sizes : from 0.15-0.25 mm (Mycoplasma)
up to 1.5 mm (10 mm
length in Bacilli and Clostridia, 20 mm
length in Spirochaetales;
to 80 mm in swarming forms of Proteus).
cytoplasmic or plasma membrane
or plasmalemma (a.k.a. innermembrane in Gram -ve
Lipids are unbranched fatty acids linked to glycerol by ester bonds
pyrophilus has ether linked lipids). The
fatty acids of Escherichia
mostly palmitic (16:0), palmitoleic (16:1), and cis-vaccenic (18:1).
These all contain an even number of C atoms : traces of longer and shorter
fatty acids also occur. Eukarya and Cyanobacteria have fatty
acids with 2 or more double bonds, whereas most Bacteria contain
only mono-unsaturates : only Mycobacteria have polyunsaturated fatty
acids (PUFAs). Insertion of double bond may occur by 2 mechanisms.
anaerobes and facultative anaerobes
simply omit a reductive step during synthesis. When precursor reaches C10,
they produce a cis double bond which cannot be further reduced (they
can only reduce trans double bonds). Further elongation gives palmitoleic
and cis-vaccenic acids. Another enzyme can isomerize cis =>
trans at the double bond, thus producing a mixture of cis and
C10 precursors. The trans precursors go on to become
saturated FA, while the cis ones become unsaturated. Note that the
previous reaction has two enzymes: a "short" isoenzyme for C8
and below and a "long" isoenzyme for C12 and above.Similar O2
dependent hydroxylation is required for steroid synthesis, but only
the cell wall-less Bacteria has sterols in the plasma membrane.
obligate aerobes introduce the double bond
after full elongation of the FA chain. Hydroxylation using molecular O2
is followed by removal of H2O to leave C=C. May be repeated
to give polyunsaturates.
Most represented lipids are PE (65%), PG (18%) and DPG (a.k.a. cardiolipin)
(17%) : PC (lecithin), PS and PI are rare, on the contrary of Eukarya.
can be identified on peculiar phospholipid composition if growing under
standard conditions. Cocci present abundant aminoacyl- (Lys-, Ala-,
Orn- and/or Gly-) PG and -DPG. . In stationary phase
coli converts its UFAs to cyclopropane FAs (the methylene group
comes from the one carbon pool via S-adenosyl Met) : this is thought
to be a protective mechanism but this theory is unproven. In
the change is due to increase in synthesis of only cis-vaccenic
acid but not palmitoleic one. E. coli contains 2 fatty acid condensing
enzymes, which catalyze the elongation reaction. Enzyme I works well up
to the C14 precursor for C16 products. It cannot
elongate C16 to C18. Enzyme II can elongate C16
to C18, but only if C16 precursor is unsaturated.
Hence, all the cis-vaccenic acid produced in E. coli is due
to operation of condensing enzyme II. Enzyme II is inherently sensitive
to temperature. At low temperatures, a lot of cis-vaccenate is made;
at high temperatures, much less. In Bacillus, where double bonds
are made by the O2 insertion pathway the desaturation enzymes
are induced by a drop in temperature and inactivated by an upshift. Plasma
membrane also contains :
transport systems: membrane transport proteins are crucial
for maintaining a selective internal cellular environment
glycerol is the only known substrate that undergoes facilitated diffusion
in some Bacteria
active transports may occur
in the classical (non-modifying) pathway
(in anaerobes and facultative anaerobes) through group translocation
[e.g. Glc entry within the cell with the phosphoenolpyruvate:phosphotransferase
(PEP:PTS) system : PEP =(enzyme I)=> HPr => enzyme III-P => enzyme
II-P => Glc/GlcN/2-dGlc/Fru/Man-P. For Man transport no enzyme III is necessary.
