If this is the primary cause of loss of glycolytic capacity, one would expect the cells to regulate their glycolytic capacity through decreasing simultaneously and proportionally the cap
Trang 1between metabolic and gene-expression regulation
during nitrogen starvation in baker’s yeast
Karen van Eunen1, Jildau Bouwman1,*, Alexander Lindenbergh1, Hans V Westerhoff1,2
and Barbara M Bakker1,3
1 Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, The Netherlands
2 Manchester Centre for Integrative Systems Biology, University of Manchester, UK
3 Department of Pediatrics, University of Groningen, The Netherlands
Introduction
Living organisms have the option to regulate their
molecular activities by altering expression of the
cor-responding genes For example, in the yeast
Saccharo-myces cerevisiae changes in glycolytic flux have
frequently been found to be accompanied by changes
in enzyme capacities [1–3] or amounts [4] However, a
change in flux through a certain enzyme can also be regulated through the interaction of that enzyme with altering concentrations of its substrate(s), product(s) and⁄ or modifier(s) (metabolic properties) To quantify the extent to which the change in flux through an individual enzyme is regulated by a change in enzyme
Keywords
fermentative capacity; glycolysis; regulation
analysis; Saccharomyces cerevisiae;
systems biology
Correspondence
B M Bakker, Department of Pediatrics,
Center for Liver, Digestive and Metabolic
Diseases, University Medical Center
Groningen, University of Groningen,
Hanzeplein 1, NL-9713 GZ Groningen,
The Netherlands
Fax: +31 50 361 1746
Tel: +31 50 361 1542
E-mail: b.m.bakker@med.umcg.nl
*Present address
Physiological Genomics, TNO Quality of
Life, Zeist, The Netherlands
(Received 11 February 2009, revised 6 July
2009, accepted 23 July 2009)
doi:10.1111/j.1742-4658.2009.07235.x
Time-dependent regulation analysis is a new methodology that allows us to unravel, both quantitatively and dynamically, how and when functional changes in the cell are brought about by the interplay of gene expression and metabolism In this first experimental implementation, we dissect the initial and late response of baker’s yeast upon a switch from glucose-lim-ited growth to nitrogen starvation During nitrogen starvation, unspecific bulk degradation of cytosolic proteins and small organelles (autophagy) occurs If this is the primary cause of loss of glycolytic capacity, one would expect the cells to regulate their glycolytic capacity through decreasing simultaneously and proportionally the capacities of the enzymes in the first hour of nitrogen starvation This should lead to regulation of the flux which is initially dominated by changes in the enzyme capacity However, metabolic regulation is also known to act fast To analyse the interplay between autophagy and metabolism, we examined the first 4 h of nitrogen starvation in detail using time-dependent regulation analysis Some enzymes were initially regulated more by a breakdown of enzyme capacity and only later through metabolic regulation However, other enzymes were regulated metabolically in the first hours and then shifted towards regula-tion via enzyme capacity We conclude that even initial regularegula-tion is subtle and governed by different molecular levels
Abbreviations
ADH, alcohol dehydrogenase; ALD, aldolase; GAPDH, glyceraldehyde 3-phosphate dehydrogenase; GPM, phosphoglycerate mutase; HXK, hexokinase; PDC, pyruvate decarboxylase; PFK, phosphofructokinase; PGI, phosphoglucose isomerase; PGK, 3-phosphoglycerate kinase; PYK, pyruvate kinase.
