1 Wageningen Centre for Food Sciences, Diedenweg 20, 6700 AN, Wageningen, The Netherlands
2 TNO Quality of Life, Utrechtseweg 48, 3700 AJ Zeist, The Netherlands
Correspondence
Bart Pieterse
Bart.Pieterse{at}BDS.nl
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ABSTRACT |
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INTRODUCTION |
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Several theories have been postulated to explain the toxic effect of organic acids in more detail. One of these considers organic acids as uncouplers that transport protons towards the inside of the cell, which is a pH-driven process. Eventually, this influx could lead to a complete dissipation of the proton motive force (Axe & Bailey, 1995
; Kashket, 1987
). A second aspect relates to the deleterious effects of the lower intracellular pH, caused by the influx of lactic acid. However, whereas many organisms aim at maintaining a constant intracellular pH (Padan et al., 1981
; Shelef, 1994
), most anaerobic fermenting species avoid a large
pH by allowing for a lower intracellular pH, and as a result increase their tolerance to organic acids (Booth, 1985
; Cook & Russell, 1994
; Diez-Gonzalez & Russell, 1997
). This is also the case for L. plantarum, which can grow at intracellular pH values as low as 4·64·8 (McDonald et al., 1990
). A third factor explaining the inhibitory effect of organic acids is the intracellular accumulation of anions, which could lead to both end-product inhibition and a loss of water activity (Russell, 1992
; Russell & Diez-Gonzalez, 1998
). For lactic acid bacteria, end-product inhibition by lactic acid could result in a disturbance of the regeneration of the cofactor NAD+, especially under anaerobic conditions in which the cell does not have the possibility of NAD+ regeneration by NADH oxidase.
The recent sequencing of the genome of L. plantarum WCFS1 (Kleerebezem et al., 2003) revealed several genes for which homologues in other prokaryotes have been found to play a role in pH control or in the maintenance of the proton motive force: a proton-translocating F1F0-ATPase (Cotter & Hill, 2003
); several sodium-proton antiporters (Cotter et al., 2001
); amino acid decarboxylases that use an intracellular hydrogen ion for the decarboxylation of an imported amino acid (Azcarate-Peril et al., 2004
; Cotter & Hill, 2003
; van de Guchte et al., 2002
); and the genes involved in malolactic fermentation, during which extracellular malate is imported and decarboxylated. The lactate that is produced is secreted via an electrogenic uniport, which results in a membrane potential that can be applied to the generation of ATP (Olsen et al., 1991
).
The genomic sequence of L. plantarum gives insight into potential responses of the cells to counteract the anticipated deleterious aspects of extracellular lactic acid accumulation. Nevertheless, the genomic data give little clue to the exact effects of lactic acid and the response of the cells towards this stress. Functional genomics techniques offer good opportunities for gaining a better understanding of the physiological state and the specific response of the cell. In recent years, the acid stress response of several prokaryotes has been studied with both proteomics and transcriptomics approaches (Ang et al., 2001; Fisher et al., 2002
; Giard et al., 2001
; Len et al., 2004
; Lim et al., 2000
; Merrell et al., 2003
; Stancik et al., 2002
; Wen et al., 2003
; Wilkins et al., 2002
). A few reports describe the use of these approaches to study the organic acid stress response caused by lactate (Hartke et al., 1996
), acetate (e.g. Arnold et al., 2001
; Kirkpatrick et al., 2001
; Polen et al., 2003
), propionate (Polen et al., 2003
) and formate (Kirkpatrick et al., 2001
). None of these studies, however, allows for discrimination between the effects of the undissociated and the dissociated forms of lactic acid. Moreover, the negative effect that the organic acid could have on the growth rate of the organism, and the secondary effects on gene expression resulting thereby, are usually neglected.
The aim of this study was to obtain a better insight into the effect of lactic acid on L. plantarum, and to obtain a genome-wide view of the transcriptional response towards this stress factor. To this end, an experimental design was developed that allows discrimination of the effects of pH, lactic acid in its dissociated and undissociated forms, and the secondary effect of a diminished maximum growth rate.
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METHODS |
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Cultivation and cell harvesting.
