Pantothenate auxotrophy of Methylobacterium spp. isolated from living plants

A number of pink-pigmented facultative methylotrophs (PPFMs) belonging to Methylobacterium spp. isolated from living plant samples were found to require B vitamins for their growth in minimal medium, and most B vitamin-auxotrophic PPFMs required pantothenate (vitamin B_⁵). Further investigation of pantothenate auxotrophy using the representative strain Methylobacterium sp. OR01 demonstrated that this strain cannot synthesize β-alanine, one of the precursors of pantothenate. β-alanine and several precursors of pantothenate restored the growth of Methylobacterium sp. OR01 in minimal medium. Furthermore, this strain could colonize leaves of Arabidopsis thaliana cultivated in medium without pantothenate or its precursors. Pantothenate, β-alanine and several precursors were detected in the suspension of A. thaliana leaves. These results suggest that pantothenate-auxotrophic PPFMs can symbiotically colonize the surface of plant leaves by acquiring β-alanine and other precursors, in addition to pantothenate. Finally, the fitness advantage of B vitamin auxotrophy of PPFMs in the phyllosphere environment is discussed.     

Reaction intermediate analogues as bisubstrate inhibitors of pantothenate synthetase

The biosynthesis of pantothenate, the core of coenzyme A (CoA), has been considered an attractive target for the development of antimicrobial agents since this pathway is essential in prokaryotes, but absent in mammals. Pantothenate synthetase, encoded by the gene panC, catalyzes the final condensation of pantoic acid with β-alanine to afford pantothenate via an intermediate pantoyl adenylate. We describe the synthesis and biochemical characterization of five PanC inhibitors that mimic the intermediate pantoyl adenylate. These inhibitors are competitive inhibitors with respect to pantoic acid and possess submicromolar to micromolar inhibition constants. The observed SAR is rationalized through molecular docking studies based on the reported co-crystal structure of 1a with PanC. Finally, whole cell activity is assessed against wild-type Mtb as well as a PanC knockdown strain where PanC is depleted to less than 5% of wild-type levels.     

The effects of pantothenate deficiency and acetate addition on anaerobic batch fermentation of glucose by Saccharomyces cerevisiae

 Physiological effects of deficiency of pantothenate, a necessary precursor in the synthesis of coenzyme A, were studied using the yeast strain Saccharomyces cerevisiae CBS 8066. Cells were grown on defined media in anaerobic batch cultures with glucose (50 g/l) as the carbon and energy source. Batch cultures containing more than 60 μg/l pantothenate showed no significant differences with respect to growth rates and product yields. However, with an initial pantothenate concentration of 30 μg/l, the average glucose consumption rate was 50% lower than in rich medium and, at even lower concentrations of pantothenate, the culture did not consume all the glucose in the medium. Furthermore, pantothenate deficiency caused the acetate and pyruvate yields to increase and the biomass yield to decrease, compared to the yields in pantothenate-rich medium. The increased acetate formation could be counteracted by initial addition of acetate to the medium, and thereby the glycerol yield could be decreased. An initial addition of acetate of 1.6 g/l to pantothenate-deficient medium (30 μg/l) caused a 35% decrease in glycerol yield and a 6% increase in ethanol yield. Furthermore, the time required for complete conversion of the glucose decreased by 40%. Acetate addition affected the acetate and glycerol yields in a similar way in pantothenate-rich medium (1000 μg/l) also. Received: 27 December 1995/Received revision: 3 May 1996/Accepted: 9 May 1996     

Semisynthetic culture medium for growth and dihydroxyacetone production by Gluconobacter oxydans

Only three vitamins (pantothenate, p-amino benzoic acid, nicotinic acid) and two amino acids (serine, glutamine) were required in the growth medium for Gluconobacter oxydans which allowed the concentration of yeast extract to be reduced to 5–10% of the previous concentration. When compared with data from cultivations with complex media, the new medium gave a lower yield (about 0.02 g biomass per g glycerol) and comparable growth rate (0.24 to 0.38 h–1) but a higher productivity (10.3 g dihydroxyacetone/gh).     