Trang 2capacity (Vmax) and by changes in the interactions of
the enzyme with the rest of metabolism, regulation
analysis was developed [5–7]
To date, regulation analysis has been applied to
compare two steady states Previous studies have
revealed a diversity of regulation which remained
visi-ble after the cells ultimately adjusted their enzyme
capacities to the new steady state [5,8,9] In order to
obtain insight into adaptation strategies of organisms,
it would be more informative to follow the patterns of
regulation during the transition from one steady state
to another To this end, time-dependent regulation
analysis has been developed [10]
Regulation analysis has the rate through an enzyme
(v) vary proportionally to a function f that depends on
enzyme concentration (e), and to a function g that
depends on metabolic effects (X, K)
Regulation of the gene-expression cascade leading to
the enzyme in question, changes f(e) Most often,
f(e) = Vmax Changes in function g are caused by
changes in the concentrations of substrates, products
and effectors (X), and by changes in the affinities
(1⁄ K) of enzyme e towards its substrates, products
and effectors (K) As derived previously [6,7], gene
expression and metabolic regulation can be dissected
as follows:
1¼D log Vmax
D log J þ
D log gðX; KÞ
D log J ¼ qhþ qm ð2Þ
Here J denotes the flux through the pathway, which at
a steady state equals the enzyme rate v D denotes the
difference between two steady states The hierarchical
regulation coefficient qh quantifies the relative
contri-bution of changes in enzyme capacity (Vmax) to the
regulation of the flux through the enzyme of interest
The hierarchical regulation coefficient is associated
with changes in the entire gene expression cascade all
the way from transcription to protein synthesis,
stabil-ity and modification [8,9], hence the name
‘hierar-chical’ The relative contribution of changes in the
interaction of the enzyme with the rest of metabolism
is reflected in the metabolic regulation coefficient qm
Together the two regulation coefficients should
describe regulation completely, i.e add up to 1
Experimentally, the hierarchical regulation
coeffi-cient is the one that is more readily determined,
because it requires only measurements of the Vmax of
the enzyme and the flux through it, under two
condi-tions, according to:
qh¼D log Vmax
The metabolic regulation coefficient can then be calculated from the summation law (qm= 1) qh) For a more elaborate description and discussion of the method, see Rossell et al [6]
Time-dependent regulation analysis is an extended version that quantifies the regulation coefficients as a function of time [10] For this study, we used the inte-grative version of time-dependent regulation analysis, which integrates all the regulation between time points
t0 (the start of the perturbation) and t This results in the following equations:
1¼ qhðtÞ þ qmðtÞ ð4Þ
qhðtÞ ¼log VmaxðtÞ log Vmaxðt0Þ
log vðtÞ log vðt0Þ ð5Þ
We denote the in vivo rate through the enzyme with
v rather than J because we are now considering transient rather than steady states
In this study, we applied time-dependent regulation analysis to the case of the nitrogen starvation of yeast cells A brief period of nitrogen starvation is applied at the end of the production process of industrial baker’s yeast (S cerevisiae) in order to increase its carbohy-drate content, which in turn increases the storage sta-bility of the yeast [11,12] This period of nitrogen starvation leads to partial loss of the fermentative capacity, which is defined as the specific rate of carbon dioxide and ethanol production immediately upon introduction of the yeast into an anaerobic, glucose excess environment (i.e the dough) The production of carbon dioxide plays a major role in leavening of the dough and gives bread its open structure It is believed that the loss in fermentative capacity is mainly caused
by the degradation of proteins Unspecific bulk degra-dation of cytosolic proteins and small organelles via autophagy is enhanced [13,14] within 30 min of nitro-gen starvation and protein half-lives of < 1 h are mea-sured [15,16] If autophagy is the primary cause of the observed changes in fermentative flux, one would expect that regulation of the loss of the fermentative flux is mainly at hierarchical level However, several studies have shown strong changes in glycolytic meta-bolites, notably adenine nucleotides and fructose-1,6-bisphosphate upon nitrogen starvation [17,18] In general, metabolic regulation is known to be relatively fast However, these studies do not analyse the extent
to which the observed metabolite changes actually affect enzyme rates Therefore, regulation analysis is
