Bacteria - Sensing the Environment
Getting about in the world

Bacteria have a wide variety of means of locomotion, depending on the type. Some bacteria are non-motile, relying
entirely upon passive flotation and Brownian motion for dispersal. However, most are motile; at least during some stage of
their lifecycle. Motile bacteria move with "intent", gathering in regions which are hot or cold, light or dark, or of favourable
chemical/nutrient content. This is obviously a useful attribute. Many species glide across the substratum. This may involve
specific organelles, such as the filament bearing goblet-shaped structures in the walls of Flexibacter (Moat, 1979). Often,
however, no specific organelles appear to be involved and gliding may be attributable to the slime covering of some
bacteria or the streaming of outer membrane lipids of others (e.g. Cytophaga (Moat, 1979)) or to other mechanisms
currently being elucidated (see section 2). The spiral-shaped Spiroplasma corkscrews its way through the medium by
means of membrane-associated fibrils resembling eukaryotic actin (Boyd, 1988). Gonogoocci exhibit twitching motility
(intermittent, jerky movements) due to the presence of pili (fine filaments, 7 nm diameter, less than one micrometer long)
which branch and rejoin to form an irregular surface lattice. However, more than half of motile bacteria use one or more
helical, whip-like appendages, about 24 nm diameter and up to 10 mm long, called
flagella (sing. flagellum).

Flagella would be of limited use if bacteria could not sense their environment - they might help disperse cells to new
environments but energy would be better used if bacteria could sense where they were going and respond appropriately.
The success of flagella is evident from their wide occurrence and high expense (each flagellum comprises 1% of a
bacterium's protein (Neidhardt, 1987) and about 2% of its genome (some 50 genes) for their synthesis and control.
Perhaps the main advantage of flagella propulsion is their speed. Escherichia coli is 2 mm long and has a single flagellum
that propels it at about 20 mm/s. In contrast speeds for gliding motility range from 1-10 mm/s. Flagella, therefore, allow
bacteria to respond faster to changes in stimuli and enhance dispersal over a large area. The pattern of flagellation varies
with each species. Some classification schemes divide flagellated bacteria into two groups: the Pseudomonadales have
one or more flagella at one or both poles of the cell (they are polarly flagellated). The Eubacteriales have a random
distribution of flagella, sometimes covering the whole surface of the cell (they are peritrichously flagellated).

Chemosensing mode in Escherichia coli

Bacteria can move towards or away from stimuli. In the vast majority of bacteria (all except the very largest) this occurs by
chemokinesis, when the stimulus is a chemical such as a food substance or a noxious irritant. Chemokinesis is an indirect
process in which the bacterium alternately swims for a stretch and then changes direction and changes its frequency of
turning in response to environmental stimuli, which it can be demonstrated by computation leads to the bacteria gathering
near food sources whilst avoiding noxious stimuli. Note that the definition used here of chemokinesis is in keeping with
classical zoological and botanical definitions, but bacteriologists usually define the terms differently and refer to the
phenomenon just described as chemotaxis. Call it what you like, the mechanism will now be described.

When unstimulated, free-swimming
Escherichia coli swarmer cells make long straight runs with infrequent tumbles (see
figure below).
During the straight runs, the flagella rotate CCW (counter-clockwise) and the flagella come together
and work as a single bundle, possibly driven together by hydrodynamic forces (note that the cell body rotates in the
opposite sense, CW, to the flagella).
During the tumbles, the flagella reverse rotation to the CW (clockwise)
sense
, the wavelength of their filaments also changes and the pitch increases and the flagella mechanically uncouple
and fly apart and the cell tumbles (rotates randomly). Chances are that after a tumble when the flagella resume CCW
rotation and reform a bundle that the bacterium will start off in a new direction – it has turned by a random number of
degrees. Recent evidence shows that only one or two flagella in a bundle are required to uncouple to effect a tumble.