Only enzymes II and III are substrate specific]
the largest subset of membrane transport proteins is the major facilitator
superfamily (MFS), which convert electrochemical gradients into substrate
concentration gradients, and transport ions, sugars, sugar-phosphates,
drugs, amino acids and other hydrophilic solutes. In bacteria, MFS proteins
are primarily responsible for nutrient uptake, although some act as drug-efflux
pumps and are involved in the development of antibiotic resistance. Protonation
and binding of substrates induce several conformational changes resulting
in switching of the opening of the hydrophilic cavity from the periplasm
(outward-facing) to the cytoplasm (inward-facing), thereby allowing transport
of substrates across the membrane.
while simple membrane bilayers are inherently moderately permeable to ammonia,
the transport protein AmtB (11 membrane-spanning helices), present
in the bacterial inner membrane between the cytoplasmic and periplasmic
spaces, may serve to accelerate uptake at sites where ammonia diffusion
is too slow for physiological needs. AmtB has the same trimeric structure
when crystallized in both the absence and presence of ammonia : it is a
channel rather than a transporter that should have flexible elements involved
in translocation of the substrate. At either ends of the pore, broader
vestibules contain ammonia in equilibrium with ammonium. In AmtB's center
midway through the membrane is a hydrophobic pore element roughly 20 angstroms
long that allow ammonia to pass but not ammonium or other ions. The trimeric
structure of AmtB uncovered now suggests how the 3 Rh polypeptides (to
which AmtB is genetically related) of RBCs form the Rh antigen complex
in the erythrocyte plasma membrane. They add that these findings could
help predict how Rh-related proteins in the mammalian kidney collecting
duct and liver mediate ammonia transport.
lactose permease (LacY) catalyses the symport of b-galactosidase
glycerol-3-phosphate transporter (GlpT) catalyses the exchange of glycerol-3-phosphate
with inorganic phosphate.
enzymes for the late stages in biosynthesis
of phospholipids, lipopolysaccharide, peptidoglycan and other envelope
enzymes for energy transduction (including
both energy generation by respiratory chain and energy consumption) :
terminal reductases (cytochrome
complex, cytochrome d complex, nitrate reductase, fumarate reductase,
trimethylamine oxide reductase)
enzymes using proton motive force (PMF)
(ATP synthase, flagellar motor, energy linked transhydrogenase,
Although chemiosmosis occurs mainly in mesosomes, sometimes it involves
non infolded plasma membrane.
nucleoid or nuclear region = the region in which the aploid genome
is contained (not to be confonded with the nucleoid in Eukarya
peroxisome !). As they are aploid, every missense mutation in the genome
become immediately detectable under phenotype analysis (e.g. Ames
for detecting mutagenic compounds). It usually consists of a single negatively
supercoiled (by DNA gyrase and topoisomerase IV) circular
dsDNA molecule, but in Streptomyces and Borrelia it is linear,
while in Rhodobacter
sphaeroides there are 2 chromosomes. Only polyamines and histone-like
proteins (e.g. : HU and H in E.coli) are associated with DNA, but
they are far less represented than in Archaea ("naked" molecule).
genomes that have been sequenced at NCBI.
chromosome : in bacterial genetics, a closed circle of double-stranded
DNA that contains the genetic material of the cell and is attached to the
cell membrane; the bulk of the material forms a compact bacterial nucleus
(called also chromatinic body).
genome size varies from 0.58 Mbp in Mycoplasma genitalium to 4.4
Mbp in Mycobacterium tuberculosis and Escherichia coli
G+C percentage contents (melting point analysis) varies between 28% (in
to 72% (in Sarcina).
preferential positioning of bacterial genes in the leading strand
was thought to result from selection to avoid high head-on collision rates
between DNA and RNA polymerases. Here we show, however, that in Bacillus
subtilis and Escherichia coli, essentiality (the transcript
product), not expressiveness (the collision rate), selectively drives the
biased gene distribution
DNA duplication occurs via rolling circle (s
structure) or via Cairns model (q structure).
RNA primers are synthetized by RNA polymerase or by primase. Other required
proteins are :
DNA pol I aeqbtgd (secondary 5'=>3' polymerase,
3'=>5' and 5'=>3' exonuclease)
DNA pol II (?)