Trang 3fundamentally different from other types of analysis
because it quantifies the overall importance of
meta-bolism versus gene expression before examining
specific metabolites
Earlier regulation analysis studies of nitrogen
starva-tion in yeast revealed mixed and diverse regulastarva-tion [9]
Both gene expression and metabolism contributed to
the overall regulation, but to different extents for
dif-ferent enzymes However, because this analysis was
not time resolved, but rather measured the endpoint of
regulation, secondary regulation events may have
taken place, obscuring a more decisive regulation
strategy put in place by the cells immediately upon
starvation
In this study, we investigated how regulation
devel-ops over time while yeast adapts to nitrogen
starva-tion If unspecific bulk degradation of proteins is the
primary reason for the loss of fermentative capacity,
we hypothesize that the initial regulation will be purely
hierarchical Such ‘multisite regulation’ [19] would lead
to initial metabolite homeostasis and a lack of
meta-bolic regulation Alternatively, metameta-bolic regulation
may be involved from the beginning, which will
become visible as a mixed regulation or even a
com-plete metabolic regulation in the early time points To
our knowledge, this is the first experimental study ever
in which regulation is studied in this way with
quanti-tative time resolution
Results
Growth and perturbation condition
S cerevisiaestrain CEN.PK113-7D was grown in
aero-bic glucose-limited chemostat cultures at a dilution
rate of 0.35 h)1 Under these conditions, a
respiro-fermentative metabolism was observed (Table 1), in
agreement with literature data [20] To induce nitrogen
starvation, cells were transferred from steady-state
chemostat cultures to a batch culture in medium
lack-ing nitrogen but with excess glucose The addition of
glucose served to prevent additional starvation for the
carbon source To discriminate between the effects
caused by nitrogen starvation and by the shift from
glucose limitation to glucose excess, control experi-ments were performed in which cells were shifted to glucose excess, but in the continued presence of nitro-gen Samples were taken from steady-state cultures and at 0, 1, 2, 3, 4 and 24 h after the start of the per-turbation The 24-h sample was only taken during nitrogen starvation, because in the presence of nitro-gen, glucose was depleted within 5–6 h of the start of the perturbation
Figure 1A shows that the total cell protein remained constant during nitrogen starvation In cells shifted to glucose excess in the presence of nitrogen, the total protein in the cultures increased with time (Student’s t-test, P < 0.05) In both cultures, cell numbers increased over time (Fig 1B) However, the cell num-ber increased exponentially in cells shifted to glucose excess in the continued presence of nitrogen, whereas the cells stopped dividing after 4 h of nitrogen starva-tion This suggests that the cells finished their division during nitrogen starvation, and further growth did not occur This was substantiated by Coulter counter data that during nitrogen starvation a peak of smaller cells occurred and persisted, indicating that the cells after division did not grow anymore in volume (data not shown)
Fermentative capacity and steady-state fluxes First, the fermentative capacity, i.e the ethanol flux under anaerobic conditions at glucose excess, was mea-sured in an off-line assay Because the fermentative capacity was measured in an off-line assay after trans-fer to fresh medium, the extracellular metabolic condi-tions were equal for all samples This implies that any metabolic regulation can only be caused by changes in intracellular metabolite concentrations
Samples were taken from the perturbed cultures at the different time points The cells were washed and transferred to an anaerobic vessel containing fresh and complete (with 38 mm ammonium sulfate) defined min-eral medium [21] with an excess amount of glucose (56 mm) This condition mimics the situation of baker’s yeast in dough [2] Apart from the ethanol flux, the fluxes of glucose, glycerol, acetate, succinate,
Table 1 Physiological parameters of the aerobic glucose-limited chemostat cultures from which cells were taken to be subjected to nitro-gen starvation and glucose excess conditions or glucose and nitronitro-gen excess conditions Dilution (growth) rate was set to 0.35 h)1 Errors represent SEM of seven independent chemostat cultures.
Yield glu,X (gÆg)1) q O 2
a q CO 2
b RQ c q glucosea q ethanolb Dry weight(gÆL)1) Carbon recovery(%)
a mmol consumed per gram biomass per hour b mmol produced per gram biomass per hour c Respiratory quotient (qCO2=q O 2 ).
