Glucose as an energy donor in acetate growing Acinetobacter calcoaceticus

Bioconversion of 5-Hydroxymethylfurfural (HMF) to 2,5-Furandicarboxylic Acid (FDCA) by a Native Obligate Aerobic Bacterium, Acinetobacter calcoaceticus NL14

2,5-Furandicarboxylic acid (FDCA), one of the top biomass-based platform chemical, is highly promising for resins and polymers, and it can be prepared from the bio-oxidation of hydroxymethyl furfural (HMF), which can be obtained mainly from lignocellulosic glucose that has a high production potential from not edible biomass.A native strain, Acinetobacter calcoaceticus NL14, that could convert HMF into FDCA is used for combining degradation and fermentation by consolidated bioprocessing (CBP). In this study, it was observed that the initial HMF concentration and pH neutralizer played important roles in the bioconversion of HMF, 5 g/L of HMF could be converted by 100% within 48 h with 0.5 g/L sodium carbonate (Na₂CO₃) with the production of 0.31 g/L FDCA. Extra glucose and hydrogen peroxide (H₂O₂) addition could further promote the production of FDCA to 0.54 g/L with 100% HMF conversion and a higher conversion rate. This report could provide a potential native bacterium for furan chemicals bioconversion and bioelimination, especially for FDCA bioproduction.

The complete genome and phenome of a community-acquired Acinetobacter baumannii

Many sequenced strains of Acinetobacter baumannii are established nosocomial pathogens capable of resistance to multiple antimicrobials. Community-acquired A. baumannii in contrast, comprise a minor proportion of all A. baumannii infections and are highly susceptible to antimicrobial treatment. However, these infections also present acute clinical manifestations associated with high reported rates of mortality. We report the complete 3.70 Mbp genome of A. baumannii D1279779, previously isolated from the bacteraemic infection of an Indigenous Australian; this strain represents the first community-acquired A. baumannii to be sequenced. Comparative analysis of currently published A. baumannii genomes identified twenty-four accessory gene clusters present in D1279779. These accessory elements were predicted to encode a range of functions including polysaccharide biosynthesis, type I DNA restriction-modification, and the metabolism of novel carbonaceous and nitrogenous compounds. Conversely, twenty genomic regions present in previously sequenced A. baumannii strains were absent in D1279779, including gene clusters involved in the catabolism of 4-hydroxybenzoate and glucarate, and the A. baumannii antibiotic resistance island, known to bestow resistance to multiple antimicrobials in nosocomial strains. Phenomic analysis utilising the Biolog Phenotype Microarray system indicated that A. baumannii D1279779 can utilise a broader range of carbon and nitrogen sources than international clone I and clone II nosocomial isolates. However, D1279779 was more sensitive to antimicrobial compounds, particularly beta-lactams, tetracyclines and sulphonamides. The combined genomic and phenomic analyses have provided insight into the features distinguishing A. baumannii isolated from community-acquired and nosocomial infections.

Pseudomonas putida KT2440 responds specifically to chlorophenoxy herbicides and their initial metabolites

Pseudomonas putida KT2440 is often used as a model to investigate toxicity mechanisms and adaptation to hazardous chemicals in bacteria. The objective of this paper was to test the impact of the chlorophenoxy herbicides 2,4-dichlorophenoxyacetic acid (2,4-D) and 2-(2,4-dichlorophenoxy)propanoic acid (DCPP) and their metabolites 2,4-dichlorophenol (DCP) and 3,5-dichlorocatechol (DCC), on protein expression patterns and physiological parameters. Both approaches showed that DCC has a different mode of action and induces different responses than DCPP, 2,4-D and DCP. DCC was the most toxic compound and was active as an uncoupler of oxidative phosphorylation. It repressed the synthesis of ferric uptake regulator (Fur)-dependent proteins, e.g. fumarase C and L-ornithine N5-oxygenase, which are involved in oxidative stress response and iron uptake. DCPP, 2,4-D and DCP were less toxic than DCC. They disturbed oxidative phosphorylation to a lesser extent by a yet unknown mechanism. Furthermore, they repressed enzymes of energy-consuming biosynthetic pathways and induced membrane transporters for organic substrates. A TolC homologue component of multidrug resistance transporters was found to be induced, which is probably involved in the removal of lipophilic compounds from membranes.