DNA pol III (main 5'=>3' polymerase, 3'=>5' and 5'=>3' exonuclease)
type I and type II (a.k.a. DNA gyrase ab) topoisomerases
It is often slower (106 bp / 5 x 104 bpm = 40' average)
than cell cycle period and therefore new rounds of synthesis are initiated
by the cell even though the previous copy has not fully replicated. Chromosomes
are always plasma membrane-bound.
modification : a mantainance methylase create N6-methylA
and N4-methylC (less than 1%) during chromosome
replication using SAM as donor.
restriction : some plasmid
or chromosome-coded restriction endonucleases specifically degrade
viral DNA but not bacterial (modified) DNA.
bacterial transformation : the exchange
of genetic material between strains of competentBacteria
(i.e. expressing a DNA binding protein) by the transfer of a fragment of
naked DNA from a donor cell to a recipient cell, followed by recombination
in the recipient chromosome. DNAase sensitive.
in Gram +ve Bacteria an ectoendonuclease degrades environmental
DNA up to 7-10 kbp fragments : ssDNA molecules enter the cytoplasm
in Gram -ve Bacteria dsDNA molecules enter the cytoplasm
specialized transduction by temperate lysogenic (bacterio)phages
(e.g. l) (once every 106-7 times
prophage excision isn't precise and a deleted / substituted particle
results, containing gene(s) adjacent one side of insertion site : when
it loses the tail and b genes; when l
it loses int,
xis and N)
generalized transduction by virulent lytic (bacterio)phages
(e.g. P1) (after endonuclease digestion, a randomly chosen chromosome
segment may be inserted into the capsid)
The recipient spectrum is extablished by host spectrum of the carrier virus.
As next infected cell becomes a partial diploid (merozygote : homogenote
if homozygotic; heterogenote if heterozygotic), some recombinations
may occur between exogenote (the extra piece of genetic information
introduced by transduction into the recipient cell by the donor cell) and
(the recipient cell's own complement of genetic information).
abortiveoradditional transduction (Campbell
model : no recombination occurs and so the acquired DNA is lost in following
conjugation : in replicative transfer
a nick in oriT creates a 3' end in a plasmid,
which enter the pilus of the F+(male) Bacteria
reaches pilus receptor OmpA on the F- (female) cell (average
speed : 40 Kbp / min at 37°C). Then pilus depolymerization allows cells
to come nearer and the transfer occurs. At the end of the process both
cells are F+. No recombination occurs with the host chromosome,
except for site-specific integration (plasmid => episome) : if the latter
occurs, the bacterium is named F'.
F-duction = F' x F-. If episome
exiting is poorly precise, also chromosomal genes can be transuced. At
the end of the process the F- cell remains F- because
the tra genes can be transferred only after all the chromosome genes
have been transduced : as such a process would require an average total
duration of 1h 40', it has a very low likelihood to occur. Interrupted
conjugation may be used to create a map (in minutes) of the chromosome
genes. As the recipient Bacteria becomes a partial diploid (merozygote
: if homozygote : homogenote; if heterozygotic : heterogenote),
or general recombination
may occur between esogenote and endogenote.
Bacteria contain one only kind of RNA polymerase with abb'sw
coded respectively by rpoA, rpoB, rpoC and rpoD
genes. Promoters contain -35 and -10 (Pribnow box) consensus sequences.
Transcription occurs at an operon level and
regulatory networks exist => polycistronic mRNAs. E.g. :
lac operon : lacZ (b-galactosidase),
(lactose permease), lacA (thiogalactoside transacetylase),
(aporepressor). The lactose catabolite allolactose acts as and inducer
preventing the repressor from binding the operator, but anyway,
when glucose is available, [cAMP]i is too low to activate CAP
and so the latter cannot activate the promoter (see also diauxia).
transcription ending may be poly-A dependent or Rho-(stem-loop)-dependent.
mRNA average life is 40" at 37°C (degraded by RNAase III). Few kinds
of RNA processing (no gene contains introns).