Trang 4pyruvate and trehalose were also measured over a
per-iod of 30 min In these 30 min, biomass production
was not measurable, consistent with earlier research
[22], and therefore we neglected fluxes in biomass in
our calculations (see Experimental procedures) The
production fluxes of acetate, pyruvate and succinate
were always < 1% of the rate of glucose consumption
(Tables S1 and S2); the other fluxes are given in
Table 2 In the nitrogen-starvation experiment, the
car-bon consumed in the off-line assay matched that
produced, within the bounds of experimental error
(Table S1) In the experiment in which cells were
shifted to glucose excess in the presence of nitrogen,
the carbon balance matched only in the 0-h sample In
the other samples the assessed carbon production rates
were 17–21% lower than the carbon consumption rates
(Table S2) The assumption that the difference is in
the glycogen flux is not realistic in this case, because
glycogen is usually consumed rather than produced
during glucose excess conditions The most likely
explanation is that the missing carbon ends up in
bio-mass and biobio-mass-related CO2 Note that CO2was not
measured in the fermentative-capacity assay and the reported CO2 flux is calculated based on the catabolic fluxes We recalculated the fluxes through the enzymes
by assuming that the gap in the carbon balance was caused by a flux from pyruvate to biomass Although this had an effect on the absolute fluxes, it had little impact on the regulation analysis reported below However, if the gap was caused by drainage at other points in glycolysis and if the relative flux through such a branch differed between time points, this may somewhat affect the reported regulation coefficients in the control experiment
The fluxes through the individual enzymes were cal-culated from the measured off-line fluxes (Table 2) as described in Experimental procedures Figure 2 shows the results A shift to glucose excess resulted in an upregulation of the fluxes through all glycolytic and fermentative enzymes The same shift in glucose con-centration but accompanied by nitrogen starvation resulted in a downregulation of the same fluxes In Fig 2, the flux through alcohol dehydrogenase and through the enzymes in the lower branch of glycolysis
Fig 1 Whole-cell protein and cell numbers per liter of cell culture were measured after a shift to nitrogen-starvation and glucose-excess (closed circles) or glucose- and nitrogen-excess conditions (open circles), from glucose-limited chemostat conditions The error bars in the figure of whole-cell protein represent the SEM of four independent nitrogen-starvation experiments and of three independent glucose-excess experiments carried out on a total of seven different chemostat cultures The error bars in the figure of cell number represent SEM of two independent experiments of both perturbation conditions carried out on a total of four different chemostat cultures.
Table 2 Experimentally measured fluxes expressed in mmolÆmin)1Æg)1for the various time points (tndenoted as n hours after the start of the perturbation) for both perturbations Negative values represent consumption of the metabolite by the pathway, and positive values repre-sent the production of the metabolite The errors reprerepre-sent SEM of three independent experiments carried out on different chemostat cultures (two for t24in nitrogen-starvation experiment) Fluxes were not determined (n.d.) at t24in the glucose excess experiment.
Nitrogen starvation Glucose )0.40 ± 0.02 )0.40 ± 0.02 )0.37 ± 0.00 )0.33 ± 0.02 )0.31 ± 0.02 )0.17 ± 0.02
Ethanol 0.66 ± 0.04 0.60 ± 0.02 0.56 ± 0.01 0.54 ± 0.01 0.56 ± 0.03 0.53 ± 0.01 Glycerol 0.08 ± 0.00 0.08 ± 0.00 0.09 ± 0.00 0.08 ± 0.00 0.08 ± 0.00 0.05 ± 0.01 Trehalose 0.00 ± 0.00 0.00 ± 0.00 0.00 ± 0.00 )0.01 ± 0.00 )0.01 ± 0.00 )0.04 ± 0.01 Glucose excess Glucose )0.37 ± 0.03 )0.52 ± 0.01 )0.56 ± 0.02 )0.57 ± 0.02 )0.60 ± 0.06 n.d.
Glycerol 0.08 ± 0.00 0.09 ± 0.00 0.09 ± 0.00 0.09 ± 0.01 0.09 ± 0.01 n.d Trehalose 0.00 ± 0.00 0.00 ± 0.00 0.00 ± 0.00 0.00 ± 0.00 0.00 ± 0.00 n.d.