Impact of membrane fatty acid composition on the uncoupling sensitivity of the energy conservation of Comamonas testosteroni ATCC 17454

The fatty acid composition of pyruvate-grown Comamonas testosteroni ATCC 17454 was analyzed after growth at 30 and 20 degrees C and after half-maximum growth inhibition caused by different membrane-active chemicals at 30 degrees C. Palmitic acid (16:0), palmitoleic acid (16:1 omega7c) and vaccenic acid (18:1 omega7c) were the dominant fatty acids. At 20 degrees C, the proportion of palmitic acid decreased and those of palmitoleic and vaccenic acid increased. Saturation degree was also lowered when half-maximum growth inhibition was caused by 4-chlorosalicylic acid, 2,4-dichlorophenoxyacetic acid and 2,4-dinitrophenol and, to a lesser extent, in the presence of 2,4-dichlorophenol, phenol and ethanol. It appeared that the dissociated forms of the former group of chemicals were preferentially incorporated near the head group region of the lipid bilayer, thereby somewhat extending the outer region of the membranes, and that the increased amount of bent, unsaturated fatty acids helped to maintain membrane integrity. Irrespective of how the decrease of the saturation degree was triggered, it caused electron transport phosphorylation (adenosine triphosphate synthesis driven by n-hexanol oxidation) to become more sensitive to uncoupling. Apparently, the viscosity and phase stability of the cytoplasmic membrane of C. testosteroni were maintained at the price of a reduced protection against energy toxicity.

Regulation of catabolic enzymes during long-term exposure of Delftia acidovorans MC1 to chlorophenoxy herbicides

Delftia acidovorans MC1 is able to grow on chlorophenoxy herbicides such as 2,4-dichlorophenoxypropionic acid (2,4-DCPP) and 2,4-dichlorophenoxyacetic acid as sole sources of carbon and energy. High concentrations of the potentially toxic organics inhibit the productive degradation and poison the organism. To discover the target of chlorophenoxy herbicides in D. acidovorans MC1 and to recognize adaptation mechanisms, the response to chlorophenoxy acids at the level of proteins was analysed. The comparison of protein patterns after chemostatic growth on pyruvate and 2,4-DCPP facilitated the discovery of several proteins induced and repressed due to the substrate shifts. Many of the induced enzymes, for example two chlorocatechol 1,2-dioxygenases, are involved in the metabolism of 2,4-DCPP. A stronger induction of some catabolic enzymes (chlorocatechol 1,2-dioxygenase TfdC(II), chloromuconate cycloisomerase TfdD) caused by an instant increase in the concentration of 2,4-DCPP resulted in increased rates of productive detoxification and finally in resistance of the cells. Nevertheless, the decrease of the (S)-2,4-DCPP-specific 2-oxoglutarate-dependent dioxygenase in 2D gels reveals a potential bottleneck in 2,4-DCPP degradation. Well-known heat-shock proteins and oxidative-stress proteins play a minor role in adaptation, because apart from DnaK only a weak or no induction of the proteins GroEL, AhpC and SodA was observed. Moreover, the modification of elongation factor Tu (TufA), a strong decrease of asparaginase and the induction of the hypothetical periplasmic protein YceI point to additional resistance mechanisms against chlorophenoxy herbicides.

Assimilatory detoxification of herbicides by Delftia acidovorans MC1: induction of two chlorocatechol 1,2-dioxygenases as a response to chemostress

Proteome analysis of bacteria that can detoxify harmful organic compounds enables the discovery of enzymes involved in the biodegradation of these substances and proteins that protect the cell against poisoning. Exposure of Delftia acidovorans MC1 to 2,4-dichlorophenoxypropionic acid and its metabolites 2,4-dichlorophenol and 3,5-dichlorocatechol during growth on pyruvate as a source of carbon and energy induced several proteins. Contrary to the general hypothesis that lipophilic or reactive compounds induce heat shock or oxidative stress proteins, no induction of the GroEL, DnaK and AhpC proteins that were used as markers for the induction of heat shock and oxidative stress responses was observed. However, two chlorocatechol1,2-dioxygenases, identified by amino terminal sequence analysis, were induced. Both enzymes catalyse the conversion of 3,5-dichlorocatechol to 2,4-dichloro-cis,cis-muconate indicating that biodegradation is a major mechanism of resistance in the detoxifying bacterium D. acidovorans MC1.

Suitability of the trans/cis ratio of unsaturated fatty acids in Pseudomonas putida NCTC 10936 as an indicator of the acute toxicity of chemicals

This study explored the suitability of using the trans/cis ratio of unsaturated fatty acids as an indicator of the acute toxicity of membrane active hazardous chemicals. The conversion of cis into trans fatty acids in Pseudomonas putida NCTC 10936 in response to 4-chlorophenol and temperature changes was compared with the results from another kind of toxicity test using the same organism, based on the sensitivity of its xylose oxidation-driven ATP synthesis to uncoupling. The response of both indicators is believed to be largely due to changes in the fluidity of the cytoplasmic membrane. However, the electron transport phosphorylation reacted faster and more sensitively to the fluidizing effect of 4-chlorophenol than the isomerization of unsaturated fatty acids. Therefore, measuring the trans/cis ratio does not provide as good early warning signals of acute toxicity as monitoring the response of the electron transport phosphorylation. If used as an indicator of chemostress, with Pseudomonas species as test organisms, the ratio should only be used in conjunction with other parameters reflecting the energetic state of the cells.