DNA invertases segregate into 2 evolutionarily distinct families
of site-specific recombinases : Tyr-specific recombinases (Tsrs) and Ser-specific
recombinases (Ssrs). They can modulate gene expression at multiple loci
scattered throughout the genome.
ribosomes = about 104 per Bacteria cell (less
than in Archaea), sometimes membrane-attached in a polysome-like
manner. 70S complexes [30S subunit (= 21 S proteins, 16S rRNA (about 1542
nucleotides)) + 50S subunit (= 34 L proteins, 23S rRNA (about 2900 nucleotides))].
The initiator amino acid in protein synthesis is N-formylMet,
obtained by formylation of Met-tRNAMet. 40÷60 different
tRNAAaa exist. The translation framing is ensured by interaction
between Shine-Dalgarno sequence at 5' end of mRNA and 3' end of
post-translational modifications : few kinds
N-deformylation of Met
inclusion bodies(not surrounded
by membranes, on the contrary of Eukarya inclusion bodies !) =
volutin : a complex molecule containing large
amounts of orthophosphate polymers (polymetaPi),
nucleoprotein, and lipid, occurring as cytoplasmic granular inclusions
(granules) in certain bacteria (e.g. Babes-Ernst granules in Corynebacterium
yeasts, yeastlike fungi, and protozoa, and serving as an intracellular
phosphate reserve. Because volutin granules stain red with blue basic dyes
they are sometimes called metachromatic granules
polar bodies : metachromatic granules located at one or both ends
of a bacterial cell.
poly-b-hydroxybutirate (PHB) or other b-alkanoic
S = only in some photosynthetic Monera
mesosome = a localized infold in the plasma
membrane (more abundant in Gram +ve). This is the site for chemiosmosis
in nitrifying Bacteria, chromatophores in purple sulfur Bacteria,
cylindrical vesicle in green Bacteria and multilayered membrane
thylakoids in Cyanobacteria. They bind the chromosome and, like
the latter, duplicate themselves during binary fission, when an accessory
cell wall = the multilayered sacculusthat
surrounds the plasma membrane (absent constitutively in Mycoplasma,
genera and temporarily in L-phase variant of certain bacteria, induced
by osmotic shock, temperature shock, or the presence of antibiotics, and
consisting of a spherical or ellipsoidal body without a rigid cell wall.
The cells are capable of growth and multiplication; they may be stable
or may revert to a normal bacterial cell)
It confers resistance to osmotic shock allowing intracellular concentration
up to 1 M, corresponding to an osmotic pressure p
= s . M .
R . T ~ 1 .
103. 8,31 .
310 ~ 15÷20 atm. It is mainly made up of peptidoglycans
(PGN) / mureins / mucopeptides, whose synthesis occurs as follows :
cytosolic phase (N-acetylmuramylpeptide synthesis) : note
that assembly is reversed relative to direction in protein synthesis (please
note often GlcNAc and MurNAc are wrongly referred as NAG and NAM, respectively).
Fru-6-P + Gln ===> Glu + GlcN-6-P
GlcN-6-P + acetyl-CoA ===> GlcNAc-6-P
GlcNAc-6-P ===> GlcNAc-1-P
GlcNAc-1P + UTP ==> UDP-GlcNAc + PPi
UDP-GlcNAc + PEP =PEP transferase===> UDP-GlcNAc-enol
+ 5 Gly-tRNAGly ====> undecaprenol-P-P-MurNAc(-GlcNAc)-L-Ala-D-g-isoGln-diaminoacid(-L-Gly)5-D-Ala-D-Ala+
5 tRNAGly ] (only in Gram +ve Bacteria, see below)
membrane flippase (?)
parietal phase (formation of crosslinks among base unit and peptidoglycan
chains). The cross-linking reaction occurs outside
the cytoplasmic membrane where there is no supply of ATP : energy comes
from hydrolysis of terminal D-Ala-D-Ala
bond. The outermost D-Ala is lost and the inner D-Ala
is bound either to the 5th glycine (Gram +ve Bacteria)
or to the side chain carboxyl of DAP (Gram -ve Bacteria).