Trang 5corresponds to the fermentative capacity Upon the
shift from glucose limited to glucose excess conditions
(in the presence of nitrogen) the fermentative capacity
increased by 40% When the same shift was
accompa-nied by the shift to nitrogen starvation a 20% decrease
in fermentative capacity was observed This suggests
that the decrease in fermentative capacity is an effect
of the nitrogen starvation itself, but was counteracted
by the shift from glucose-limited to glucose excess
conditions Both the decrease in the fermentative
capacity during nitrogen starvation and the increase
during glucose excess (in the presence of nitrogen) in
glucose consumption and ethanol production were
significant (Student’s t-test, P < 0.05)
Enzyme capacities
We also measured how the catalytic capacities (Vmax)
of the enzymes involved in fermentation developed in
time Figure 3 shows these Vmaxvalues as a percentage
of their values at t0 (absolute enzyme capacities are presented in Tables S3 and S4) During the first 4 h of nitrogen starvation, all enzymes except for phospho-glucose isomerase (PGI) and glyceraldehyde 3-phos-phate dehydrogenase (GAPDH) were downregulated significantly Importantly, after 24 h of nitrogen star-vation the capacities of the enzymes 3-phosphoglycer-ate kinase (PGK), phosphoglycer3-phosphoglycer-ate mutase (GPM) and pyruvate kinase (PYK) had returned to their original levels of t0(Fig 3 and Table S3)
When the cells were transferred from glucose limited
to glucose excess conditions in the presence of nitro-gen, the capacities of hexokinase (HXK), aldolase (ALD), PGK, GPM, PYK and pyruvate decarboxylase (PDC) were upregulated The capacity of alcohol dehy-drogenase (ADH) was downregulated and the capaci-ties of PGI, phosphofructokinase (PFK) and GAPDH remained constant PGI was only downregulated at
Fig 2 Fluxes through the glycolytic and fermentative pathways under anaerobic glucose excess conditions in cells that had undergone the shift to nitrogen starvation and glucose excess or to glucose excess conditions in the presence of nitrogen Cells were transferred to the off-line assay system at various time points during nitrogen-starvation and glucose-excess (closed circles) or during glucose- and nitrogen-excess conditions (open circles) In this simplified scheme of the glycolytic and fermentative pathways, enzymes with the same flux are depicted in the same box Measured fluxes are depicted in bold Branching metabolites connect the boxes Fluxes were calculated based on the stoichi-ometry of the glycolytic and fermentative pathways (described under Experimental procedures) In the graphs, the fluxes through the glyco-lytic and fermentative pathways are plotted as a function of time Fluxes are depicted in percentage with respect to the flux at t0 The error bars represent the SEM of three independent experiments carried out on cells from different chemostat cultures (two for t 24 in the nitrogen-starvation experiment).
Trang 64 h The trend, that more enzymes were upregulated
than downregulated, parallels the observed
upregula-tion of the fluxes under this condiupregula-tion
Time-dependent regulation analysis during the
first 4 h
If the initial regulation during nitrogen starvation was
dominated by unspecific bulk degradation of cytosolic
proteins and small organelles, all hierarchical
regula-tion coefficients should be equal to 1 initially
Accord-ing to the summation theorem (Eqn 4) all metabolic
regulation coefficients should then equal zero If,
alter-natively, metabolic regulation comes into play early
on, one might expect mixed or pure metabolic
regula-tion, exemplified by hierarchical regulation
coeffi-cients < 1 in the early time points To test these
possibilities quantitatively, time-dependent regulation
analysis was applied to the data to assess how the
fluxes under the conditions of the fermentative
capac-ity were regulated as a function of the time into
nitro-gen starvation (or, in the control experiment the time
into glucose and nitrogen excess)
Hierarchical coefficients were calculated as a func-tion of time into starvafunc-tion according to the integrative form of time-dependent regulation analysis (Eqns 4 and 5) The results for the two perturbations are shown in Fig 4 (shift from glucose limitation to nitro-gen starvation and glucose excess) and Fig 5 (relief from glucose limitation only) Instead of the antici-pated hierarchical regulation, a diversity of regulation was observed in the first 4 h of nitrogen starvation and even within the first hour (Fig 4) In the shift to glu-cose excess experiments, in the presence of nitrogen, the regulation was different, but again diverse Below, the different categories of regulation and the shifts from one to another that were observed during the first 4 h, are discussed
Purely metabolic regulation Enzymes with a metabolic regulation coefficient (qm) close to 1 and a hierarchical regulation coefficient (qh) close to 0 were found in cells adjusting to nitrogen starvation, as well as in cells accommodating excess glucose The changes in fluxes through these enzymes
D
Fig 3 The V max values of the glycolytic and fermentative enzymes expressed as percentages with respect to their values at t 0 , during shift
to nitrogen-starvation and glucose-excess (closed circles) or to glucose-excess conditions in the presence of nitrogen (open circles) Error bars represent the SEM of three (two for t 24 in nitrogen-starvation experiment) independent experiments carried out on cells from different chemostat cultures Absolute values are reported in Tables S3 and S4.