Optimization of ethanol production in Saccharomyces cerevisiae by metabolic engineering of the ammonium assimilation

Ethanol is still one of the most important products originating from the biotechnological industry with respect to both value and amount. In addition to ethanol, a number of byproducts are formed during an anaerobic fermentation of Saccharomyces cerevisiae. One of the most important of these compounds, glycerol, is produced by yeast to reoxidize NADH, formed in synthesis of biomass and secondary fermentation products, to NAD+. The purpose of this study was to evaluate whether a reduced formation of surplus NADH and an increased consumption of ATP in biosynthesis would result in a decreased glycerol yield and an increased ethanol yield in anaerobic cultivations of S. cerevisiae. A yeast strain was constructed in which GLN1, encoding glutamine synthetase, and GLT1, encoding glutamate synthase, were overexpressed, and GDH1, encoding the NADPH-dependent glutamate dehydrogenase, was deleted. Hereby the normal NADPH-consuming synthesis of glutamate from ammonium and 2-oxoglutarate was substituted by a new pathway in which ATP and NADH were consumed. The resulting strain TN19 (gdh1-A1 PGK1p-GLT1 PGK1p-GLN1) had a 10% higher ethanol yield and a 38% lower glycerol yield compared to the wild type in anaerobic batch fermentations. The maximum specific growth rate of strain TN19 was slightly lower than the wild-type value, but earlier results suggest that this can be circumvented by increasing the specific activities of Gln1p and Glt1p even more. Thus, the results verify the proposed concept of increasing the ethanol yield in S. cerevisiae by metabolic engineering of pathways involved in biomass synthesis.     

Metabolic flux distribution for γ-linolenic acid synthetic pathways in<Emphasis Type="Italic">Spirulina platensis</Emphasis>

Spirulina produces γ-linolenic acid (GLA), an important pharmaceutical substance, in a relatively low level compared with fungi and plants, prompting more research to improve its GLA yield. In this study, metabolic flux analysis was applied to determine the cellular metabolic flux distributions in the GLA synthetic pathways of twoSpirulina strains, wild type BP and a high-GLA producing mutant Z19/2. Simplified pathways involving the GLA synthesis ofS. platensis formulated comprise of photosynthesis, gluconeogenesis, the pentose phosphate pathway, the anaplerotic pathway, the tricarboxylic cycle, the GLA synthesis pathway, and the biomass synthesis pathway. A stoichiometric model reflecting these pathways contains 17 intermediates and 22 reactions. Three fluxes—the bicarbonate (C-source) uptake rate, the specific growth rate, and the GLA synthesis rate—were measured and the remaining fluxes were calculated using linear optimization. The calculation showed that the flux through the reaction converting acetyl-CoA into malonyl-CoA in the mutant strain was nearly three times higher than that in the wild-type strain. This finding implies that this reaction is rate controlling. This suggestion was supported by experiments, in which the stimulating factors for this reaction (NADPH and MgCl₂) were added into the culture medium, resulting in an increased GLA-synthesis rate in the wild type strain.     

Relationship between astaxanthin production and the intensity of anabolic processes in the yeast <Emphasis Type="Italic">Phaffia rhodozyma</Emphasis>

The astaxanthin synthesis in the yeast Phaffia rhodozyma was shown to depend on the rate of growth occurring in the first two days of cultivation. The growth rate of the yeast culture studied was preset by the cultivation conditions, among which the C : N ratio was decisive. The intense anabolic processes coupled with active culture growth during the first 24 h significantly inhibited the synthesis of the key enzymes involved in astaxanthin synthesis, which led to a marked decrease in the carotenoid production. It was demonstrated that, for the maximum yield of astaxanthin to be obtained from 1 l of nutrient medium, it is necessary to carry out cultivation, beginning with the first day, at a growth rate significantly lower than µ_max. The optimum budding rate of the mutant strain Ph. rhodozyma VKPM Y-2409 consistent with the maximum astaxanthin synthesis was determined. The specific astaxanthin productivity of the strain studied was about 7.0 mg/g of dry biomass at a budding rate of <0.5.Translated from Mikrobiologiya, Vol. 73, No. 6, 2004, pp. 751–757.Original Russian Text Copyright © 2004 by Vustin, Belykh, Kishilova.     