In Gram -ve multiple random cross links between many chains occur. In Gram
+ve relatively few cross links occur and many side chains are not cross-linked
: DD-carboxypeptidase I removes terminal D-Ala
"inactivating" some side chains. In E.coli there are at least
6 different penicillin-binding proteins (PBPs) : p91PBP1
and p66PBP2 have only transpeptidase
activity, p60PBP3 has both transpeptidase
and transglycosylase activities, p49PBP4
has endopeptidase and carboxypeptidase activities,
p42PBP5 and p40PBP6 are DD-carboxypeptidase.
NAM in lipid II is linked by the transglycosylase activity of PBP
to a NAG in the peptidoglycan
Gram +ve Bacteria. Theircell
walls are thick, consisting of
about 50 layers of highly cross-linked peptidoglycan. NAM is linked to
peptide, which then transpeptidase cross-links to L-Ala
in another peptide via e-Lys amino group. The
(D-Gly)5 bridge allows binding among different
layers of peptidoglycan : it is absent in Micrococcus spp..
... a- and/or b-phosphodiesters
: the latter forms an ester with the C-6 OH- in NAM of peptidoglycan. Absent
in Micrococcus spp..
lipoteichoic acid (LTA) (in Streptococcus
spp.) : it arise from the outer layer of the plasma membrane.
polysaccharide C (in Streptococcus spp.)
protein M(in Streptococcus spp.)
protein A (in Staphylococcus spp.) : binds to Fcg
preventing binding to FcgRs.
Please note that although some Mycobacterium
spp. and some Nocardia spp. are classified as Gram +ve Bacteria
(due to their thick peptidoglycan layers), they often give a weak or a
variable gram reaction caused by the presence (in the cell wall) of lipids
Such a cell wall resists many stainings, but not alcohol-
and acid-fast Ziehl-Neelsen differential staining.
In peptidoglycan MurNAc is substituted by MurNglycolyl and tetrapeptide
as in Gram -ve Bacteria (see below), but, on the contrary of these,peptide
crosslinks may occur even between mesoDap residues.
Protoplast = a Gram +ve Bacterium which appears as Gram
-ve because deprived of its cell wall (by using lysozime) and maintained
in hypertonic solution to prevent osmotic shock. It is still alive but
cannot undergo repliction.
Gram -ve Bacteria. Theircell
walls consist of ...
... outer (or parietal) membrane that confers negativity at Gram
staining. On the contrary of the common biological membranes, it is unpermeable
to lipophilic compounds and permeable to hydrophilic compounds. It contains
in both the inner and the outer layers
protein A : binds peptidoglycan
phospolipids : more PE and less PG than in the inner membrane
p38OmpF decreases in high p
(receptor for TuIa, T2 and ColA phages)
p37OmpC increases in high p
(receptor for TuIb, Mel and 434 phages)
p34OmpD in Salmonella typhimurium
PhoE porin favorites entry of phosphate (or similar
anions) during phosphate limitation (receptor for TC45 phage)
LamB porin is induced by Mal (receptor for
Porins cover approximately 60% of cell surface. They
are often named according to electrophoresis migration pattern (protein
B, C,...) : sometimes wrongly named matrix proteins. Their pore
have Ø ~ 1 nm ; they have no contact with peptidoglycan. They are
also present in the outer membrane of mitochondria in Eukarya cells,
supporting endosymbiotic theory.
minor proteins are mostly receptors for molecules
too large to get through pores formed by porins. Most are also receptors
for phage and colicins (as are the major proteins), or are involved in
biological iron chelators
/ enterobactin is a cyclic trimer of 2,3-dihydroxybenzoylserine (DHBS),
OM receptor is p81FepA protein (also a receptor for ColB
and ColD phages). The FepB protein is the inner membrane permease. The
Fes protein is an esterase which hydrolyses Fe3+
- enterochelin into DHBS-Fe3+monomers.
Such monomers may be easily reduced to the Fe2+
form which is used in biosynthesis. E. coli synthesizes enterochelin.