Glucose-limited continuous cultivation of L. plantarum WCFS1 was performed in duplicate on 25 % MRS medium (13·75 g l1, Difco) with additional sodium chloride or sodium lactate (as specified in Table 1), at 37 °C in an Applikon bioreactor with a working volume of 1 l. Glucose limitation was confirmed by the fact that the addition of a concentrated glucose solution to the steady-state culture resulted in an increased cell density. A constant pH was maintained (pH 6·0 or 4·8) by automatic titration with 10 M sodium hydroxide. The culture was kept anoxic by a continuous overlay with nitrogen gas. The dilution rate was set at 0·3 h1 or 0·05 h1.
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RNA isolation.
RNA was isolated from the cells according to the Macaloid/phenol-based protocol, as previously described (Pieterse et al., 2005). RNA purity and concentrations were determined both spectrophotometrically and on agarose gel. The RNA isolates were checked for residual RNase activity by comparing samples that were incubated for 1 h at 42 °C with the initial material on an agarose gel.
Array design.
The microarray used is a clone-based array, containing 3714 identified unique fragments from the genomic L. plantarum WCFS1 library in pBlueScript SK+ (Kleerebezem et al., 2003). The mean size of the fragments is 1·2 kb, with a standard deviation of 0·3 kb. The microarray contains approximately 80 % of the L. plantarum WCFS1 genome (Pieterse et al., 2005
).
Fluorescent labelling and hybridization.
Differential transcript levels were determined by two-colour fluorescent hybridizations of the corresponding cDNAs on the L. plantarum clone array. The RNA samples were labelled by in vitro reversed transcription with either Cy5- or Cy3-labelled dUTP, using random hexamer primers. Labelling, hybridization and washing were performed as previously described (Pieterse et al., 2005). The fluorescent labels were swapped for the labelling of the biological duplicates in order to avoid false positives due to dye-specific effects.
Image analysis.
The fluorescent signals from the two different labels on the hybridized arrays were quantified with a ScanArray Express scanner (Packard Bioscience) and Imagene 4.2 software (BioDiscovery, Inc.). Spots for which the difference between the mean signal of the spot and the mean signal of the background was smaller than two times the background standard deviation were excluded from further analysis. Spots for which the signal in one or both of the channels exceeded the detection limit of the scanner were also excluded. After removal of the empty spots and the spots for which the signal exceeded the detection limit of the scanner, 2787 spots (75 %) remained for further analysis.
Normalization.
Within-slide, intensity-dependent normalizations were performed with the scatter plot smoother LOWESS from the software program Datafit (Oakdale Engineering). The user-defined fraction of data used for smoothing at each point was set at 20 % for all slides.
Significance analysis.
Prior to significance analysis, a data transformation was applied to the normalized ratios in order to obtain a distribution around zero that approached the normal distribution (Pieterse et al., 2005). Significance analysis was performed by one-way ANOVA. Subsequently, a Tukey HSD test was performed to determine whether a significant differential expression level (99 % confidence interval) was observed under a specific condition. If genes or predicted operons were present on multiple spots on the array, these spots were considered as replicates in the significance analysis.
By comparison of overlapping regions of the genomic fragments on the array, we were able to predict which of the specific genes present in the clones were the ones affected.
Hierarchical clustering.
For the hierarchical clustering and visualization of the results, the programs CLUSTER and TREEVIEW were applied (Eisen et al., 1998). Only those genes or operons were included that fell within the 99 % confidence interval of the Tukey HSD test for at least one of the six conditions. Average linkage clustering was performed on the natural logarithm of the expression ratios of the genes or operons, based on all replicate spots. The outcome of the clustering was influenced by assigning weight values to the different experiments. For the experiments in which the effect of lactate was studied, a weight value of 1 was applied. The dataset in which the effect of the lower pH value was studied was assigned a weight value of 0·75, the 800 mM sodium chloride dataset 0·5 and the 300 mM sodium chloride dataset 0·25.
In silico analysis of cell surface proteins.
The intracellular, extracellular and transmembrane regions of proteins that were annotated as cell surface proteins were predicted using a hidden Markov model-based tool (http//www.cbs.dtu.dk/services/TMHMM; Krogh et al., 2001). Multiple protein alignments (gap open penalty of 10; gap extension penalty of 1; GONNET-matrix), and pI predictions were performed in DNAman version 5.2.9. (Lynnon BioSoft). The motif LPQTxE is the L. plantarum orthologue of the well-known cell-wall-anchoring LPxTG pentapeptide (Fischetti et al., 1990
; Kleerebezem et al., 2003
).