Trang 7were regulated purely by interactions with their
sub-strate(s), product(s) or other metabolites and not by
changes of Vmax GAPDH was regulated metabolically
in both perturbations, PGI only upon nitrogen
starva-tion and PFK only after the shift to glucose-excess
conditions in the presence of nitrogen
Purely hierarchical regulation
Few enzymes were found to have a qh value close to 1
during the first 4 h The flux through these enzymes
was mainly regulated through the change in Vmax The
contribution of their interaction with their substrate(s)
and product(s) to the regulation of their capacity was
thereby negligible During nitrogen starvation, only
PGK was regulated hierarchically and GPM came
closest in the shift to glucose excess, in the presence of
nitrogen (Fig 5)
Antagonistic regulation directed by metabolism
A negative qhvalue is obtained when the flux changes
in the opposite direction compared with the Vmax This
implied that metabolic regulation dominated and was counteracted by hierarchical regulation The regulation
of ADH during glucose-excess conditions in the pres-ence of nitrogen was the prime example of this category, to an extent increasing with time
Progression towards more hierarchical regulation
In this category, any time profile was classified that showed an increasing contribution by hierarchical reg-ulation This could be a shift of qh from 0 to 1, but also any other time profile in which qhincreased This means that, as time progressed, changes in Vmax became more important at the cost of metabolic regu-lation The enzymes PFK, GPM and ADH belonged
to this category when the cells were starved of nitro-gen PGK was regulated in this way in the cells shifted
to glucose excess in the presence of nitrogen HXK, ALD, PYK and PDC showed increasing hierarchical regulation upon both perturbations However, upon the shift from limiting to excess glucose with excess nitrogen throughout, all these enzymes showed decreased hierarchical regulation after 3 or 4 h
Fig 4 Hierarchical regulation coefficients quantifying the regulation upon shift to nitrogen-starvation and glucose-excess conditions Regula-tion coefficients were calculated according to the integrative time-dependent regulaRegula-tion analysis (see IntroducRegula-tion) The error bars represent SEM of three independent experiments carried out on cells from four different chemostat cultures The dashed lines indicate a qhof 1.0 and the dotted lines indicate a qhof 0.
Trang 8Progression towards metabolic regulation
This category is the opposite of the previous one In
this case, metabolic regulation becomes more
impor-tant over time The behaviour of PGI during
glucose-excess conditions in the presence of nitrogen is an
example of this form of regulation
A summary of all regulation is given in Table 3 This
shows visually that 5 of 10 enzymes exhibit a similar
regu-lation pattern upon the two different perturbations
Furthermore, there is large variation between the
condi-tions, although under starvation condicondi-tions, 7 of 10 enzymes tend to an increased contribution by gene expression as a function of time Altogether, the results indicate that at no point into starvation did the enzyme capacities reduce proportional to each other and to the flux With initially four enzymes predominantly regu-lated metabolically (HXK, PGI, PFK, GAPDH, qhclose
to zero at 1 h), five enzymes dominated by gene expres-sion (ALD, PGK, GPM, PDC, ADH, qh‡ 1 at 1 h) and one enzyme with cooperative regulation (PYK,
0 < qh< 1 at 1 h), one cannot state that autophagy
Table 3 Categories of regulation Enzymes were classified to the various categories based on the regulation during the first 4 h after the start of the perturbations, i.e nitrogen-starvation and glucose-excess conditions (closed circles) or glucose- and nitrogen-excess conditions (open circles) ADH, alcohol dehydrogenase; ALD, aldolase; GAPDH, glyceraldehyde 3-phosphate dehydrogenase; GPM, phosphoglycerate mutase; HXK, hexokinase; PDC, pyruvate decarboxylase; PFK, phosphofructokinase; PGI, phosphoglucose isomerase; PGK, 3-phosphoglycer-ate kinase; PYK, pyruv3-phosphoglycer-ate kinase.