Iron-laden enterochelin (or dihydroxybenzoyl-serine, a breakdown product
of enterobactin) is bound by lipocalin
ferrichrome is not synthetized by E. coli
but only by Fungi, e.g. Penicillium. Despite this, many Bacteria
have receptors for Fe3+/ferrichrome, hence
stealing the fungal siderophores. Albomycin is an antibiotic analog
of ferrichrome, made by the Fungi to kill such dishonest Bacteria
OM receptor is p78FhuA/TonA (also a receptor for
Tl, T5, f80 and
ColM phages), while inner membrane receptor is FhuB.
aerobactin and its receptor system are made
by E. coli carrying the ColV plasmid (also coding for colicin V,
which eliminates competing E. coli by binding to the p74Cir,
a carrier for Fe3+ which is also a receptor for ColI and ColV
phages). Such E. coli are often virulent
- due, in part, to aerobactin which can scavenge Fe from transferrin, while
most other bacterial siderophores bind iron less strongly.
The 2 siderophore variants produced by M. tuberculosis, the cell-associated
and soluble mycobactins (MBTs), and the Y. pestis siderophore, yersiniabactin
all have salicyl-capped non-ribosomal peptide-polyketide hybrid scaffolds
: carrier for nucleosides; receptor for T6 and ColK
: carrier for vitamin B12; receptor for BF23 and ColE
carrier for Fe-aerobactin, receptor for CloacinDF13 (on ColV plasmid)
: carrier for Fe-coprogen
: carrier for Fe-citrate
: carrier for Fe3+
in the inner layer only :
p7lipoprotein (Braun protein)
: it is bound via its -NH2 group of C-terminal
Lys to carboxyl group of every 10-12th (on average) Dap residue
in peptidoglycan. N-terminus is glyceryl-Cys : 2 fatty acids are
attached to glycerol moiety by ester links and a fatty acid is bound to
Cys by amide bond. Only one lipoprotein out of 3 is linked to peptidoglycan.
in the outer layer only :
enterobacterial common Ag (ECA) is an acidic
polysaccharide of GlcNAc, ManUANAc and 4-acetamido-4,6-dideoxy-D-Gal,
covalently bound to a phospholipid.
K antigens are specific capsular polysaccharides
made by most Enterobacteriaceae. Some are anchored by lipid tails.
colanic acidcontains Glc, Gal, Fuc
and GlcUA. It is made in response to adverse environmental conditions (high
low T, or dessication).
OmpA protein is the receptor for the F-pilus
/ endotoxins are synthetized on the inner membrane via the undecaprenol-P
pathway and then transfered in the outer one. Look here for purification
and biological effects.
Assembly occurs on cytoplasmic membrane: then it
is translocated to OM via the Bayer patches. LPS covers approximately 30%
of cell surface. It is made up of ... :
lipid A (the immunogenic portion of LPS)
class I (GlcN-b(1->6)-GlcN-glycophospholipid).
C-4' and C-1 bind P groups, C-3' binds KDO, N binds 3(or b)-hydroxymiristic
acid (BHM), C-4 and C-6' bind lauritic, palmitic or D3-miristoxymiristic
class II (3-aminoGlcN-b(1->6)-GlcN-glycophospholipid).
No phosphate groups. It is less immunogenic than class I.
constant R core (-2-keto-3-deoxyoctonic acid (KDO)-L-glycero-D-mannoeptose-GlcNAc-Gal-Glc-).
Ra, Rb, Rc, Rd and Re mutants have defective R cores due to different mutations
in the rfa operon.
variable side chain or somatic O antigen (D-Abe(a1->3)Man(a1->4)L-Rha(b1->3)Gal(b1->3))n-40.
Stabilized by Ca2+ and Mg2+. Other sugars in the
side chain may be Fru, Tet, 4-aminoAra, GlcU, GalU : sometimes the side
chain is immunogenic (Bacteroides fragilis), alternatively it may
be substituted by haptens (e.g. Ag T1 (polyRib+polyRibGal), Ag
T2 (GlcA) and the enterobacterial common Ag (ECA : poly(GlcNAc-ManUANAc-4-acetamido-4,6-dideoxy-D-Gal),
partially esterified with palmitic acid)) : the latter may become immunogenic).