Scanning electron microscopy.
Nucleopore polycarbonate membranes (Costar) with 1 µm pores were coated with poly-L-lysine (30 min in 0·01 % poly-L-lysine, 0·1 M Tris/HCl buffer). For scanning electron microscopy, several drops of bacteria from duplicate steady-state cultures were transferred to the membrane immediately upon harvesting, and stored for 5 min at 100 % humidity. Fixation was achieved by 30 min incubation in the bacterial growth medium with additional 3 % glutaraldehyde. The membranes were subsequently rinsed three times in water for 10 min. Dehydration was performed by immersing in a series of ethanol washes (30, 50, 70, 90, and three times 100 %). Membranes were critical point dried in CO2 (Balzers CPD 020, Balzers Union). The dry membranes were mounted on the sample holders by carbon adhesive tabs (Electron Microscopy Sciences). Sample holders were put inside the preparation chamber (CT 1500 HF, Oxford Instruments) attached to the microscope. Samples were sputter coated with 5 nm platinum and analysed in a field emission scanning electron microscope (JEOL 6300F) at 5 kV. Images were recorded digitally, and photo processing was done with Adobe PhotoShop 5.5.
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RESULTS AND DISCUSSION |
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The effect of extracellular pH on gene expression was studied by comparing mRNA levels from L. plantarum cultured at pH 4·8 with those of L. plantarum cultured at pH 6·0 (Table 1, row C).
As the presence of lactic acid also influences the growth rate of the organism, changes in gene expression are expected that are not caused by the primary effect of the sodium lactate, but by the secondary effect of an altered absolute or relative growth rate. In this study, the effect of a different absolute growth rate was avoided by using identical dilution rates for the cultures for which the transcription profiles were compared. In order to determine whether relative growth rate (i.e. the ratio between the set growth rate and the maximum growth rate under the given conditions in a batch culture) also affected gene expression, the transcription profile of the culture with sodium lactate at pH 4·8 and a dilution rate of 0·05 h1 was also compared with that of the culture with 300 mM sodium chloride at pH 4·8 and a dilution rate of 0·3 h1. The relative growth rates of these cultures were alike (Table 1, row F).
Furthermore, transcriptome datasets from two independent duplicate cultures in which the effect of additional sodium chloride (0 mM versus 300 mM/0 mM versus 800 mM) was studied, were generated (Table 1, rows A and B). These were added to study whether osmotic stress mechanisms are initiated in the presence of lactic acid.
Hierarchical cluster analysis
Hierarchical clustering was performed in order to group genes or operons that showed similar expression patterns under the different experimental conditions (Fig. 2).
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Striking differences occurred in the two datasets that represent the effect of lactic acid, but vary in growth rate/relative growth rate. In order to determine lactic acid-specific effects, we concentrated on the genes that are marked with boxes 1 and 2 in Fig. 2. The corresponding genes and their expression data are listed in Tables 27
.
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Probably the most striking feature from this group of genes was the multiple cell surface protein-encoding genes that were found. Analysis of the corresponding regions of these genes on the L. plantarum genome indicated that three operons encoding cell surface proteins could be identified, not all the genes of which were represented in our datasets. The corresponding proteins showed low similarity to other proteins in database searches. Prediction of transmembrane helices, cell wall anchors, expected pI values and amino acid lengths from the complete sets of genes revealed a structural homology between these three operons (Fig. 3). This structural conservation might indicate that the proteins within a single operon interact. Multiple sequence alignment of the amino acid sequences from the corresponding genes showed a limited number of highly conserved regions (data not shown). The array data indicated that, under inducing conditions, the absolute expression level of the lp_3679lp_3676 operon was among the highest transcript levels measured. This would suggest that the corresponding proteins are abundantly present on the cell surface. Indeed, scanning electron microscopy revealed striking morphological differences between the stressed and non-stressed cells (Fig. 4
): whereas the cells that were not subjected to lactic acid stress showed a smooth appearance, the stressed cells had a remarkably rough surface. These structures were mainly situated on the longitudinal sides of the cells. It is tempting to speculate that these cell surface proteins may have a structural, physical function in combating lactic acid stress. To our current knowledge, a specific role for structural cell surface proteins in the organic acid stress response has not been implicated before.