Protein synthesis patterns in Acinetobacter calcoaceticus induced by phenol and catechol show specificities of responses to chemostress

The proteins induced in Acinetobacter calcoaceticus by the potentially toxic growth substrates phenol and catechol were analyzed by 2D-electrophoresis of cell extracts and compared with those induced by heat shock and oxidative stress. Although both aromatic compounds are quite similar, the only difference being that catechol has an additional hydroxyl group, the responses obtained differed considerably. Phenol has greater lipophilicity and mainly induced heat shock proteins, whereas catechol, which causes the production of reactive oxygen species, predominantly induced oxidative stress proteins. Furthermore, some special proteins were induced by phenol or catechol, which might be useful as biomarkers for chemostress, and could be involved in the catalytic degradation of potentially toxic compounds.

Induction of heat shock proteins in response to primary alcohols in Acinetobacter calcoaceticus

Cells of Acinetobacter calcoaceticus 69-V, a species able to metabolize a range of aliphatic hydrocarbons and alcohols, were confronted with ethanol, butanol, hexanol or heat shock during growth on acetate as sole source of carbon and energy. The primary alcohols and the heat shock led to the synthesis of new proteins or amplified expression of specific, common and general proteins, which were detected by silver staining after two-dimensional gel electrophoresis. Some of the alcohol-inducible proteins were identified as heat shock proteins by comparing protein patterns of alcohol-shocked cells with those of heat-shocked cells, and by N-terminal amino acid sequencing. DnaK was found to be amplified after all treatments, but GroEI only after heat shock and ethanol treatment. The N-terminal amino acid sequence of the protein, which was considerably amplified after alcohol treatment and heat shock, shows homology to HtpG (high temperature protein G). Some of the heat shock proteins induced by ethanol differ from those induced by butanol and hexanol, suggesting there are at least two different signals for the induction of some heat shock proteins by primary alcohols. This could be due to the different localization of ethanol, butanol and hexanol in the membrane, or because higher cytoplasmic concentrations of ethanol than of butanol or hexanol were applied in these tests in order to keep concentrations of the alcohols in the membrane roughly similar. Besides heat shock proteins, a group of proteins were observed which were only induced by butanol and hexanol, possibly indicating the existence of a further defense mechanism against high concentrations of hydrophobic substrates preventing protein denaturation and membrane damage.

The biochemistry, physiology and genetics of PQQ and PQQ-containing enzymes

Pyrrolo-quinoline quinone (PQQ) is the non-covalently bound prosthetic group of many quinoproteins catalysing reactions in the periplasm of Gram-negative bacteria. Most of these involve the oxidation of alcohols or aldose sugars. PQQ is formed by fusion of glutamate and tyrosine, but details of the biosynthetic pathway are not known; a polypeptide precursor in the cytoplasm is probably involved, the completed PQQ being transported into the periplasm. In addition to the soluble methanol dehydrogenase of methylotrophs, there are three classes of alcohol dehydrogenases; type I is similar to methanol dehydrogenase; type II is a soluble quinohaemoprotein, having a C-terminal extension containing haem C; type III is similar but it has two additional subunits (one of which is a multihaem cytochrome c), bound in an unusual way to the periplasmic membrane. There are two types of glucose dehydrogenase; one is an atypical soluble quinoprotein which is probably not involved in energy transduction. The more widely distributed glucose dehydrogenases are integral membrane proteins, bound to the membrane by transmembrane helices at the N-terminus. The structures of the catalytic domains of type III alcohol dehydrogenase and membrane glucose dehydrogenase have been modelled successfully on the methanol dehydrogenase structure (determined by X-ray crystallography). Their mechanisms are likely to be similar in many ways and probably always involve a calcium ion (or other divalent cation) at the active site. The electron transport chains involving the soluble alcohol dehydrogenases usually consist only of soluble c-type cytochromes and the appropriate terminal oxidases. The membrane-bound quinohaemoprotein alcohol dehydrogenases pass electrons to membrane ubiquinone which is then oxidized directly by ubiquinol oxidases. The electron acceptor for membrane glucose dehydrogenase is ubiquinone which is subsequently oxidized directly by ubiquinol oxidases or by electron transfer chains involving cytochrome bc1, cytochrome c and cytochrome c oxidases. The function of most of these systems is to produce energy for growth on alcohol or aldose substrates, but there is some debate about the function of glucose dehydrogenases in those bacteria which contain one or more alternative pathways for glucose utilization. Synthesis of the quinoprotein respiratory systems requires production of PQQ, haem and the dehydrogenase subunits, transport of these into the periplasm, and incorporation together with divalent cations, into active quinoproteins and quinohaemoproteins. Six genes required for regulation of synthesis of methanol dehydrogenase have been identified in Methylobacterium, and there is evidence that two, two-component regulatory systems are involved.

