Fatty acid degradation in Caulobacter crescentus

Specialized acyl carrier protein used by serine palmitoyltransferase to synthesize sphingolipids in Rhodobacteria

Serine palmitoyltransferase (SPT) catalyzes the first and committed step in sphingolipid biosynthesis condensating L-serine and acyl-CoA to form 3-oxo-sphinganine. Whenever the structural gene for SPT is present in genomes of Rhodobacteria (α-, β-, and γ-Proteobacteria), it co-occurs with genes coding for a putative acyl carrier protein (ACP) and a putative acyl-CoA synthetase (ACS). In the α-proteobacterium Caulobacter crescentus, CC_1162 encodes an SPT, whereas CC_1163 and CC_1165 encode the putative ACP and ACS, respectively, and all three genes are known to be required for the formation of the sphingolipid intermediate 3-oxo-sphinganine. Here we show that the putative ACP possesses a 4'-phosphopantetheine prosthetic group, is selectively acylated by the putative ACS and therefore is a specialized ACP (AcpR) required for sphingolipid biosynthesis in Rhodobacteria. The putative ACS is unable to acylate coenzyme A or housekeeping ACPs, but acylates specifically AcpR. Therefore, it is a specialized acyl-ACP synthetase (AasR). SPTs from C. crescentus, Escherichia coli B, or Sphingomonas wittichii use preferentially acyl-AcpR as thioester substrate for 3-oxo-sphinganine synthesis. Whereas acyl-AcpR from C. crescentus is a good substrate for SPTs from distinct Rhodobacteria, acylation of a specific AcpR is achieved by the cognate AasR from the same bacterium. Rhodobacteria might use this more complex way of 3-oxo-sphinganine formation in order to direct free fatty acids toward sphingolipid biosynthesis.

CspC regulates the expression of the glyoxylate cycle genes at stationary phase in Caulobacter

Background

The Cold Shock proteins are RNA binding proteins involved in various cellular processes, including adaptation to low temperature, nutritional stress, cell growth and stationary phase. They may have an impact on gene expression by interfering with RNA stability and acting as transcription antiterminators. Caulobacter crescentus cspC is an essential gene encoding a stationary phase-induced protein of the Cold Shock Protein family and this work had as goal investigating the basis for the requirement of this gene for survival at this phase. In this work we investigate the role of CspC in C. crescentus stationary phase and discuss the molecular mechanisms that could be involved.

Results

The expression of cspC increased significantly at stationary phase in complex media and in glucose depletion, indicating a putative role in responding to carbon starvation. Global transcriptional profiling experiments comparing cspC and the wild type strain both at exponential and stationary phases as well as comparing exponential and stationary phase in wild type strain were carried out by DNA microarray analysis. The results showed that the absence of cspC affected the transcription of 11 genes at exponential phase and 60 genes at stationary phase. Among the differentially expressed genes it is worth noting those encoding respiratory enzymes and genes for sulfur metabolism, which were upregulated, and those encoding enzymes of the glyoxylate cycle, which were severely downregulated in the mutant at stationary phase. mRNA decay experiments showed that the aceA mRNA, encoding isocitrate lyase, was less stable in the cspC mutant, indicating that this effect was at least partially due to posttranscriptional regulation. These observations were supported by the observed arrested growth phenotype of the cspC strain when grown in acetate as the sole carbon source, and by the upregulation of genes for assimilatory sulfate reduction and methionine biosynthesis.

Conclusions

The stationary phase-induced RNA binding protein CspC has an important role in gene expression at this phase, and is necessary for maximal expression of the glyoxylate cycle genes. In the case of aceA, its downregulation may be attributed to the shorter half-life of the mRNA in the cspC mutant, indicating that one of the possible regulatory mechanisms is via altering RNA stabilization.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1845-1) contains supplementary material, which is available to authorized users.

