Journal of Robotics, Networking and Artificial Life, Vol. 1, No. 1 (June 2014), 17-21

Intelligent mechanisms in E. coli in processing carbon sources
Zhongyuan Tian

Graduate School of Science and Engineering, Yamaguchi University,1677-1 Yoshida, 753-8512 Yamaguchi-shi, Yamaguchi, Japan
Hiroshi Matsuno

Graduate School of Science and Engineering, Yamaguchi University,
1677-1 Yoshida, 753-8512 Yamaguchi-shi, Yamaguchi, Japan
Tel/Fax : +81-83-933-5697
E-mail: matsuno@sci.yamaguchi-u.ac.jp

Abstract
E. coli is “wise” enough to take suitable responding time, and suitable responding behaviors, when facing different kinds andintensities of stimulations. In a network of glycogen metabolism, a shorter time stimuli result in the post translation level reactions forquicker response, and a longer time stimuli will activate more time consuming the central dogma level reactions. In addition, different
intensities of signals caused by different actions was illustrated by using gene products expression system based on ppGpp
concentration.

Keywords: chemotaxis, PTS, ATP, ppGpp, the central dogma, post translation

1. Introduction
A human’s body will initiatively or positively takereactions via reflex arc system or deep tendon reflexes
system, facing to different kinds and intensities ofstimulations. E. coli, a bacterium, is it “wise” enough totake suitable reactions towards the variety signals? Herethe word “suitable” includes suitable responding time,and suitable responding behaviors. Our answer is “Yes”.
In E. coli, different kinds, time length or intensities ofsignals can drive suitable functioning units (e.g.
proteins) on suitable levels to make suitable reactions.
According to the time cost of a respond to a signal,
we divide the intracellular processes into 2 levels:
central dogma level and post translation level (Fig 1).

The central dogma level includes the whole process of agene transcribed to an mRNA then translated to aprotein. The post translation level includes otherintracellular process of non direct relation with genetic
DNA or mRNA, for example protein-protein interaction,
protein-metabolite interaction, protein localization,protein motion, etc. The time consuming for an action in
the central dogma level is longer than that in the posttranslation level.
For E. coli, the average length of coding sequences
is 1068 bp [1], and the maximal transcription speed isabout 40-80 bp/sec [2, 3], the maximal translation speed
is about 20 aa/sec [3, 4], then the average time cost for agene expression in an optimal condition is about 40second. But in reality, a g ene’s expression may costs

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17Fig. 1 According to the time cost of i ntracellular action, we
divide the intracellular processes into two levels: the central
dogma level and the post translation levelfrom several minutes to several days. And the time
consuming in post translation level is commonly much
shorter then that of central dogma level. For example,
the for a chemotaxis reaction in E. coli, only need few
seconds, or even in a sub-second time scale [5], which
includes at least 6 steps actions of the post translationlevel from a s ignal to a c hemoreceptor, …, at last to aflagella.
In this context, examples (a) uses a systematicalmodel of PTS-Chemotaxis-glycogen to describe
different levels’ responds resulted from a same kind ofstimuli coming with different time lengths.
According to intensity of a signal, the respond should beclassified into low, mid and high intensity cases, which
is illustrated by the example (b): Using a ppGpp-RNAP
model to explain different kinds of actions are causedby different intensities of the stimuli.
2. Example (a): the same kind of stimuli comingwith different time lengths result in different
levels’ responds
In studies on E. coli, PTS, glycogen, and flagellum
are common objects, but always studied separately. PTS
is the transport system for an E. coli intaking cultural
glucose [6]. Glycogen is a polymer functioning as acarbohydrate intracellular storage [7]. Flagellum
together with FilM and CheY forms the E. coli motion
driver, which gives in time response to the five kinds ofchemoreceptors [8].
Intra these 3 systems, EI, HPr, EIIAGlc and ATP are key
mediators. Un-phosphorylated EI (EI) inhibits the autophosphorylation of CheA (P~CheA), which in turn stops
the transferring of phosphate group from P~CheA to theflagella motor CheY; this will causes flagella rotating inclock-wise (CW) direction and E. coli will tumbling

Fig. 2 Shorter time stimulation causes responses on the posttranslation level, which is realized by the network of P TS,
glycogen and chemotaxis system.

here [6]. The binding of un-phosphorylated HPr (HPr)with GlgP (HPr::GlgP) catalyzes a quicker glycogendecomposition, EIIAGlc regulates expression levels ofglgBXCAP, ptsHIcrr and ptsG, indirectly via
cAMP/CRP complex [9]. ATP is a necessary member of
CheA auto-phosphorylation (Equ. 1) and ADPG
synthesis (Equ. 2) [10]. We can find, despite EIIAGlc
works up to the central dogma level, all the other 3
mediators are mainly functioning in the post translationlevel.
𝐶ℎ𝑒𝑒 + 𝐴𝐴𝐴 ⇋ 𝑃~𝐶ℎ𝑒𝑒 + 𝐴𝐴𝐴(1)
𝐺1𝑃 + 𝐴𝐴𝐴

𝐺𝐺𝐺𝐺⟹

𝐴𝐴𝐴𝐴 + 𝑃𝑃𝑃(2)