The toxicity of substituted phenolic compounds to a detoxifying and an acetic acid bacterium

In the detoxifying bacterium Acinetobacter calcoaceticus 69-V and in the acetic acid bacterium Acetobacter methanolicus MB 58, glucose and xylose are oxidized, respectively, via PQQ-dependent membrane-bound dehydrogenases, which are linked to the respiratory chain in a manner enabling energy conservation via electron transport phosphorylation (ETP) in the cytoplasmic membrane. Neither the glucose and gluconic acid nor the xylose and xylonic acid are metabolized. Therefore, measurements of sugar oxidation-driven ATP syntheses ought not to be disturbed by ATP drainage caused by anabolic processes. Studying the effect of substituted phenolic compounds on these energization processes reveals that their toxicity increases with an increasing degree of chlorination and that A. calcoaceticus 69-V is more stable than A. methanolicus MB 58 against chlorinated phenols. On the other hand, A. methanolicus MB 58 is more stable against 2,4-dinitrophenol (2,4-DNP) and 2,4-dichlorophenoxyacetic acid (2,4-D), especially in the acidic pH range, in which the sensitivity of ATP synthesis to the uncouplers is higher than that of respiration. The toxicity caused by protonophoric activities ought to be barely detectable by respiratory and dehydrogenase tests. The luminescence system of Photobacterium phosphoreum tested in the luminescent bacteria test was much more sensitive. This test system should be used as a screening tool and the effects measured must be confirmed by toxicity tests evaluating the stability of bacteria themselves involved in processes of detoxification as well as the production of toxic metabolites, monitored with respect to their velocity and efficiency.

Quantitative aspects of glucose metabolism by Escherichia coli B/r, grown in the presence of pyrroloquinoline quinone

Escherichia coli B/r was grown in chemostat cultures under various limitations with glucose as carbon source. Since E. coli only synthesized the glucose dehydrogenase (GDH) apo-enzyme and not the appropriate cofactor, pyrroloquinoline quinone (PQQ), no gluconate production could be observed. However, when cell-saturating amounts of PQQ (nmol to mumol range) were pulsed into steady state glucose-excess cultures of E. coli, the organisms responded with an instantaneous formation of gluconate and an increased oxygen consumption rate. This showed that reconstitution of GDH in situ was possible. Hence, in order to examine the influence on glucose metabolism of an active GDH, E. coli was grown aerobically in chemostat cultures under various limitations in the presence of PQQ. It was found that the presence of PQQ indeed had a sizable effect: at pH 5.5 under phosphate- or sulphate-limited conditions more than 60% of the glucose consumed was converted to gluconate, which resulted in steady state gluconate concentrations up to 80 mmol/l. The specific rate of gluconate production (0.3-7.6 mmol.h-1.(g dry wt cells)-1) was dependent on the growth rate and the nature of the limitation. The production rate of other overflow metabolites such as acetate, pyruvate, and 2-oxoglutarate, was only slightly altered in the presence of PQQ. The fact that the cells were now able to use an active GDH apparently did not affect apo-enzyme synthesis.

The growth rate-limiting reaction in methanol-assimilating yeasts

The maximum growth rate of methylotrophic yeasts during growth on methanol is about 0.2 h-1. Since they are able to grow faster on substrates such as glucose we tried to identify the putative limiting step in methanol metabolism within the assimilatory pathway, leading to the formation of a major precursor for biosyntheses, or within the linear dissimilatory sequence. Growth experiments with mixed substrates and determination of some kinetic parameters allowed us to restrict the number of possible pacemaker enzymes. The dissimilatory sequence does not seem to be growth-rate limiting. This also applies to transketolase, transaldolase and fructose-1,6-bisphosphatase. Surprisingly, methanol oxidase appears to be the prime candidate.