Pantothenate and coenzyme A in bacterial growth

Toennies, G. (Temple University School of Medicine, Philadelphia, Pa.), D. N. Das, and F. Feng. Pantothenate and coenzyme A in bacterial growth. J. Bacteriol. 92:707-713. 1966.-The effect of environmental pantothenate levels on the growth of Streptococcus faecalis 9790 was studied in terms of growth rate, depletion phenomena, cellular coenzyme A (CoA) content, and differential rates of wall and membrane synthesis. Low concentrations of pantothenate yielded normal exponential growth curves up to peak turbidities which are a function of pantothenate concentration. Attainment of these peaks was followed by lysis. Under such conditions, bacterial CoA increased initially in proportion with cell substance, but attained a peak level much earlier than cell substance, and then gradually decreased down to vanishing amounts. With higher pantothenate concentrations, cellular CoA levels increased to a maximum, and, under these conditions, the CoA content remained constant during exponential growth. Four-fifths of the pantothenate requirement of growing cells was eliminated by environmental oleate and palmitate. When CoA disappeared during growth on low pantothenate levels, cell wall synthesis seemed to continue at nearly normal rates, but membrane synthesis was severely curtailed. The data suggest that in fermentative organisms pantothenate action might be confined to wall and membrane synthesis, that these two processes differ in their quantitative dependence on pantothenate, and that pantothenate might occur in the form of acyl carrier protein as well as CoA.     

SECRETION OF VITAMINS AND AMINO ACIDS INTO THE ENVIRONMENT BY OCHROMONAS DANICA1,2

Ochromonas danica grown on a chemically defined medium under controlled conditions in the light synthesized the following vitamins: ascorbate, B₆, N⁵-methyltetrahydrofolate, tetrahydrofolate polyglutamates, oxidized folate monoglutamates, nicotinate, pantothenate, riboflavin, vitamin A, β-carotene, and vitamin E but no vitamin. B₁₂. The cells also secreted molecules into their growth medium including the vitamins ascorbate, B₆, the above folates, nicotinate, pantothenate, riboflavin, vitamin E, and the amino acids alanine, aspartic acid, leucine, and valine. The role of such secretions in nature is discussed.     

Preparation of high-specific-activity D-[3-3H]pantothenic acid

High-specific-activity D-[3-3H]pantothenic acid (5 Ci/mmol) was prepared from commercially available beta-[3-3H]alanine employing Escherichia coli strain DV1 (panD2 pan F1). This strain is defective in beta-alanine synthesis and pantothenate uptake, and under appropriate growth conditions converted 85 to 90% of the input beta-[3-3H]alanine to extracellular D-[3-3H]pantothenate. The radiolabeled vitamin was purified from the medium by thin-layer chromatography followed by reverse-phase high-performance liquid chromatography. The overall yield of D-[3-3H]pantothenic acid was 30% and radiochemical purity was greater than 99%.     

Maintenance energy demand affects biomass synthesis but not cellulase production by a mesophilicClostridium

Summary Secretion of cellulolytic activity by the mesophilClostridium strain C7 was studied while the bacterium underwent progressive carbon/energy starvation and the ensuing continuous decline in growth rate. In the slowest range of growth rates studied the organism was in full response to the global regulation imposed by guanosine 5, 3-bispyrophosphate (ppGpp). The exoenzymes of the cellulase complex were produced at the same volumetric rate whether or not the response was active. However, the volumetric rate of biomass synthesis was reduced 45% or more by the response. Energy necessary to maintain the ppGpp-regulated state (i.e., maintenance energy) was, therefore, diverted from energy going to synthesis of biomass but not from that going to exoenzyme synthesis, making the yield of cellulase activity per mole of carbon-energy substrate independent of growth rate and the exoenzyme complex produced from the substrate with equal efficiency at all growth rates. The primary consideration in improving exoenzyme productivity by bacteria with this type of energy distribution between secretion, growth, and maintenance is simply increasing yield per mole of carbon-energy substrate, with growth rate effects on yield a secondary and minimum concern.     