Characterization of long-chain fatty acid uptake in Caulobacter crescentus

Studies evaluating the uptake of long-chain fatty acids in Caulobacter crescentus are consistent with a protein-mediated process. Using oleic acid (C18:1) as a substrate, fatty acid uptake was linear for up to 15 min. This process was saturable giving apparent V(max) and K(m) values of 374 pmol oleate transported/min/mg total protein and 61 μM oleate, respectively, consistent with the notion that one or more proteins are likely involved. The rates of fatty acid uptake in C. crescentus were comparable to those defined in Escherichia coli. Uncoupling the electron transport chain inhibited oleic acid uptake, indicating that like the long-chain fatty acid uptake systems defined in other gram-negative bacteria, this process is energy-dependent in C. crescentus. Long-chain acyl CoA synthetase activities were also evaluated to address whether vectorial acylation represented a likely mechanism driving fatty acid uptake in C. crescentus. These gram-negative bacteria have considerable long-chain acyl CoA synthetase activity (940 pmol oleoyl CoA formed/min/mg total protein), consistent with the notion that the formation of acyl CoA is coincident with uptake. These results suggest that long-chain fatty acid uptake in C. crescentus proceeds through a mechanism that is likely to involve one or more proteins.

Liquid culture carbon, nitrogen and inorganic phosphate source regulate nematicidal activity by fluorescent pseudomonads in vitro

AIMS

The aim of the present investigation was to determine the influence of nutrients on the nematicidal activity by Pseudomonas aeruginosa strain IE-6S+ and Ps. fluorescens strain CHA0 in vitro.

METHODS AND RESULTS

Culture filtrate of IE-6S+ and CHA0 obtained from chemically defined medium caused mortality of Meloidogyne javanica juveniles in vitro and that growth medium amended with various C, N or inorganic phosphate (Pi) sources markedly influenced nematicidal activity of the two bacteria. Glycerol (C source), propionate (fatty acid precursor) and L-lysine (N source) enhanced nematicidal activity while glucose (C), L-valine (N) and Pi substantially repressed nematicidal activity of the two bacteria.

CONCLUSION

Liquid culture amendments with various C, N or Pi sources modulate the biosynthesis of nematicidal agents to a different extent in vitro.

SIGNIFICANCE AND IMPACT OF THE STUDY

Developing bacterial strains more responsive to certain environmental signals can be exploited for increased secondary metabolite production in pharmaceutical fermentations and offers new avenues to improve biocontrol.

Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media

Microarray analysis was used to examine gene expression in the freshwater oligotrophic bacterium Caulobacter crescentus during growth on three standard laboratory media, including peptone-yeast extract medium (PYE) and minimal salts medium with glucose or xylose as the carbon source. Nearly 400 genes (approximately 10% of the genome) varied significantly in expression between at least two of these media. The differentially expressed genes included many encoding transport systems, most notably diverse TonB-dependent outer membrane channels of unknown substrate specificity. Amino acid degradation pathways constituted the largest class of genes induced in PYE. In contrast, many of the genes upregulated in minimal media encoded enzymes for synthesis of amino acids, including incorporation of ammonia and sulfate into glutamate and cysteine. Glucose availability induced expression of genes encoding enzymes of the Entner-Doudoroff pathway, which was demonstrated here through mutational analysis to be essential in C. crescentus for growth on glucose. Xylose induced expression of genes encoding several hydrolytic exoenzymes as well as an operon that may encode a novel pathway for xylose catabolism. A conserved DNA motif upstream of many xylose-induced genes was identified and shown to confer xylose-specific expression. Xylose is an abundant component of xylan in plant cell walls, and the microarray data suggest that in addition to serving as a carbon source for growth of C. crescentus, this pentose may be interpreted as a signal to produce enzymes associated with plant polymer degradation.

