmid-bearing E. coli cells were ascertained by flow cytometry. Differences in the cellular DNA and protein content (15-20%) permit discrimination of control and plasmid-bearing cells, as well as adaptation to continuous cultivation conditions in both freely suspended and immobilized states to be monitored. Moreover, the observed metabolic burden due to maintenance and over-expression of plasmid-coded genetic material and slow cell growth in poorly-viable immobilized cells were found to be the main factors contributing to strain stabilization.

Chemoenzymatic dynamic kinetic resolution of rac-1-phenylethanol in ionic liquids and ionic liquids/supercritical carbon dioxide systems.

Continuous dynamic kinetic resolution processes in different ionic liquid/supercritical carbon dioxide biphasic systems were carried out by simultaneously using both immobilized Candida antarctica lipase B (Novozym 435) and silica modified with benzenosulfonic acid (SCX) catalysts at 40 degrees C and 10 MPa. SCX was seen to act as an efficient heterogeneous chemical catalyst for the racemization of (S)-1-phenylethanol in different ionic liquid media ([emim][NTf(2)], [btma][NTf(2)] and [bmim][PF(6)]). Coating both chemical and enzymatic catalysts with ILs greatly improved the efficiency of the process, providing a good yield (76%) of (R)-1-phenylethyl propionate product with excellent enantioselectivity (ee = 91-98%) in continuous operation.

Model of central and trimethylammonium metabolism for optimizing L-carnitine production by E. coli.

The application of metabolic engineering principles to the rational design of microbial production processes crucially depends on the ability to make quantitative descriptions of the systemic ability of the central carbon metabolism to redirect fluxes to the product-forming pathways. The aim of this work was to further our understanding of the steps controlling the biotransformation of trimethylammonium compounds into L-carnitine by Escherichia coli. Despite the importance of L-carnitine production processes, development of a model of the central carbon metabolism linked to the secondary carnitine metabolism of E. coli has been severely hampered by the lack of stoichiometric information on the metabolic reactions taking place in the carnitine metabolism. Here we present the design and experimental validation of a model which, for the first time, links the carnitine metabolism with the reactions of glycolysis, the tricarboxylic acid cycle and the pentose-phosphate pathway. The results demonstrate a need for a high production rate of ATP to be devoted to the biotransformation process. The results demonstrate that ATP is used up in a futile cycle, since both trimethylammonium compound carriers CaiT and ProU operate simultaneously. To improve the biotransformation process, resting processes as well as CaiT or ProU knock out mutants would yield a more efficient system for producing L-carnitine from crotonobetaine or D-carnitine.

Understanding structure-stability relationships of Candida antartica lipase B in ionic liquids.

Two different water-immiscible ionic liquids (ILs), 1-ethyl-3-methylimidizolium bis(trifluoromethylsulfonyl)imide and butyltrimethylammonium bis(trifluoromethylsulfonyl)imide, were used for butyl butyrate synthesis from vinyl butyrate catalyzed by Candida antarctica lipase B (CALB) at 2% (v/v) water content and 50 degrees C. Both the synthetic activity and stability of the enzyme in these ILs were enhanced as compared to those in hexane. Circular dichroism and intrinsic fluorescence spectroscopic techniques have been used over a period of 4 days to determine structural changes in the enzyme associated with differences in its stability for each assayed medium. CALB showed a loss in residual activity higher than 75% after 4 days of incubation in both water and hexane media at 50 degrees C, being related to great changes in both alpha-helix and beta-strand secondary structures. The stabilization of CALB, which was observed in the two ILs studied, was associated with both the maintenance of the 50% of initial alpha-helix content and the enhancement of beta-strands. Furthermore, intrinsic fluorescence studies clearly showed how a classical enzyme unfolding was occurring with time in both water and hexane media. However, the structural changes associated with the incubation of the enzyme in both ILs might be attributed to a compact and active enzyme conformation, resulting in an enhancement of the stability in these nonaqueous environments.

Fluorescence and CD spectroscopic analysis of the alpha-chymotrypsin stabilization by the ionic liquid, 1-ethyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]amide.