A
E
I
B
F
J
C
G
D
H
Fig 5 Hierarchical regulation coefficients quantifying the regulation upon the transition to glucose-excess conditions in the presence of nitrogen Regulation coefficients were calculated according to the integrative time-dependent regulation analysis (see Introduction) The error bars represent SEM of three independent experiments carried out on ditto-different chemostat cultures The dashed lines indicate a q h of 1.0 and the dotted lines indicate a q h of 0.
Trang 9precedes metabolic regulation or vice versa (Fig 4).
Apparently, both mechanisms contribute from the
begin-ning Seven of ten enzymes exhibited a shift in regulation
between 1 and 4 h, always in the direction of hierarchical
regulation
Integrated regulation after 24 h
In this study, the growth condition prior to the nitrogen
starvation differed from the conditions used in the
ear-lier study of Rossell et al [9] Here, we have grown
yeast under glucose-limited conditions (chemostat
culti-vation at a high dilution rate), whereas in the study of
Rossell et al [9] cells were grown in glucose excess
(batch cultivation) To compare the two studies, we
cal-culated the regulation coefficients after 24 h of nitrogen
starvation from our data and compared the results to
those from the earlier batch study Table 4 shows the
results The initial growth condition did not have any
effect on the type of regulation of HXK, PGI, ALD,
PDC and ADH In both cases, regulation was
domi-nated by gene expression (qh close to 1 or higher),
although the precise numbers differed substantially
between the two conditions Under both initial growth
conditions, PGK was regulated by metabolism (qhclose
to 0) Because the SEM of the enzyme GAPDH was
considerable in the study by Rossell et al [9] is unclear
whether the discrepancy between the two studies in the regulation of GAPDH is real However, the enzymes PFK, GPM and PYK were clearly regulated differently under the two growth conditions Apparently, the regu-lation of the flux through these enzymes upon the intro-duction of nitrogen starvation is sensitive to the growth conditions prior to nitrogen starvation
Transcript levels The diversity in the time profiles of the Vmax values suggested that, apart from unspecific bulk degradation
of proteins, other more specific regulation mechanisms
of protein regulation were involved in the response to nitrogen starvation To investigate the extent to which such regulation took place at the mRNA level, we measured the transcript levels of nearly all glycolytic and fermentative genes using qPCR (Fig 6) First, the
Vmax levels of PGI and GAPDH remained constant
We wondered whether (possible) degradation of these proteins would be compensated for by increased syn-thesis driven by increased transcription, but we found
no increase in the mRNA levels of these enzymes Figure 6A shows that the transcript level of PGI1 did not change significantly The transcript levels of the TDH genes, which code for GAPDH, were changed significantly (Student’s t-test, P < 0.05) TDH1 was increased, and TDH2 and TDH3 were both decreased (Fig 6B) However, because TDH3 was the most abundant of the three, the total transcript level of the TDH genes was decreased Second, trends observed in the Vmax during the first 4 h were sometimes reversed
at the 24 h time point For example, the Vmax values
of PGK, GPM and PYK decreased during the first
4 h, but recovered to their original values at 24 h Recovery of the Vmax of PGK was, however, not pre-ceded by a significant increase in transcript level In the case of PYK, one isoform increased and the other decreased at the mRNA level Again one of the tran-scripts, in this case PYK1, was highly abundant, which resulted in lower total PYK mRNA levels Because of problems with the primer sets, transcript levels of GPM were not measured Finally, in most cases, the changes in transcript levels predicted changes in isoen-zyme distributions, but no overall up- or downregula-tion It seems that the hierarchical part of the regulation is quite subtle and cannot be attributed to a single process in the gene expression cascade
Discussion
Time-dependent regulation analysis quantifies the rela-tive importance of metabolism and gene expression in
Table 4 Comparison of the regulation coefficients after 24 h of
nitrogen starvation of cells that started off as respiro-fermentative
growing cells in a chemostat culture at D = 0.35 h)1and cells that
started off as growing exponentially in a batch culture [9] The
errors represent, SEM of two independent experiments carried out
on different chemostat cultures (this study) and SEM of four
inde-pendent experiments carried out on different batch cultures ADH,
alcohol dehydrogenase; ALD, aldolase; GAPDH, glyceraldehyde
3-phosphate dehydrogenase; GPM, phosphoglycerate mutase;
HXK, hexokinase; PDC, pyruvate decarboxylase; PFK,
phosphofruc-tokinase; PGI, phosphoglucose isomerase; PGK,
3-phosphoglycer-ate kinase; PYK, pyruv3-phosphoglycer-ate kinase.