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Two other genes that may serve a specific role in the counteracting of lactic acid stress are squalene synthase and phytoene synthase, which are involved in the biosynthesis of sterols. Sterols can increase the rigidity of the membrane (van der Rest et al., 1995), which could possibly limit the influx of lactic acid.
Moreover, two predicted regulators were represented in the group of genes that showed increased expression in response to lactic acid. These are especially interesting because of their potential role in the regulation of an organic acid stress response.
Identification of genes with a specifically decreased expression in response to lactic acid
Group 2 (Fig. 2, Table 3
) contains 10 genes or operons that showed a decreased expression in response to lactic acid regardless of absolute and relative growth rate, several of which also showed a decreased expression in response to a lower pH alone and to lactate at pH 6·0. The putative functions of these genes vary widely.
Effect of lactic acid on the expression of genes that are known for their role in (in)organic acid response
In addition to the genes that were found to show differential expression in response to lactic acid, we studied the expression of a number of genes that have been associated with the prokaryotic (organic) acid response in earlier studies.
Although the role of the F1F0-ATPase in acid adaptation has been clearly demonstrated in studies with both a mutant strain and a strain with an increased F1F0-ATPase activity (Drici-Cachon et al., 1996; van de Guchte et al., 2002
), no differential expression of these genes could be observed in this study. It should be noted that these effects were observed at low pH values in the presence of inorganic acids. It is doubtful whether this system plays a significant role in the stress attributed to lactic acid. The amount of energy that this system would require when the cell has to cope with a massive influx of lactate could ultimately lead to a cessation of growth (Bond & Russell, 1996
).
If the uncoupling effect is the main factor responsible for lactic acid stress, one would expect major problems in proton motive force-dependent transport processes, whereas the results that are presented in this paper do not indicate a lactic acid-specific adaptation of the expression of genes encoding transport proteins. Furthermore, no increase of lactic acid-specific expression was observed for genes that could play a role in restoring the membrane potential, such as cation transporters and the malolactic fermentation genes. Remarkably enough, a cation transporter (lp_0124) that did respond to lactic acid showed decreased expression (Table 3).
Metabolic rerouting under the combined effects of lactic acid and a lower absolute growth rate
Groups 5 and 3 (Fig. 3, Tables 4
and 5
) contain genes and operons that were differently expressed in cells grown in the presence of lactic acid and with a lower absolute growth rate. Within these clusters, several genes involved in energy metabolism showed a differential expression, which could indicate a shift towards alternative fermentation pathways. The complete dataset was studied in more detail to determine whether other genes in these pathways showed similar trends. An overview of the expression of these genes and the metabolic routes in which they are involved is presented in Table 8
and Fig. 5
.
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The genes encoding phosphoenolpyruvate synthase (lp_1912) and phosphoenolpyruvate carboxykinase (lp_3418), responsible for the bypass from pyruvate to oxaloacetate via phosphoenolpyruvate, both showed an increased expression (Table 8). A subsequent conversion to malate by malate dehydrogenase would lead to NAD+ regeneration. The flux through this pathway seems to be further stimulated by the down-regulation of the pyruvate carboxylase (lp_2136) and pyruvate kinase genes (lp_1897; statistically non-significant) under the same conditions (Table 8
).
The increased expression of lp_2596, the formate acetyl transferase activating enzyme (Table 8), suggests the upregulation of the formate acetyl transferase gene, responsible for the conversion of pyruvate into formate and acetyl-CoA. Indeed, an increase in expression (90 % confidence interval) of this gene (lp_2598) could be observed (Table 8
). A subsequent conversion step in this pathway is that of acetyl-CoA to acetaldehyde and ethanol, during which two NAD+ molecules are regenerated. This step could be performed by the bifunctional alcohol dehydrogenase/acetaldehyde dehydrogenase (lp_3662), for which a statistically non-significant increase in expression of 150 % was observed (Table 8
). Alternatively, acetyl-CoA can be converted into acetyl-phosphate and subsequently acetate by phosphotransacetylase and acetate kinase, respectively. However, no increased expression was observed for the corresponding genes.