The stability of alpha-chymotrypsin in the ionic liquid, 1-ethyl-3-methyl-imidizolium bis[(trifluoromethyl)sulfonyl]amide ([emim][NTf2]), was studied at 30 and 50 degrees C and compared with the stability in other liquid media, such as water, 3 M sorbitol, and 1-propanol. The kinetic analysis of the enzyme stability pointed to the clear denaturative effect of 1-propanol, while both 3M sorbitol and [emim][NTf2] displayed a strong stabilizing power. For the first time, it is shown that enzyme stabilization by ionic liquids seems to be related to the associated structural changes of the protein that can be observed by differential scanning calorimetry (DSC) and fluorescence and circular dichroism (CD). The [emim][NTf2] enhanced both the melting temperature and heat capacity of the enzyme compared to the other media assayed. The fluorescence spectra clearly showed the ability of [emim][NTf2] to compact the native structural conformation of alpha-chymotrypsin, preventing the usual thermal unfolding which occurs in other media. Changes in the secondary structure of this beta/beta protein, as quantified by the CD spectra, pointed to the great enhancement (up 40% with respect to that in water) of beta-strands in the presence of the ionic liquid, which reflects its stabilization power.

Criteria to design green enzymatic processes in ionic liquid/supercritical carbon dioxide systems.

Five different ionic liquids (ILs) based on quaternary ammonium cations, with functional side chains ((3-hydroxypropyl)-trimethyl-, (3-cyanopropyl)-trimethyl-, butyl-trimethyl-, (5-cyanopentyl)-trimethyl- and hexyl-trimethyl-) associated with the same anion (bis(trifluoromethane)sulfonyl amide)), were synthesized, and their suitability for Candida antarctica lipase B (CALB)-catalyzed ester synthesis in IL/supercritical carbon dioxide (scCO(2)) biphasic systems was assayed. Catalytic efficiency of the system has been analyzed as a function of both enzyme properties and mass-transfer phenomena criteria. First, the suitability of these ILs as enzymic reaction media was tested for the kinetic resolution of rac-phenylethanol. All ILs were found to be suitable media for enzyme catalysis, the best catalytic parameter (5.3 U/mg specific activity, 94.9% selectivity) being obtained for the (5-cyanopentyl)-trimethylammonium. Second, enzyme stability in all of the ILs was studied at 50 degrees C over a period of 50 days, and data were analyzed by a two-step kinetic deactivation model. All of the ILs were shown to act as stabilizing agents with respect to hexane, producing an increase in the free energy of deactivation (to 25 kJ/mol protein) and an improvement in the half-life time of the enzyme (2000-fold), which agrees with the observed increased hydrophobicity of the cation alkyl side chain (measured by Hansen's solubility parameter, delta). By using two different CALB-IL systems with different hydrophobicity in the cation, continuous processes to synthesize six different short chain alkyl esters (butyl acetate, butyl propionate, butyl butyrate, hexyl propionate, hexyl butyrate, and octyl propionate) in scCO(2) at 10 MPa and 50 degrees C were carried out. Both rate-limiting parameters (synthetic activity and scCO(2)-ILs mass-transfer phenomena) were related with the delta-parameter of the ILs-alkyl chain and reagents.

Kinetic resolution of rac-2-pentanol catalyzed by Candida antarctica lipase B in the ionic liquid, 1-butyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]amide.

The ionic liquid, l-butyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]amide ([Bmim] [NTf2]), was used as a reaction medium for the kinetic resolution of rac-2-pentanol catalyzed by free Candida antarctica lipase B, using vinyl propionate at 2% (v/v) water content. The synthetic activity of lipase in [Bmim] [NTf2] was up 2.5-times greater than in hexane, and showed high enantioselectivity (ee > 99.99%). The optimal temperature and pH were 60 degrees C and 7, respectively. A decrease in water activity (aw) produced a decay in synthetic activity, and an exponential increase in selectivity.