Decarboxylase activity involved in methyl ketone production by Staphylococcus carnosus 833, a strain used in sausage fermentation

Staphylococcus carnosus strain 833, inoculated into sausage, increased the levels of methyl ketones which contributed to the cured aroma. These ketones were predicted to arise from incomplete beta-oxidation followed by a decarboxylation. To check this hypothesis, we measured the beta-decarboxylase activity in resting cells of S. carnosus grown in complex or in synthetic medium, using as substrate a beta-ketoacid, which can be an intermediate of the beta-oxidation pathway. This activity was present throughout the growth period. The enzyme appeared to be constitutive because no induction was observed. High aeration, a pH of 5 and the presence of nitrate promoted the production of methyl ketones.

Identification of beta-oxidation and thioesterase activities in Staphylococcus carnosus 833 strain

Staphylococcus carnosus 833, inoculated into sausage meat, increased the level of methyl ketones, which contributed to the cured aroma. These ketones can arise from incomplete beta-oxidation followed by two enzymatic activities: a thioesterase and a decarboxylase. In this study we identified the beta-oxidative pathway (through the measure of 3-hydroxyacyl-CoA dehydrogenase activity) and the thioesterase activity in extracts of S. carnosus cells grown in the presence of different methyl esters. The beta-oxidative system was induced by methyl esters and highest induction was found with a 12-carbon substrate. It was specific for medium chain length fatty acyl CoA substrates. Its maximal activity was observed at the end of stationary growth phase. HPLC analyses of acyl-CoA after incubation of cell extracts with palmitoyl-CoA showed that the beta-oxidation system released preferentially long chain hydroxyacyl-CoAs, enoyl-CoAs, and acyl-CoAs. The time-course of intermediate formation indicated a precursor product relationship indicative of a model of free intermediates which could be further deacylated by a thioesterase. The thioesterase activity was enhanced when S. carnosus was grown in the presence of methyl esters with at least 12 carbons and this enzyme was specific for short chain acyl-CoAs. The maximal activity was reached at the stationary growth phase.

Purification and characterization of fatty acid beta-oxidation enzymes from Caulobacter crescentus

Acetoacetyl coenzyme A (acetoacetyl-CoA) thiolase, an enzyme required for short-chain fatty acid degradation, has been purified to near homogeneity from Caulobacter crescentus. The relative heat stability of this enzyme allowed it to be separated from beta-ketoacyl-CoA thiolase. The purification scheme minus the heating step also permitted the copurification of crotonase and 3-hydroxyacyl-CoA dehydrogenase. These activities are in a multienzyme complex in Escherichia coli, but a similar complex was not observed in C. crescentus. Instead, separate proteins differing in enzymatic activity were detected, analogous to the beta-oxidation enzymes that have been isolated from Clostridium acetobutylicum and from mitochondria of higher eucaryotes. In these cells, as appears to be the case with C. crescentus, the individual enzymes form multimers of identical subunits.

Proliferation of microbodies in Saccharomyces cerevisiae

The development of microbodies in the yeast Saccharomyces cerevisiae was studied in response to different conditions of growth. Various strains of S. cerevisiae were investigated, using cells from the exponential growth phase on glucose as an inoculum in all transfer experiments. Electron microscopy, including serial sectioning, revealed that these cells generally contained one to four small microbodies which were localized in the vicinity of the cell wall and characterized by the presence of catalase. Transfer of these glucose-grown cells into media supplemented with various compounds known to induce microbody proliferation in other yeasts--i.e. uric acid, alkylated amines, amino acids, C2-compounds such as ethanol or acetate, in the presence or absence of compounds that induce oxygen radical formation--did not result in a significant change in the number of microbody profiles observed. Marked microbody proliferation was, however, observed after a shift of cells into media containing oleic acid and was associated with the induction of activities of beta-oxidation enzymes. In addition, catalase and isocitrate lyase were present in enhanced levels. Kinetic experiments suggested that these microbodies developed from those originally present in the inoculum cells. In thin sections up to 14 microbody profiles were occasionally observed, often present in small clusters. Their ultimate volume fraction amounted to 8-10% of the cytoplasmic volume.