Escherichia coli adenylate cyclase at

Comments: Diauxie

Comments are by M. Crasnier-Mednansky (martine [at] minst [dot] org)

Sci Rep. 2016
The lag-phase during diauxic growth is a trade-off between fast adaptation and high growth rate
Chu D, Barnes DJ
This comment was originally posted on Feb 1, 2017 at PubMed Commons

It is astounding that the authors totally ignore the specific effects of cAMP on the lag phase of the glucose-lactose diauxie.  Not only does addition of cAMP eliminate the diauxic lag, it also clearly impairs growth on glucose (see figure 1 in Ullmann A, 1968).  An increased level of cAMP triggers a 'leaky' expression of CRP-cAMP-dependent genes and operons thereby affecting growth on glucose.  Leaky expression of genes reduces fitness in glucose, with a trade-off for a shorter diauxic lag (or, as in figure 1 mentioned above, a complete elimination of the lag phase resulting in biphasic growth).  In the Escherichia coli glucose-lactose diauxie, there is a correlation between the cAMP level and the cost-benefit trade-off.

Sci Rep. 2016
Glucose becomes one of the worst carbon sources for E. coli on poor nitrogen sources due to suboptimal levels of cAMP
Bren A, Park JO, Towbin BD, Dekel E, Rabinowitz JD, Alon U
This comment was originally posted on May 4, 2016 at PubMed Commons

There are several discrepancies in this paper which cannot be reconciled.  For example, Figure 1a and Table S1 indicate a growth rate of 0.76 hr-1 for maltotriose with ammonia as nitrogen source.  The glucose-maltotriose diauxie with ammonia (Figure 2a, upper and middle panel) indicates a growth rate for maltotriose of 0.37 hr-1.  In diauxie, the growth rate on each sugar is characteristic of that sugar (Monod, 1942).  Therefore, the glucose-maltotriose diauxie should exhibit a growth rate of 0.76 hr-1 for maltotriose.  It is likely that the presence of the reporter gene in the diauxie experiment (Figure 2) is affecting the growth rate on maltotriose.

J Bacteriol. 2015
Acetate Exposure Determines the Diauxic Behavior of Escherichia coli during the Glucose-Acetate Transition
Enjalbert B, Cocaign-Bousquet M, Portais JC, Letisse F
This comment was originally posted on Jan 16, 2017 at PubMed Commons, updated February 28, 2019

Growth of Escherichia coli on excess glucose under aerobic conditions is not diauxic (Wolfe AJ, 2005), and the acetate switch is certainly not "classically described as a diauxie".  It is therefore extraordinary that the authors are now showing that "diauxic behavior does not occur under such conditions".  A diauxie in the presence of both glucose (not in excess) and acetate in the culture medium was reported by Kao KC, 2005.
Unfortunately, growth on excess glucose was still described as being diauxic by Succurro A, 2019 who erroneously stated: A classical and yet still actively studied example of adaptation to dynamic environments is the diauxic shift of Escherichia coli, in which cells grow on glucose until its exhaustion and then transition to using previously secreted acetate.

Nucleic Acids Res. 2013
Structures of the Escherichia coli transcription activator and regulator of diauxie, XylR: an AraC DNA-binding family member with a LacI/GalR ligand-binding domain
Ni L, Tonthat NK, Chinnam N, Schumacher MA
This comment was posted on January 24, 2013 at

Introduction states, "With the broader goal of generating an E. coli biocatalyst that can co-metabolize all biomass sugars, it would be necessary to also eliminate the diauxie between D-xylose and L-arabinose, as these two sugars comprise 95% of the total sugar hemicellulose (Kim JH, 2010; Inada T, 1996)".  Xylose and arabinose are two class B sugars for E. coli as defined by Jacques Monod, and there is no report of a diauxic growth between xylose and arabinose, even though E. coli was reported to preferentially utilize arabinose when grown in a mixture of xylose and arabinose.  In addition, Kim JH, 2010 and Inada T, 1996 do not report a diauxie with xylose and arabinose.  Kim JH, 2010 report, in the presence of glucose, xylose and arabinose were simultaneously consumed in E. coli ptsG mutant strains, lacking Enzyme IICBGlc, as in such mutants Enzyme IIAGlc remains phosphorylated thus eliminating inducer exclusion and cAMP-dependent catabolite repression.  Reference to Inada T, 1996 is inappropriate for supporting the existence of a diauxie with xylose and arabinose.

Mol Syst Biol. 2010
Bacterial adaptation through distributed sensing of metabolic fluxes
Kotte O, Zaugg JB, Heinemann M
This comment was originally posted on Mar 13, 2015 at PubMed Commons

Escherichia coli cells growing on excess glucose (Fig. 3, Environment G) do not consume acetate after glucose depletion (the acetate switch occurs before glucose is fully depleted).  In fact, cells utilize both glucose and acetate during entry into the stationary phase of growth (see Fig. 1A in Wolfe AJ, 2005).  Failure to assimilate acetate before glucose depletion was reported for a specific mutant strain and resulted in a diauxic type of growth (Nyström T, 1993).