Enzyme
Respiro-fermentative
growing cells (this
study)
Exponential growing cells Rossell et al [9]
Trang 10flux regulation In this study, we applied the method
to dissect the primary mechanism(s) of flux regulation
when yeast cells were adapting to nitrogen starvation
Our results showed that after 1 h of nitrogen
star-vation some enzymes were dominated by metabolic
regulation, whereas others were predominantly
hierar-chically regulated GPM, PGK and to a lesser degree
PYK exhibited hierarchical regulation during the first
hour of nitrogen starvation and metabolic regulation
after 24 h, which would be in line with a primary role for autophagy HXK, PFK and PGI, however, were initially rather regulated by metabolism and showed more hierarchical regulation after 24 h This shows that on its own, neither autophagy nor metabolism could be the primary cause of the loss of fermentative capacity Rather, a subtle interplay between the two was observed from the beginning
The diversity of regulation observed during the first few hours of nitrogen starvation cannot be explained simply from the addition of high glucose to the starva-tion medium Not only did we observe a decrease in many enzyme capacities during nitrogen starvation in the presence of high glucose and an increase upon glu-cose excess in a full growth medium, there was no (inverse) correlation between the degree of downregu-lation under nitrogen starvation and the degree of upregulation upon glucose excess
We compared the measured flux and Vmax data to earlier reports Both fermentative capacity and enzyme capacities measured at time point 0 h (nonstarved yeast cells) were highly comparable to the data obtained by Van Hoek et al for yeast grown under identical conditions [20] In addition, we calculated whether the measured Vmax values can support the fluxes measured under both perturbations This is true for all enzymes, with the exception of PFK in the nitrogen-excess experiment The fact that PFK has quite a few allosteric regulators, i.e ATP, citrate, fructose-2,6-bisphosphate, etc., might complicate mea-suring the actual Vmax However, fructose-2,6-bisphos-phate is no longer commercially available, which limits the possibilities for rapid further measurements Alto-gether our results were similar to literature data and make sense to the yeast cell physiology
Because both metabolic and hierarchical regulation played a role in the adaptation of the yeast cell to nitrogen starvation, we discuss the mechanisms acting
at each level The hierarchical regulation can be divided into several levels, i.e mRNA synthesis and degradation, protein synthesis and degradation and protein modification
The finding that some Vmax values decreased faster than others is not consistent with the simple view of unspecific bulk degradation of cytosolic proteins The simplest explanation might be that degradation of some enzymes is rapidly compensated by new synthe-sis The synthesis of proteins can be regulated via the concentrations of the corresponding mRNAs or the translation of these mRNAs Although we observed some regulation of glycolytic mRNA levels (Fig 6), there was no direct correlation with the time profiles
of the corresponding Vmax values Notably, restoration
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Fig 6 The ratios of [mRNA]t ⁄ [mRNA]t ss of the glycolytic and
fer-mentative genes during nitrogen starvation Data were normalized
to the mean of the control gene PDI1 and the steady-state samples
of the nitrogen starvation experiments The error bars represent
the SEM of three independent experiments carried out on different
chemostat cultures (two for time point t24).