What do we mean by frequency of tumbling? The bacterial flagella have a switch mechanism, alternating between two
states: CW rotation and CCW rotation, with the rotation rate remaining more or less constant. The Gibbs free energy for
the CCW (swimming) → CW (tumbling) transition is about +40 kJ mol-1, and this energy is provided for by random thermal
fluctuations. When the cell is triggered to tumble more, it simply increases the probability of tumbling by
reducing the free energy required, making it more likely that thermal noise will provide the necessary energy.
When Escherichia coli nears the source of an attractant chemical, moving up a concentration gradient, it’s tumbling
frequency decreases and it makes longer runs. If tumbling frequency was simply inversely proportional to attractant
concentration, then computer simulations reveal that this will actually lead to a repellent effect – the bacterium will tend to
move away from the attractant source. However, when the computerised virtual cell is given a memory, allowing it to
compare the concentration at different points in time, it is able to measure the gradient rather than simply the
concentration. By reducing tumbling as it moves up the gradient toward the attractant source, then it will indeed become
‘attracted’ to the source (meaning that it spends longer near the source) (fig. 19). This is indeed found to be the case –
bacteria have a memory of a few minutes that allows them to make temporal comparisons of chemical concentrations in
their environment.
Above left - a computer-simulated ‘random walk’ of a bacterial cell starting
at the centre of the arena and tumbling at random intervals. Right - two
such simulated cells tracked over 15000 seconds each. Despite starting at
the centre they soon reach the edge of the arena (by random chance);
they have been programmed to bounce of the walls at the arena’s edge.
Repellents work in a converse manner – the bacteria tumble more frequently as they approach the repellent (as the
gradient increases) and so tend to avoid it:
Computer-simulated bacterial cells programmed to respond to the
(exponential) concentration gradient of a chemo-attractant placed in the
centre of the arena. Each cell has been given a one second memory with
which to measure changes in attractant concentration over time. The cells
tumble less if they move up the concentration gradient and tumble more if
they travel down the gradient (within preset minimum and maximum tumbling
frequencies). Each picture shows 4 cells traced for 5000 seconds each.
Left - each cell started at the edge of the arena at the bottom right corner at
about 5 o’clock. Right -: the bacteria start nearer to the arena centre. Note
how the bacteria remain near the attractant even though they are in constant
motion.
Computer-simulated bacteria programmed to respond to a chemo-
repellent at the centre of the arena, by tumbling more frequently if they
travel up the gradient and tumbling less frequently if they travel down the
gradient (within preset minimum and maximum tumbling frequencies). Each
cell had a one second memory to enable temporal comparisons in
repellent concentration. Left – one cell starting at the centre and was
tracked for 15000 seconds. Right – 3 cells began in the centre of the
arena and were tracked for 15000 seconds each. They can be seen to
clearly avoid the repellent and stay near the edge of the arena.
Chemosensing modes in other flagellated bacteria

Some alpha-subgroup bacteria also have a CW/CCW flagella switch, for example in Caulobacter crescentus CW
rotation leads to swimming, CCW rotation to tumbling (the opposite sense as in
Escherichia coli). Others, however,
have flagella that rotate in one direction only. In other members of this group very different strategies are employed.
Rhodobacter sphaeroides has a single right-handed flagellum in a lateral position which can push the cell at up to ~35
mm/s. This flagellum rotates only CW (or CCW in some variants). If an anaerobically grown cell detects a decreasing
gradient  of chemoattractant (if it is moving from the source of the attractant) then its probability of turning increases
(note that this response is opposite in sense to that of E. coli, but equivalent). During turning, the flagellum stops and
assumes the form of a planar spiral. This whole flagellum spiral slowly rotates, turning the cell by a random amount.
Sinorhizobium meliloti has 2-6 short, peritrichously or lophotrichously arranged right-handed flagella with fixed CW
rotation, during which they form a propulsive bundle. The flagella rotate continuously, however, asynchronous rates of
rotation cause the bundle to fly apart and the cell to tumble. more information on these other sensory response
modes can be found
here.
Mechanism of chemosensing

This section of the article is advanced (tech level 4+).

The best-studied chemosensing mechanism of
Escherichia coli is the Che phosphorelay system summarised in the
diagram below. In
Escherichia coli the chemosensors are methyl-accepting chemotaxis proteins (MCPs) that span
the inner membrane as dimers (pairs). These are connected to a phosphorelay system. In such phosphorelay
systems, the signal is relayed by
protein phosphorylation, which involves enzymes called phosphatases (which
remove phosphate)
phosphorylases (which attach phosphate) and kinases (which transfer phosphate from one
molecule to another). These receptors tend to be concentrated at the cell poles. Together with several of the
chemotaxis (Che) proteins they form a
MCP:CheW:CheA:CheY receptor complex.

When stimulated by a repellent

CheW functions as a relay linker, connecting the MCP to CheA. When an MCP is stimulated by a chemorepellent
binding to it, the receptors cluster in groups of about 7 MCP dimmers together with about 7 CheA dimers and are in
their activated state. This state activates CheA which autophosphorylates (phosphorylates itself) to CheA-P.

CheA-P is an active kinase and phosphorylates CheY to the active CheY-P form.