The mixed substrate concept, applied for microbial syntheses of metabolites

Microbial overproduction of metabolites is a response to suboptimal conditions for growth and multiplication. It is an energy-wasting process in terms of life insofar as a part of energy of the carbon source remains in the metabolite. From an energetic point of view microbial overproduction can be divided into two categories: i) energy-consuming, ii) energy-yielding. The amount of energy required or made available is considered to be responsible for discrepancies between carbon metabolism-determined possible and experimentally obtained yields. Since the expenditure of energy must be provided by oxidation of carbon source more substrate is consumed than required according to the metabolic pathway. In the case of energy-yielding synthesis energy must be discharged. Various possibilities exist. Since metabolic sequences not involved in the synthesis of the proper product are not switched off completely other synthetic processes and even growth can occur. The energy is thus discharged at the expense of substrate. To increase the experimental yield the energy produced or consumed has to be maintained low. This can be achieved by means of substrate mixtures. The synthesis of by-products and growth are difficult to prevent completely. However, growth can be quite desirable since the catalyst is renewed thus making the product synthesis possible.

Factors relevant in bacterial pyrroloquinoline quinone production

Quinoprotein content and levels of external pyrroloquinoline quinone (PQQ) were determined for several bacteria under a variety of growth conditions. From these data and those from the literature, a number of factors can be indicated which are relevant for PQQ production. Synthesis of PQQ is only started if synthesis of a quinoprotein occurs, but quinoprotein synthesis does not depend on PQQ synthesis. The presence of quinoprotein substrates is not necessary for quinoprotein and PQQ syntheses. Although the extent of PQQ production was determined by the type of organism and quinoprotein produced, coordination between quinoprotein and PQQ syntheses is loose, since underproduction and overproduction of PQQ with respect to quinoprotein were observed. The results can be interpreted to indicate that quinoprotein synthesis depends on the growth rate whereas PQQ synthesis does not. In that view, the highest PQQ production can be achieved under limiting growth conditions, as was shown indeed by the much higher levels of PQQ produced in fed-batch cultures compared with those produced in batch experiments. The presence of nucleophiles, especially amino acids, in culture media may cause losses of PQQ due to transformation into biologically inactive compounds. Some organisms continued to synthesize PQQ de novo when this cofactor was administered exogenously. Most probably PQQ cannot be taken up by either passive diffusion or active transport mechanisms and is therefore not able to exert feedback regulation on its biosynthesis in these organisms.

Effects of growth rate and oxygen tension on glucose dehydrogenase activity in Acinetobacter calcoaceticus LMD 79.41

The regulation of the synthesis of the quinoprotein glucose dehydrogenase (EC 1.1.99.17) has been studied in Acinetobacter calcoaceticus LMD 79.41, an organism able to oxidize glucose to gluconic acid, but unable to grow on both compounds. Glucose dehydrogenase was synthesized constitutively in both batch and carbon-limited chemostat cultures on a variety of substrates. In acetate-limited chemostat cultures glucose dehydrogenase levels and the glucose-oxidizing capacity of whole cells were dependent on the growth rate. They strongly increased at low growth rates at which the maintenance requirement of the cells had a pronounced effect on biomass yield. Cultures grown on a mixture of acetate and glucose in carbon and energy-limited chemostat cultures oxidized glucose quantitatively to gluconic acid. However, during oxygen-limited growth on this mixture glucose was not oxidized and only very low levels of glucose dehydrogenase were detected in cell-free extracts. After introduction of excess oxygen, however, cultures or washed cell suspensions almost instantaneously gained the capacity to oxidize glucose at a high rate, by an as yet unknown mechanism.

Bacterial NAD(P)-independent quinate dehydrogenase is a quinoprotein

Acinetobacter calcoaceticus LMD 79.41 produced significant amounts of pyrrolo-quinoline quinone (PQQ) in its culture medium when grown on quinic acid or shikimic acid. Studies with LMD 79.41 and PQQ- -mutants of this strain demonstrated that this organism contains an NAD(P)-independent quinate dehydrogenase (QDH) (EC 1.1.99.-), catalyzing the first degradation step of these compounds, and that the enzyme contains PQQ as a cofactor, i.e. is a quinoprotein. Synthesis of QDH was induced by protocatechuate and the enzyme appeared to be particle-bound. Acinetobacter Iwoffi RAG-1 produced a quinoprotein QDH apoenzyme since growth on quinic acid only occurred in the presence of PQQ. The results obtained with the PQQ- -mutants of strain LMD 79.41 also provided some insight into the regulation of PQQ biosynthesis and assemblage of quinoprotein enzymes in the periplasmic space. Since two species of Pseudomonas also contained a quinoprotein QDH, it is assumed that bacterial NAD(P)-independent quinate dehydrogenase is a quinoprotein.