Mutant selection and phenotypic and genetic characterization of ethanol-tolerant strains of <Emphasis Type="Italic">Clostridium thermocellum</Emphasis>

Clostridium thermocellum is a model microorganism for converting cellulosic biomass into fuels and chemicals via consolidated bioprocessing. One of the challenges for industrial application of this organism is its low ethanol tolerance, typically 1–2% (w/v) in wild-type strains. In this study, we report the development and characterization of mutant C. thermocellum strains that can grow in the presence of high ethanol concentrations. Starting from a single colony, wild-type C. thermocellum ATCC 27405 was sub-cultured and adapted for growth in up to 50 g/L ethanol using either cellobiose or crystalline cellulose as the growth substrate. Both the adapted strains retained their ability to grow on either substrate and displayed a higher growth rate and biomass yield than the wild-type strain in the absence of ethanol. With added ethanol in the media, the mutant strains displayed an inverse correlation between ethanol concentration and growth rate or biomass yield. Genome sequencing revealed six common mutations in the two ethanol-tolerant strains including an alcohol dehydrogenase gene and genes involved in arginine/pyrimidine biosynthetic pathway. The potential role of these mutations in ethanol tolerance phenotype is discussed.     

Pantothenate limitation does not induce uncoupled growth of Zymomonas in chemostat culture

Summary Growth coefficients ofZymomonas mobilis were compared in glucose-limited chemostat culture using a complex medium and a defined minimal growth medium at non inhibitory concentrations of ethanol. Under carbon and energy limited conditions in the complex medium containing yeast extract, the max. molar growth yield (Y_G ^max) and maintenance energy coefficient (m_e) were 10.8 g cell/mol glucose and 8.3 mmol glu/g cell/hr, respectively. Glucose-limited growth in the minimal medium with NH₄Cl as nitrogen source promoted slight energetic uncoupling, as reflected in the decrease in the maximum growth yield. The growth yield with respect to calcium pantothenate was calculated to be 1.4×10⁴ g cell/g Ca-pantothenate. However, pantothenate-limited growth did not result in a decrease in growth yield nor an increase in the specific rate of glucose catabolism. Steady-state growth measurements failed to confirm the previously held view of Belaïchet al. (1972) that pantothenate deficiency induces energetic uncoupling inZymomonas.     

Biosynthesis and degradation both contribute to the regulation of coenzyme A content in Escherichia coli.

Escherichia coli mutants [coaA16(Fr); Fr indicates feedback resistance] were isolated which possessed a pantothenate kinase activity that was refractory to feedback inhibition by coenzyme A (CoA). Strains harboring this mutation had CoA levels that were significantly elevated compared with strains containing the wild-type kinase and also overproduced both intra- and extracellular 4'-phosphopantetheine. The origin of 4'-phosphopantetheine was investigated by using strain SJ135 [panD delta(aroP-aceEF)], in which synthesis of acetyl-CoA was dependent on the addition of an acetate growth supplement. Rapid degradation of CoA to 4'-phosphopantetheine was triggered by the conversion of acetyl-CoA to CoA following the removal of acetate from the media. CoA hydrolysis under these conditions appeared not to involve acyl carrier protein prosthetic group turnover since [acyl carrier protein] phosphodiesterase was inhibited equally well by acetyl-CoA or CoA. These data support the view that the total cellular CoA content is controlled by modulation of biosynthesis at the pantothenate kinase step and by degradation of CoA to 4'-phosphopantetheine.     

Metabolic Basis for the Isoleucine, Pantothenate or Methionine Requirement of ilvG Strains of Salmonella typhimurium

Salmonella typhimurium strain DU501, which was found to be deficient in acetohydroxy acid synthase II (AHAS II) and to possess elevated levels of transaminase B and biosynthetic threonine deaminase, required isoleucine, methionine, or pantothenate for growth. This strain accumulated α-ketobutyrate and, to a lesser extent, α-aminobutyrate. We found that α-ketobutyrate was a competitive substrate for ketopantoate hydroxymethyltransferase, the first enzyme in pantothenate biosynthesis. This competition with the normal substrate, α-ketoisovalerate, limited the supply of pantothenate, which resulted in a requirement for methionine. Evidence is presented to support the conclusion that the ambivalent requirement for either pantothenate or methionine is related to a decrease in succinyl coenzyme A, which is produced from pantothenate and which is an obligatory precursor of methionine biosynthesis. The autointoxification by endogenously produced α-ketobutyrate could be mimicked in wild-type S. typhimurium by exogenously supplied α-ketobutyrate or salicylate, a known inhibitor of pantothenate biosynthesis. The accumulation of α-ketobutyrate was initiated by the inability of the residual AHAS activity provided by AHAS I to efficiently remove the α-ketobutyrate produced by biosynthetic threonine deaminase. The accumulation of α-ketobutyrate was amplified by the action of transaminase B, which decreased the isoleucine pool by catalyzing the formation of α-keto-β-methylvalerate and aminobutyrate from isoleucine and α-ketobutyrate; this resulted in release of threonine deaminase from end product inhibition and unbridled production of α-ketobutyrate. Isoleucine satisfied the auxotrophic requirement of the AHAS II-deficient strain by curtailing the activity of threonine deaminase. Additional lines of evidence based on genetic and physiological experiments are presented to support the basis for the autointoxification of strain DU501 as well as other nonpolarigenic ilvG mutant strains.     