CheY-P then dissociates from the receptor complex and diffuses to the flagella motor where it binds FliM in the C ring
(see flagella structure) and it also binds the regulator phosphatase
CheZ which undergoes delayed activation as it
oligomerises to its active form. This binding to CheZ
increases the probability of tumbling (CW rotation) by
reducing the activation energy of the switch. After a delay CheZ becomes active and this acts as a phosphatase,
removing phosphate from CheY-P to yield CheY which reassociates with the receptor complex. Thus, CheZ acts as a
time-delay which resets the system, a form of adaptation which helps confer the memory needed for the system to
respond to concentration gradients.

A second adaptation system also exists, which is methyl-dependent. CheA-P not only phosphorylates and activates
CheY, but it also phosphorylates and activates
CheB, at a slower rate, producing CheB-P after a time-delay. CheB-P
is a specific methyl-esterase which cleaves a methyl group from MCP (MCP-Me → MCP). The methylated form is the
active form which stimulates CW flagella rotation and tumbling. The demethylated form becomes inactive and
CCW
rotation and straight runs become favoured again
– returning the cell to its pre-stimulus state. Chemorepellents
thus stimulate MCP demethylation. This periodic resetting of the receptor occurs every few minutes, giving the cell a
memory of an equivalent duration. CheR also helps to reset the system by antagonising CheB-P as CheR is a methyl
transferase which methylates MCPs.
When stimulated by an attractant

Attractants work in a converse manner. When an attractant binds to the MCP, the receptors deactivate and de-cluster into
separate dimmers (with associated CheA dimers). This inhibits the autophosphorylation of CheA, deactivating it and
reducing the concentration of CheY-P, resulting in an increased probability of CW flagella rotation and a reduced
probability of tumbling.

Sugars are chemoattractants that do not bind MCPs directly. Instead they either bind their sugarspecific
periplasmic
binding protein (PBP)
which is involved in sugar transport into the cell as well as chemotaxis. [Recall that the periplasm
is the region between the inner and outer membranes in the envelopes of gram negative bacteria and contains various
PBPs which bind to nutrients.] Galactose, maltose and ribose work this way. At least the PBP for maltose is known to be
localised at the cell poles along with the MCPs. Alternatively, some sugars, e.g. glucose, mannose and mannitol, bind to a
specific Enzyme II of the PEP-dependent sugar phosphotransferase system (PTS) (PEP is phosphoenolpyruvate). The
PTS Enzyme I modulates the kinase activity of the MCP-CheW-CheA receptor complex by phosphorylating CheA and
simultaneously phosphorylates the sugar as it is imported through the EII/EIII proteins. [More explanation to be added
here.]

MCPs also respond to changes in pH and temperature. Oxygen acts as an attractant for
Escherichia coli and its receptor
is Aer (an MCP homologue) which is cytoplasmic and lacks methylation sites for adaptation. Aer also binds FAD (flavine
adenine dinucleotide, an electron/hydrogen carrier used in respiration) which acts as an internal signal for the redox state
of the
electron transport chain (ETC).

A summary of this complex process of chemosensing in enteric bacteria, such as
Escherichia coli, is shown in the figures
and table below:
Above: Che phosphorelay signalling system. Binding of a chemical repellent
(ligand) to the receptor (MCP) increases tumbling frequency when repellent
concentration increases. The protein CheW (W) connects the MCP to the protein
CheA (A). When the repellent binds MCP, CheA becomes activated by
autophosphorylation and then phosphorylates CheY, activating it too. The active
phosphorylated cheY diffuses to the flagellar motor and binds to it, along with
CheZ to which the active CheY also binds. This increases the probability of
tumbling by tending to switch the flagella into CW rotation mode.
Responses to other stimuli

Bacteria can also respond to a variety of other stimuli, apart from specific chemicals, and responses to temperature,
light, osmolarity, pH and touch have been observed. Photosynthetic bacteria may move towards the light to
photosynthesise, or away from it if the light is too bright and potentially damaging. One particular response we shall
look at here is the response to magnetism, in particular to the Earth's magnetic field. Bacteria that move magnetic
North or South in a magnetic field are called magnetotactic.
Magnetotactic bacteria are Gram-negative, flagellated and
motile bacteria. They swim at about 100 mms-1. They are
microaerophilic, aquatic and contain magnetosomes. These
bacteria come from many taxonomic groups. The magnetosomes
are intracellular magnetic grains that give each cell a permanent
magnetic dipole moment. The local geomagnetic field (about 0.5
G) places a magnetic torque upon the bacteria, aligning them
with the magnetic field.