Culture collections and biochemistry / Colecciones de cultivos y bioquímica

This review describes the relationships and links between culture collections, which act as sources of genomes, transcriptomes, proteome, and metabolomes, and fields of research biochemistry that demand their support and help. In addition, the invaluable but not always rewarded efforts of these organizations as a source and conservator of organism diversity is discussed. Biological waste-water treatment, ethanol as a non-finite source of energy, Rhodococcus fascians as the source of a citrus-juice debittering agent, the sporulation of filamentous fungi in liquid medium, and biotransformation with growing and resting cells are processes developed by the authors that demonstrate some of the applications of organisms from culture collections in the general field of biotechnology and related areas, including industrial biochemistry and biocatalytic synthesis (AU)

Esta revisión describe las relaciones existentes entre las colecciones de cultivos y las diferentes áreas de investigación en bioquímica que precisan de la ayuda de estos centros de recursos biológicos, que actúan como fuentes de genomas, transcriptomas, proteomas y metabolomas. Se describen los esfuerzos impagables y no siempre reconocidos de estas organizaciones como fuentes de diversidad microbiana y de conservación de dicha diversidad. Se comentan algunos ejemplos de procesos desarrollados por los autores que muestran algunos posibles usos de los organismos almacenados en las colecciones de cultivos en biotecnología y áreas relacionadas, como la bioquímica industrial y la síntesis biocatalítica. Estos ejemplos incluyen el tratamiento biológico de las aguas residuales, la producción de etanol como fuente de energía no finita, la utilización de Rhodococcus fascians para contrarrestar la acidez del zumo de cítricos, la esporulación de hongos filamentosos en medio líquido o la biotransformación mediante células en crecimiento o en estado latente (AU)

Culture collections and biochemistry.

This review describes the relationships and links between culture collections, which act as sources of genomes, transcriptomes, proteome, and metabolomes, and fields of research biochemistry that demand their support and help. In addition, the invaluable but not always rewarded efforts of these organizations as a source and conservator of organism diversity is discussed. Biological waste-water treatment, ethanol as a non-finite source of energy, Rhodococcus fascians as the source of a citrus-juice debittering agent, the sporulation of filamentous fungi in liquid medium, and biotransformation with growing and resting cells are processes developed by the authors that demonstrate some of the applications of organisms from culture collections in the general field of biotechnology and related areas, including industrial biochemistry and biocatalytic synthesis.

Lipase catalysis in ionic liquids and supercritical carbon dioxide at 150 degrees C.

Free and immobilized Candida antarctica lipase B dispersed in ionic liquids (1-ethyl-3-methylimidazolium bistriflimide and 1-buthyl-3-methylimidazolium bistriflimide) were used as catalyst for the continuous kinetic resolution of rac-1-phenylethanol in supercritical carbon dioxide at 120 and 150 degrees C and 10 MPa. Excellent activity, stability and enantioselectivity levels were recorded in continuous operation.

Ester synthesis from trimethylammonium alcohols in dry organic media catalyzed by immobilized Candida antarctica lipase B.

Twenty-one different organic solvents were assayed as possible reaction media for the synthesis of butyryl esters from trimethylammonium alcohols in dry conditions catalyzed by immobilized Candida antarctica lipase B. The reactions were carried out following a transesterification kinetic approach, using choline and L-carnitine as primary and secondary trimethylammonium alcohols, respectively, and vinyl butyrate as acyl donor. The synthetic activity of the enzyme was strictly dependent on the water content, the position of the hydroxyl group in the trimethylammonium molecule, and the Log P parameter of the assayed solvent. Anhydrous conditions and a high excess of vinyl butyrate over L-carnitine were necessary to synthesize butyryl-L-carnitine. The synthetic reaction rates of butyryl choline were practically 100-fold those of butyryl-L-carnitine with all the assayed solvents. In both cases, the synthetic activity of the enzyme was dependent on the hydrophobicity of the solvent, with the optimal reaction media showing a Log P parameter of between -0.5 and 0.5. In all cases, 2-methyl-2-propanol and 2-methyl-2-butanol were shown to be the best solvents for both their high synthetic activity and negligible loss of enzyme activity after 6 days.