Microbial maximal specific growth rate as a square-root function of biomass yield and two kinetic parameters

Understanding how growth rates changes under different perturbations is fundamental to many aspect of microbial physiology. In this work, we experimentally showed that maximal specific growth rate is a square-root function of the biomass yield, the substrate turnover number, and the maximum synthesis rate of the substrate transporter under that condition. We used Escherichia coli cultures in lactose minimal medium as a model system by introducing genetic modifications, in vitro evolution, and ethanol stress to the cell. Deletion of crr affected all three parameters in different directions while deletion of ptsG decreased only the biomass yield. Ethanol stress negatively impacted all three parameters, while anaerobicity decreased biomass yield and transporter synthesis rate. In addition, laboratory evolution increased the growth rate in lactose mostly through enhancing the expression rate of the lac operon. Despite all these changes, the growth rate of the perturbed strain was successfully related to the three parameters by the square-root equation. Thus, this square-root relationship provides insight into how growth rate is altered by different physiological parameters.     

Physiology and metabolic fluxes of wild-type and riboflavin-producing Bacillus subtilis.

Continuous cultivation in a glucose-limited chemostat was used to determine the growth parameters of wild-type Bacillus subtilis and of a recombinant, riboflavin-producing strain. Maintenance coefficients of 0.45 and 0.66 mmol of glucose g-1 h-1 were determined for the wild-type and recombinant strains, respectively. However, the maximum molar growth yield of 82 to 85 g (cell dry weight)/mol of glucose was found to be almost identical in both strains. A nonlinear relationship between the specific riboflavin production rate and the dilution rate was observed, revealing a coupling of product formation and growth under strict substrate-limited conditions. Most prominently, riboflavin formation completely ceased at specific growth rates below 0.15 h-1. For molecular characterization of B. subtilis, the total amino acid composition of the wild type was experimentally determined and the complete building block requirements for biomass formation were derived. In particular, the murein sacculus was found to constitute approximately 9% of B. subtilis biomass, three- to fivefold more than in Escherichia coli. Estimation of intracellular metabolic fluxes by a refined mass balance approach revealed a substantial, growth rate-dependent flux through the oxidative branch of the pentose phosphate pathway. Furthermore, this flux is indicated to be increased in the strain engineered for riboflavin formation. Glucose catabolism at low growth rates with reduced biomass yields was supported mainly by the tricarboxylic acid cycle.     

Influence of quorum sensing and iron on twitching motility and biofilm formation in Pseudomonas aeruginosa

Reducing iron (Fe) levels in a defined minimal medium reduced the growth yields of planktonic and biofilm Pseudomonas aeruginosa, though biofilm biomass was affected to the greatest extent and at FeCl₃ concentrations where planktonic cell growth was not compromised. Highlighting this apparently greater need for Fe, biofilm growth yields were markedly reduced in a mutant unable to produce pyoverdine (and, so, deficient in pyoverdine-mediated Fe acquisition) at concentrations of FeCl₃ that did not adversely affect biofilm yields of a pyoverdine-producing wild-type strain. Concomitant with the reduced biofilm yields at low Fe concentrations, P. aeruginosa showed enhanced twitching motility in Fe-deficient versus Fe-replete minimal media. A mutant deficient in low-Fe-stimulated twitching motility but normal as regards twitching motility on Fe-rich medium was isolated and shown to be disrupted in rhlI, whose product is responsible for synthesis of the N-butanoyl homoserine lactone (C4-HSL) quorum-sensing signal. In contrast to wild-type cells, which formed thin, flat, undeveloped biofilms in Fe-limited medium, the rhlI mutant formed substantially developed though not fully mature biofilms under Fe limitation. C4-HSL production increased markedly in Fe-limited versus Fe-rich P. aeruginosa cultures, and cell-free low-Fe culture supernatants restored the twitching motility of the rhlI mutant on Fe-limited minimal medium and stimulated the twitching motility of rhlI and wild-type P. aeruginosa on Fe-rich minimal medium. Still, addition of exogenous C4-HSL did not stimulate the twitching motility of either strain on Fe-replete medium, indicating that some Fe-regulated and RhlI/C4-HSL-dependent extracellular product(s) was responsible for the enhanced twitching motility (and reduced biofilm formation) seen in response to Fe limitation.     