Aquaspirillum magnetotacticum has Fe3O4 magnetite
(lodestone) magnetosomes. Each cell contains about 20
cuboidal-octahedral crystals. Each crystal is about 420 Å in
diameter and the crystals are arranged in a chain. Single
magnetic domains in magnetite range from 400-1000 Å. Full
alignment requires the ratio of the interactive magnetic energy
with the applied field to the thermal energy to be greater than
about 10. A ratio of 16 is obtained for 22 500 A particles. As we
shall see, there are other mechanisms that stabilize the structure
and keep the crystals aligned.

Thus, the magnetosomes function as a ferromagnetic
biocompass. At 0.5G and 30oC, 80-90% of the cells are fully
aligned. The cells clump together if they contain too many
magnetosomes. Recorded levels of magnetotactic bacteria yield
103-104 cells / ml of slurry in aquatic environments (in New
England). These bacteria are absent from heavily polluted waters
and absent in limestone caverns, thermal springs, thawed
Antarctic sediments and iron-rich seeps. They are abundant in
water purification plant settling basins, ponds with organic
sediments, and sewage-treatment oxidation ponds.

In the Northern Hemisphere, magnetotactic bacteria swim
predominantly northward, whilst in the Southern Hemisphere they
swim predominantly southward. The vertical component of the
geomagnetic field, due to Earth’s curvature, is directed upwards
in the Southern Hemisphere, is zero at the geomagnetic equator,
and is directed downwards in the Northern Hemisphere.
Therefore, the bacteria are directed downwards in both
hemispheres and so are abundant in sediments, but absent in
surface water. At the geomagnetic equator there are
approximately equal proportions of each polarity and the bacteria
swim horizontally.
Above: Magnetospirillum (Aquaspirillum)
Magnetospirillum magnetotacticum (formerly Aquaspirillum magnetotacticum) is a microaerophilic chemoheterotroph
that metabolises organic acids, like fumaric, tartaric and succinic acids as its sole carbon (and energy?) source.
Nitrate is the principle electron-acceptor for microaerobic growth on tartrate. Traces of oxygen are required. (As a
substrate for oxygenases? For haem production?). Nitrate is reduced to nitrous oxide and ammonia in the process.
Thus, this bacterium is a
denitrifier. In low oxygen tensions (< 0.2 kPa) these bacteria also reduce ethyne. In high
oxygen tension (above about 6 kPa) they do not produce magnetosomes and are not magnetotactic. This
bacterium lacks catalase activity and so is sensitive to high oxygen concentrations. They have polar or bipolar
flagellation. Pili on coccoid forms, extracellular polysaccharide on spirilla, allow them to adhere to sediment particles.

Magnetosomes are typically (though not always) arranged in one or more linear chains. Each magnetosome particle
is a single crystal of magnetite or greigite enclosed in a phospholipid bilayer membrane. This membrane is derived
by invagination of the inner membrane but contains specialized proteins. This causes some confusion in
nomenclature – does ‘magnetosome’ refer to the whole chain or just to one of the particles? Each magnetosome
particle/vesicle is a tiny magnet and the particles within each chain are aligned –(N-S)-(N-S)-(N-S)- which helps to
stabilize the chain as a magnetic north pole is attracted to a magnetic south pole. However, as anyone who has
ever played with magnets will know, this arrangement is metastable, meaning that a slight displacement of one of
the magnets can cause the whole chain to collapse into an aggregated cluster of magnets. Additional structures are
needed to stabilize this arrangement (see the diagram below). In
Magnetospirillum the actin homologue protein
MamK forms a protein filament track along which the magnetosome particles are aligned (see below). There is
evidence to suggest that the protein MamJ forms linkers that connect each vesicle to the track. It is also possible
that additional structures link neighbouring magnetosome vesicles together. (See review by Thanbichler and
Shapiro, 2008).
The magnetosome and associated stabilizing structures in Magnetospirillum.
Some bacteria have two chains of magnetosomes at opposite sides of the cell and it is possible that these are
positioned by their mutual magnetic repulsion. Large cells require a larger torque to turn them and the large rod-
shaped cells of
Magnetotacticum bavaricum, which are 8-10 mm long, have 200-1000 crystals arranged in 5 chains.
However, it is possible that this produces far more torque than needed and magnetosomes may have additional
functions.

The individual crystals of magnetite are 35-120 nm in diameter. A magnetite crystal contains one or more domains –
regions in which the molecules all have their magnetic moments aligned parallel, reinforcing one another. If the crystals
were much larger than domain boundaries would occur, where the alignment of the molecules switches between crystal
domains with magnetic poles pointing in different directions (typically opposite one another). A crystal with several
domains whose magnetic moments tend to oppose and cancel one another will have a reduced magnetic moment. If the
crystals were much smaller, then they would lose their permanent magnetism, due to the thermal motion of the atoms.
Thus, the size chosen is optimal for maximizing the intensity of the crystal’s magnetic field.