Acetate utilization by acetate-adapted cells is not diminished by glucose addition (Lowry OH, 1971).  Furthermore glucose utilization by acetate-adapted cells is inhibited by acetate.  It is therefore questionable whether acetate-adapted cells are 'adapting' to glucose when transferred to a medium containing a large excess of acetate (Fig. 3, Environment GA).  In this context, the reversible phosphotransfer reaction between phosphoacetate kinase and the phosphotransferase system (PTS), originally proposed by Fox DK, 1986 but never established in vivo, should be physiologically relevant as to regulate the rate of sugar transport by the PTS and thus the cAMP level.

Nat Rev Microbiol. 2009
cAMP does not have an important role in carbon catabolite repression of the Escherichia coli lac operon
Narang A
This comment was posted on Mar 20, 2009 at

Wanner BL, 1978 stated, "Much of the variation [in β-galactosidase synthesis] was eliminated by growing E. coli in the presence of cAMP, and this component we call cAMP-mediated catabolite repression".  The remaining repression [in the presence of cAMP] was carbon source dependent and growth related, and possibly mediated by cAMP, as concluded by the authors.  It is therefore extraordinary to read cAMP does not have an important role in carbon catabolite repression of the Escherichia coli lac operon upon analysis of data by Wanner BL, 1978.  In addition, the author fully ignores the reasoning of a previous correspondence by Crasnier-Mednansky M, 2008 indicating a crucial role for cAMP in the glucose-lactose diauxie.  Wanner BL, 1978 further indicated a large variation in β-galactosidase activity occurred in media supporting similar growth rate (thus synthesis rate is not constant).  Therefore, their data did not indicate "β-galactosidase activity is inversely proportional to the specific growth rate", as reported.  In addition, data from Wanner BL, 1978, Figure 2B, did not indicate addition of exogenous cAMP increased β- galactosidase activities less than two-fold.  In fact, media in which there was marked growth rate inhibition by cAMP also showed large stimulation of β-galactosidase synthesis, and a growth rate inhibition was not a necessary condition for an increase in the enzyme activity.

PLoS Genet. 2007
Adaptive diversification in genes that regulate resource use in Escherichia coli
Spencer CC, Bertrand M, Travisano M, Doebeli M
This comment was originally posted on May 2, 2015 at PubMed Commons

The role of cAMP in the glucose-acetate diauxie was not taken into account by the authors however if it is taken into account, interesting possibilities arise.

Acetate utilization by the fast-switchers is suppressed during growth on glucose as shown by a biphasic growth curve indicating preferential use of glucose over acetate (Figure 1A, blue circles), and a nearly constant concentration of acetate in the medium to the switch point (Figure 1C, blue circles).  In contrast, an extended diauxic lag is observed with the slow-switchers (Figure 1A, red circles).  Both switchers however show identical growth rate during the first growth phase (red and blue circles in Figure 1A), same switching point in time, and same glucose use (red and blue circles in Figure 1B).

A diauxic lag disappearance and biphasic growth are typically associated with addition of cAMP to the growth medium (Ullmann A, 1968).  It was established that, during a downshift from glucose to acetate, the CRP-cAMP complex peaked during the first hour of transition, which correlated with an increase in cAMP (Kao KC, 2004).  Therefore addition of cAMP to a typical glucose-acetate diauxie most likely will affect the diauxic lag.  Moreover, a cAMP-dependent regulation of the aceBAK operon was previously inferred by the presence of CRP-binding sites within the operon and a strong glucose repression, as indicated by transcriptome data (Table 1 in Zhang Z, 2005).

So, what if the fast-switchers are no longer 'dependent' on the cAMP signal upon entry in the second phase of growth on acetate (in other words there is no need for CRP-cAMP in the absence of IclR for the transcription of the aceBAK operon).  It is then expected that the fast-switchers with an 'ancestral' iclR will exhibit a typical diauxic growth, which is what is observed (Figure 4A).

As regards the slow-switchers, their growth pattern does not significantly vary from the growth pattern of the ancestor.  They both resume growth on acetate after an extended lag, but very poorly as compared to the fast-switchers.  It is therefore not surprising that introduction of the iclRIS1 in the ancestor bares no consequences on the growth pattern.

A final note; micromolar concentrations of glucose were used for growth in the presence of both glucose and acetate (as indicated in M&M under Growth curve assay).  The increased concentration of acetate in the medium from the slow-switchers (Figure 1C, red circles) should not occur at glucose concentrations used in Figure 1A as dissimilation of acetate occurs under aerobiosis in excess glucose.