The suggested reroutings make sense in view of the potential effects of lactic acid accumulation on the cell. Conversion of pyruvate into lactic acid is the predominant mechanism for L. plantarum to avoid NAD+ depletion under anaerobic conditions. Metabolites other than lactate have been reported as the end-product of hexose fermentation by L. plantarum, but only in cases where oxygen or citrate are present as electron acceptors (Ferain et al., 1996b; Lindgren et al., 1990
; Tseng & Montville, 1990
). Therefore, growth inhibition due to pyruvate accumulation and/or low NAD+ levels (as a consequence of end-product inhibition by lactate), form a plausible explanation of the inhibitory effect caused by lactic acid. Strategies that aim to avoid pyruvate accumulation and/or regeneration of NAD+ could be beneficial for L. plantarum. The suggested shift towards the phosphoketolase bypass and the pathways leading towards malate and ethanol formation would contribute to a limitation of the pyruvate level. Moreover, these three routes have a clear advantage with respect to cofactor regeneration. These observations indicate that diminished NAD+ regeneration due to end-product inhibition of the lactate dehydrogenase is an important growth-limiting effect of lactic acid accumulation under anaerobic conditions. This suggestion is confirmed by observations of Ferain and co-workers, who have reported that an L. plantarum strain that lacks lactate dehydrogenase activity is especially inhibited in its growth under anaerobic conditions (Ferain et al., 1996a
). Under aerobic conditions, the NAD+-regenerating function of the lactate dehydrogenase could be taken over by NADH oxidase.
The fact that these genes did not show similar trends in response to lactic acid at a higher relative growth rate may indicate that lactic acid is not the only regulatory trigger.
Growth rate-related effects
From clusters 3 and 5 versus clusters 1 and 6 in the hierarchical cluster (Fig. 2), it becomes apparent that altered growth characteristics (in comparison with the reference condition) form an important parameter in gene expression studies.
The coherence within these clusters clearly indicates that the observed changes are not coincidental: the combined effect of lactic acid and a lower absolute growth rate resulted in, among other effects, the decreased expression of genes involved in transport processes and amino acid uptake, and the previously discussed differential expression of genes involved in metabolic rerouting (Tables 4 and 5). Among the genes that responded to the effect of lactic acid and a higher relative growth rate, increased expression was observed for a remarkably high number of tRNA ligases (Table 6
). Based on the fact that the difference in absolute growth rate does not lead to a significant difference in the expression of genes that have been related to glucose limitation (unpublished results), we conclude that this difference does not increase the effect of the glucose starvation on the cells.
Especially in exponentially growing cultures, it is generally difficult to avoid changes in growth rate as a consequence of the imposed stress. The effect of altered absolute growth rate on gene expression is illustrated by three papers on proteome/transcriptome changes in Escherichia coli in response to acetate (Arnold et al., 2001; Kirkpatrick et al., 2001
; Polen et al., 2003
). Transcriptome studies of the effect of a growth-inhibiting concentration of this organic acid on exponentially growing cells reveal a decreased expression for a large number of genes involved in transcription and translation (Arnold et al., 2001
). Other studies have recognized this problem and circumvented it by using an acetate concentration that hardly affects growth rate (Kirkpatrick et al., 2001
; Polen et al., 2003
). However, for most stress-response studies this will not be desirable, since the effects on gene expression will also be limited. Experiments with steady-state cultures of E. coli confirm the effect of absolute growth rate on both metabolome and gene expression (Hua et al., 2004
; Tweeddale et al., 1998
).
Whereas the use of steady-state cultures with an equal dilution rate appears to be the method of choice to circumvent absolute growth rate-related effects, our data indicate that differences in relative growth rate should also be accounted for.
Concluding remarks
The experimental design that was applied in this study allowed the different effects of lactic acid to be distinguished, and resulted in new insights into both the effect of lactic acid stress on L. plantarum and the potential environmental response mechanisms of the organism. In particular, those genes that show increased expression towards lactic acid regardless of growth rate-related effects may be good target genes for strain improvement. The metabolic reroutings in response to lactic acid at a lower absolute growth rate suggest an inhibitory effect of lactic acid at lower growth rates due to decreased NAD+ regeneration and/or pyruvate accumulation. The fact that these effects only occur in combination with the lower absolute growth rate indicates that lactic acid itself is not the regulatory trigger for these reroutings.
The results presented in this paper demonstrate the importance of good experimental design in studies in which more than one physico-chemical parameter is affected by the subject of study. A poor discrimination of primary and secondary effects, such as growth-related effects, will complicate data interpretation and the rational selection of genes for further studies, and should therefore be avoided.
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ACKNOWLEDGEMENTS |
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Received 27 June 2005;
revised 9 September 2005;
accepted 12 September 2005.
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