Some bacteria use greigite (Fe3S4) instead of magnetite. In particular these bacteria occur in environments where
oxygen availability is low and sulphur-availability high. Greigite is less effective, however, as it makes a weaker magnet
(one third as strong). At least one known species of bacterium has crystals of both greigite and magnetite (a given
magnetosome particle must be one or the other and mixed crystals do not occur). Such bacteria encounter
environments of variable oxygen content – if oxygen is scarce then they incorporate sulphur instead.


See also
quorum sensing - how bacteria sense the presence of one-another!


Article last updated 16/9/14
For more on chemokinesis in bacteria:
MCP receptors
MCP binding repellent
Attractants bind either directly to MCPs or via periplasmic binding proteins, the latter serving as adapters to
increase the range of chemical ligands to which the MCPs can respond. The chemosensory ligand must first
diffuse across porins (protein pores or channels) in the outer membrane (OM). IM: inner membrane; OM:
outer membrane; PP: periplasm.
Above: when a repellent (or PBP + attractant) binds the Escherichia coli MCP, such as phenol, or
equivalently when an attractant dissociates from the MCP, then CheA autophosphorylates itself and then
passes the phosphate on to a second messenger called CheY (CheA may potentially phosphorylate several
CheY molecules in this way). Phosphorylated CheY, CheY-P, is active. CheB also becomes activated by
phosphorylation. This is the characteristic
two-component system (TCS) using a phosphorelay
mechanism, which is characteristic of signalling in bacteria (compare this to the eukaryotic kinase cascade).
CheW is an adapter protein, attaching CheA to the MCP so CheA can respond to ligand binding the MCP.
CheB-P demethylates the MCP. The more methylated the MCP, the more it activates cheA. Thus,
demethylation by CheB (an
esterase) reduces activity in the system by reducing CheA phosphorylation.
This resets the MCP sensor should the concentration of repellent remain unchanged, this is
adaptation to
the stimulus and is a form of
memory. It would be interesting to see to what extent adaptation occurs to
repellents compared to attractants. (There are few repellents in the
Escherichia coli case and establishing
their existence has been problematic, but other bacteria may possibly sense a wider range of repellents).
Above: when an attractant (or PBP + attractant), such as a specific sugar like galactose, binds the
Escherichia coli MCP, CheA phosphorylation and activation are reduced and so phosphorylation and
activation of CheY is also reduced. Similarly phosphorylation and activation of CheB is reduced. CheR (a
methyl transferase) remains active at a more-or-less constant rate regardless and is now able to
demethylate the MCP without competing with CheB. Methylation of the MCP is thus reduced, which tends to
increase the activity of the MCP and CheA, resetting the system should the concentration of attractant not
change. Again this is adaptation, which is crucial if the cell is to respond to
changes in stimulus
concentration
.

Note: much of the details of this system are still being elucidated by experiment. There is some uncertainty
as to the mode of CheW and CheA binding - CheW is described as linking the MCP to CheA by some
sources, whilst others claim that CheA and CheW bind to MCP competitively. Here we present only models
(the so-called 2:2:2 model) which will be altered as and when my own researches turn up positive
developments. It has also been suggested that CheA binds between the two MCP dimers, facilitating their
dimerisation.

Effect of CheY

When CheY is phosphorylated to CheY-P by CheA, it becomes active. In this active form it disassociates
from the MCP receptor and binds to FliM, a protein component of the C ring in the cytoplasm (see
bacterial
motility for a description of the flagella structure). This switches the rotation bias of the flagellum to CW
rotation, which favours tumbles. CheY-P is phosphorylated when the concentration of a repellent increases,
or equivalently, when the concentration of an attractant reduces.
MCP binding attractant
Flowchart of bacterial flagella operation - new version
Notes: CheR is active at the same basic rate in both cases (that is it is not affected by binding or
detachment of attractant or repellent from the MCP). This will methylate the MCP at a basal rate. However,
when the concentration of repellent increases (or concentration of attractant decreases) then CheB is
phosphorylated to CheB-P and activated. CheB-P demethylates the MCP, opposing the action of CheR.
Thus, when active, the methylation of MCP decreases. Binding of repellent initially activates the MCP, then
the delayed action of CheB-P deactivates it, leading to adaptation of the response.