Escherichia coli adenylate cyclase at Minst.org

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Comments: 2016

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

J Bacteriol. 2016
Classic Spotlight: When Phenotypic Heterogeneity Met Carbon Catabolite Repression
Becker A
This comment was originally posted on March 7, 2016 at PubMed Commons

Escherichia coli cells, when 'pre-induced' in the presence of the artificial inducer TMG, synthesize β-galactosidase in the presence of glucose.  COHN M, 1959 stated, "The effect of pre-induction is to restore in the presence of 10-3 M glucose about 50 per cent of the maximal differential rate obtainable on succinate".  The observation the maximal rate was not reached in the presence of glucose led the authors to argue, indeed incorrectly, that glucose was a preferential metabolic source for yielding high internal levels of repressor.  Such observation however will have an explanation later on with the discovery of the 'cAMP effect' on β-galactosidase synthesis, in agreement with the finding by COHN M, 1959 that carbon sources presently known to elicit higher cAMP levels (particularly succinate, lactate and glycerol, see Epstein W, 1975) were found to be non-inhibitory (i.e. allowing maximal differential rate).  Anke Becker’s final statement, that inhibition of lactose permease by unphosphorylated Enzyme IIA (leading to inducer exclusion) is primarily responsible for CCR of the lac operon, is therefore inappropriate as cAMP via its receptor protein (simultaneously designated as CRP by Emmer M, 1970 and CAP by Zubay G, 1970) also plays a role in CCR of the lac operon.  Furthermore, Jacques Monod (1942) reported diauxie was attenuated -but not eliminated- when cells were pre-induced (adapted to the less preferred 'B' sugar).  Diauxie was however eliminated by addition of exogenous cAMP (Ullmann A, 1968).  Therefore, inducer exclusion and the level of cAMP both contribute to CCR of the lac operon.

Lastly, unphosphorylated EIIAGlc does not inhibit adenylate cyclase.  The current model of regulation postulates dephosphorylation of Enzyme IIA during glucose transport interferes with the activation of adenylate cyclase by phosphorylated Enzyme IIAGlc.

J Bacteriol. 2016
Classic Spotlight: the Birth of the Transcriptional Activator
Silhavy TJ
This comment was originally posted on Feb 20, 2016 at PubMed Commons

Is calling AraC a repressor for araBAD in the absence of L-arabinose overreaching?  In the looped state, when a subunit of AraC is bound to O2, the non-induced basal level of araBAD expression is impaired as compared to the unlooped state.  Indeed, deletion of O2 leads to an increase in araBAD transcription when an AraC subunit binds to I2 and interacts with the I1-bound AraC subunit.  As stated in Schleif R, 2010, "a consequence of looping in the ara system is depletion of the state in which AraC is bound at I1I2 in the absence of arabinose".  Therefore, it could be construed, in the looped state, the 'apparent' repression of araBAD in the absence of arabinose actually reflects a lack of transcriptional activation by AraC.  Thus it seems AraC is more of a switcher than a repressor.  That said, the conclusion by Englesberg E, 1965 that AraC exhibits both positive and negative control was perfectly legitimate at the time.  They tentatively proposed that the repressor was converted into an activator thereby establishing an analogy with the lactose system, "…instead of the repressor being converted into an inert substance, we propose that, in the L-arabinose system, it is converted to a biologically necessary entity [an activator]".

Nucleic Acids Res. 2016
The target spectrum of SdsR small RNA in Salmonella
Fr÷hlich KS, Haneke K, Papenfort K, Vogel J
This comment was originally posted on Aug 4, 2016 at PubMed Commons

Expression of crp in Escherichia coli was found 'not to be' post-transcriptionally regulated by sRNAs including SdsR (Lee HJ, 2016).  In sharp contrast, this paper reports SdsR 'strongly' affects the expression of crp in Salmonella typhimurium.  What causes such discrepancy?

In all fairness, Lee HJ, 2016 noted "a few sRNAs (which included SdrS) were close to the twofold cutoff for repression of crp" and also noted "our translational fusions will only detect regulation in the 5’ UTR and the first 20 codons of the targets".  Therefore, it was prudently suggested that expression of crp was not affected by sRNAs.

Here, the authors observed a two-fold repression of crp by SdsR using whole genome microarray (Table 1), and an almost 2-fold repression using a gfp reporter fusion (Figure 1B).  Thus it appears there is no data discrepancy between the present work and Lee HJ, 2016.

The contention by the authors SdsR strongly affects the expression of crp is in relation to data obtained with sRNA CyaR (as reported in Figure 6).  Figure 6A indicates that, in early stationary phase, there is no synthesis of SdsR.  SdsR appears at +3h when the cells are supposedly well advanced in the stationary phase.  This suggests regulation by SdsR occurs late in the stationary phase, as mentioned by the authors.  Figure 6A also indicates constitutive SdsR is overly expressed, and most importantly the correlation between SdsR and crp mRNA is not straightforward, as observed by comparing lane 4 and 10 (or 11) in Figure 6A.

CyaR expression is positively regulated by CRP-cAMP (De Lay N, 2009), therefore a carbon source triggering a relatively high cAMP level as compared to glucose (maltose in this paper), caused an increase in the CyaR level both in the presence and absence of SdsR (Figure 6B, lane 1 to 8).  With SdsR overly expressed, the CyaR level significantly decreased for cells grown on maltose (Figure 6B, lane 11 and 12).  The authors concluded lack of CyaR is related to the repression of crp by SdsR yet the level of CRP was not monitored.

It is reasonable to conclude regulation of crp expression by sRNAs does not appear physiologically relevant during growth or entry into stationary phase.  However, this regulation may be significant upon accumulation of SdsR in nutrient-limited cells.  If this is the case, CRP-dependent synthesis of post-exponential starvation proteins, which are not essential for survival (Schultz JE, 1988), will gradually be shut off.  This attempted proposal is grounded in data from LÚvi-Meyrueis C, 2014 indicating lack of SdsR results in impaired competitive fitness however only after 2 to 3 days in stationary phase.

Mol Microbiol. 2016
Regulation of CsrB/C sRNA decay by EIIAGlc of the phosphoenolpyruvate: carbohydrate phosphotransferase system
Leng Y, Vakulskas CA, Zere TR, Pickering BS, Watnick PI, Babitzke P, Romeo T
This comment was originally posted on Dec 14, 2015 at PubMed Commons

This article is remarkable for demonstrating an interaction between unphosphorylated Enzyme IIA and the EAL domain of CsrD.  Such interaction is physiologically connected to the role of cAMP in Escherichia coli because there is an established correlation between the phosphorylation state of Enzyme IIAGlc and the level of cAMP, phosphorylation of Enzyme IIAGlc typically causing an increase in the cAMP level (and concomitantly eliminating the effect of Enzyme IIAGlc on CsrD).

The authors discussed the present regulatory interaction with no mention to the role of cAMP.  However, considering (1) the inhibitory function of (CsrD-controlled) CsrA on glycogen biosynthesis, (2) the ability of stationary-phase E. coli to accumulate glycogen as a carbon reserve, and (3) the increase in cAMP occurring upon entry into the stationary phase (Makman RS. 1965) (because of Enzyme IIAGlc rephosphorylation), it seems CsrD and CRP-cAMP both work 'in concert' for the timeliness of physiological processes during entry into stationary phase, particularly when cells are growing on glucose.