Reduction of the cytosolic fructose-1,6-bisphosphatase in transgenic potato plants limits photosynthetic sucrose biosynthesis with no impact on plant growth and tuber yield

Sucrose produced in source leaves is the predominant carbon source for developing sink tissues in most higher plants. Consequently the rate of sucrose synthesis is likely to be important for sink development and final crop yield. Two sucrose biosynthetic enzymes are believed to possess regulatory properties with respect to the rate of sucrose synthesis: (i) cytosolic FBPase and (ii) sucrose phosphate synthase. To study the impact of reduced photosynthetic sucrose biosynthesis on plant growth and crop yield a cDNA clone encoding cytosolic FBPase was isolated from a potato leaf cDNA library and used for antisense experiments in transgenic potato plants. The cDNA clone cy-F1, containing an open reading frame of 1020 bp highly homologous (85%) to other known sequences of plant cytosolic FBPases, was cloned in reversed orientation between the 35S CaMV promoter and the octopine synthase polyadenylation signal. Out of 75 independent transformants five transgenic lines having 9 to 55% of the wild-type FBPase activity were chosen for further analysis. A 45% reduction of the cytosolic FBPase activity did not cause any measurable change in metabolite concentrations, growth behaviour or photosynthetic parameters of the transgenic plants. Inhibition of cytosolic FBPase activity below 20% of the wild-type activity led to an accumulation of 3-PGA, triose-phosphates and fructose-1,6bisphosphate in source leaves. This resulted in a reduced light-saturated rate of assimilation measured via gas exchange and a decreased photosynthetic rate under conditions of the leaf disc electrode with saturating light and CO₂. Measuring photosynthetic carbon fluxes by labelling leaf discs with ¹⁴CO₂ revealed a 53–65% reduction of sucrose synthesis whereas starch synthesis decreased only by 18–24%. The flux into the anionic and cationic fraction was not altered. Despite these changes steadystate sucrose concentrations were not effected in source leaves from transgenic plants. Starch accumulated by more than a factor of 3 compared with wild-type leaves and was degraded during the night. This provides strong evidence for the hypothesis that hexoses and/or hexosephosphates are exported out of the chloroplasts, thereby circumventing the limitation of sucrose biosynthesis caused by the inhibition of cytosolic FBPase in the dark. Accordingly, plant growth and potato tuber yield remained unaltered. From these data it can be concluded that a reduced photosynthetic sucrose biosynthetic capacity can be efficiently compensated without any reduction in crop yield under greenhouse or growth chamber conditions by changing carbon export strategy. Whether the same holds true for field conditions remains to be elucidated.     

Mutations in sdh (succinate dehydrogenase genes) alter the thiamine requirement of Salmonella typhimurium.

Mutants lacking the first enzyme in de novo purine synthesis (PurF) can synthesize thiamine if increased levels of pantothenate are present in the culture medium (J. L. Enos-Berlage and D. M. Downs, J. Bacteriol. 178:1476-1479, 1996). Derivatives of purF mutants that no longer required pantothenate for thiamine-independent growth were isolated. Analysis of these mutants demonstrated that they were defective in succinate dehydrogenase (Sdh), an enzyme of the tricarboxylic acid cycle. Results of phenotypic analyses suggested that a defect in Sdh decreased the thiamine requirement of Salmonella typhimurium. This reduced requirement correlated with levels of succinyl-coenzyme A (succinyl-CoA), which is synthesized in a thiamine pyrophosphate-dependent reaction. The effect of succinyl-CoA on thiamine metabolism was distinct from the role of pantothenate in thiamine synthesis.