Shorter time stimulation causes responses on thepost translation level. The analysis in this section isbased on an assumption: proteins levels are sufficient toperform their functions. In Fig. 2, glucose and ATP are 2
stimuli of outside (in the culture) and inside(intracellular) respectively. When an E. coli meets
glucose at the first time, it quickly activates the poles
located PTS (un-phosphorylated) by passing phosphategroup to glucose. Meanwhile glucose as achemotaxis signal has been captured by poles locatedchemoreceptors. Signals form both these 2 pa thways

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repress the CheA auto-phosphorylation, which at lastresult in E. coli run-forward by rotating flagella incounter clock-wise (CCW) direction. Simultaneously,
poles located HPr::GlgP complex makes pole-locatedglycogen a quick decomposition to supply more
phosphate group as soon as possible, sinceglycogenolysis is a quicker process and needless energy
driven.
If then outside glucose disappears, chemoreceptors
will lose its inhibition on CheA auto-phosphorylation,
so as the phosphorylated EI (P~EI). Now, E. coli willstop run-forward, instead, turn direction (tumbling),
until catching another glucose.
If following the first step, the outside glucose is
there still; the un-phosphorylated CheY will continue todrive E. coli run-forward. But accompany with quick
glycogenolysis driven by EI, much more ATP isproduced in the pathway of glycolysis and TCA cycle.
Accompany with the sudden accumulation of
intracellular ATP, the glycogenesis pathway is turned
on, which is caused by glycogen content varies
inexpertly; and the CheA auto-phosphorylation process
will be returned on by the higher pressure of ATP andlower pressure of the inhibitions, which results in E. coli
tumbling-reorient.
After the aforementioned preparation period, if there
is still a glucose signal, then E. coli will “realize”: there
really has a “glucose banquet”. At this time, more
phosphate grout is transferred from PEP to PTS for
glucose uptake, ATP is in a quite flat level. E. coli runs
into the glucose now.
In all, for shorter time stimulation, when an E. colimeets glucose (outside stimulus), it quickly takes
suitable types of motion and uptake simultaneously. But
if the time length of this decision left for E. coli islimited in only a few seconds, a longer time scale would
become re-oriented by Brownian motion [5]. Whenintracellular phosphate group (ATP) lacks (insidestimuli), the corresponding flagella motion andintracellular behavior will change.
In order to clarify the relationship with glucose, ATP,glycogen and flagella, we construct a Boolean networkwith Ginsim [11] (Fig. 3a). And from the result of its
analysis (Fig. 3b), we can find, the system of double
signals (glucose and ATP) and double responses

Fig. 3 Boolean network and states transition analysis result of
the switch of ATP, glucose, glycogen and chemotaxis system.

(Flagella and glycogen) reaches 2 stable states, ofwhich: 1000 represents there is only ATP, but no glucose
and glycogen, E. coli will tumble there to reorient; 0101means if there is no ATP and glucose, but only glycogenremains, the E. coli will go straight. This mechanism
can be understood as a switch of E. coli facing shortertime stimulation. In one word, E. coli now either
tumbles there with ATP inside, or run forward withglycogen inside. We should not forget, afore-talked
mechanism only occurs at the first few seconds.
Longer time stimulation causes responses on thecentral dogma level. If an E. coli is emerged in aglucose culture, then the stimulating time is longenough to activate the reaction of the central dogma
level. This process includes a series of complex
networks, such as PEIIAGlc&cAMP and FDP&Cra
subpathways, (As show in Fig. 4), which wereexplained in the paper [9].

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genes. As all nutrition starvation occurs, Highconcentration ppGpp will be produced, which together

Fig. 5 Different intensities of p pGpp result in different kindsof RNAP actions.

with DksA binds to and drive RNAP employing RpoS
to transcribe mRNA only.

4. Conclustion
Fig. 4 Regulation mechanisms inter PTS and glycogenmetabolism: PEIIAGlc&cAMP pathway, FDP&Cra pathway
and HPr subcellular localization

3. Example (b): Using a ppGpp-RNAP model toexplain that different kinds of actions arecaused by different intensities of the stimuli
ppGpp is a stringent alarmone in E. coli, whosemechanism was clearly studied by Traxler et al. in theirseries papers [12–14]. Fig. 5 shows that the 3 “ bands”
of ppGpp intensities result in 3 types of RNAP
functions. If there is no starvation signal in an E. coli
(ppGpp is null), RNAP will employ RpoD to transcribe
mRNA and rRNA & stable genes in a proportion of
20% and 80%. If E. coli facing only amino acidstarvation, a low concentration of ppGpp is produced, asa consequence, the low concentration ppGpp will bindto and drive RNAP to on ly express rRNA & stable

E. coli, a bacterium, is an efficient system, whenfacing different circumstances. In this study, firstly, bysystematically constructing a network of glucose, PTS,
glycogen and chemotaxis system, we unveiled a f act
that the shorter time stimuli results in the posttranslation level reactions. And further longer time
stimuli will activate more time consuming the central
dogma level reaction. Secondly, different intensities ofsignals result in different kinds of actions, wasillustrated by ppGpp example.
The last but not the least, we would like to say,biology cannot be classified to higher or lower levels,
they only evolve towards different directions.
Acknowledgement
This work is partially supported by JSPS KAKENHI
Grant Number 25250028.
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