When LPS has no O chain, the strain is called R for the aspect
of their colony (rough), otherwise S (for smooth) : not to be confused
with R and S definition for capsule absence/presence ! The transfer of
the O chain from the lipid carrier to the core-lipid A complex is mediated
by rfbT (in rfb operon) and rfaT (in rfa operon)
Both LPS and OMPs may act as receptors for bacteriophages.
Receptors for P1, T4, and T7 include both protein and LPS components. Mutants
defective in LPS sugars change their phage susceptibility. Thus E. coli
adsorbs phage Omega8 (binds to the O8 O-antigen) whereas E. coli
K-12 (no O-antigen) does not. E. coli K-12 phages specific for the
LPS include : U3 (it requires presence of
Gal at the end of core), C21 (it only adsorbs
if final Gal is absent => exposure of Glc), Br10 (it requires phosphate
on heptose), Br2 (it requires inner Glc(Gal)-Glc in core) and FP1 &
T4 (they require heptose in inner core).
periplasm or periplasmic space/gel = the
region (5-7 nm) between the inner and the outer membranes (please note
sometimes it is wrongly defined as the region between the inner membrane
and the peptidoglycan layer). It contains :
the monolayered cell wall : NAM units are linked to a L-Ala-D-g-isoGlu-mesoDap-D-Ala
peptide, which then transpeptidase crosslinks to L-Ala
in another peptide via the remaining mesoDap amino group.
osmotical shock-sensitive binding protein transports, functionally linked
to the specific porins (e.g. : in E.Coli Mal enters through LamB,
and MalK; also transport systems for Ara,
Gal, His, Leu, several other amino acids and sugars, phosphate, sulfate,
vit B12 and vit B1 exist)
scavenging enzymes such as asparaginase, acid phosphatase,
alkaline phosphatase, carboxypeptidase-II, endonuclease-I, 5'-nucleotidase
protective enzymes which inactivate antibiotics
membrane derived oligosaccharides (MDO) contain
8 to 10 Glc residues linked by b(1->2)
and b(1->6) bonds
and carrying phosphoglycerol side chains. They increase when osmolarity
of the medium drops.
Bayer sites : temporary discontinuities in
peptidoglycan allow limited regions of adhesion between outer and inner
membrane. These are sites of entry for phage DNA in many cases. Uncertain
structure - also unknown whether they are short lived or permanent.
Observed under EM by phage attachment and by binding of antibody/ferritin
complex to newly made O-antigen.
Spheroplast = a Gram -ve Bacteria partially deprived of its
cell wall by using lysozime (and maintained in hypertonic solution to prevent
Secretion systems in Gram -ve Bacteria(exporting
molecules through both inner and outer membranes)
type II (the main terminal branch of the general secretory pathway)
type III (injects toxins directly into target cells through a needle
cytoskeleton : in bacteria, the cell
wall is generally considered to be the primary determinant of cell shape.
However, this has been called into question, most recently by the discovery
of the Mollicutes (Mycoplasma, Acholeplasma, and Spiroplasma).
Mollicutes are the smallest and simplest free-living and self-replicating
cells within prokaryotes, and they are enveloped only by a cholesterol-containing
cell membrane. Despite the lack of a cell wall, these cells have distinct
morphologies, and their peculiar mode of movement that occurs in the absence
of appendages normally implicated in motility (e.g., flagella or secretion
organelles) makes the existence of an internal cytoskeleton likely. Williamsonref
first reported the isolation of a cytoskeleton upon cell lysis and sodium
deoxycholate extraction of Spiroplasma isolated from Drosophila.
Cytoskeletal elements have also been released from Spiroplasma cells by
repeated freezing and thawingref.
Townsend et al.ref
also developed methods for purification of the membrane-associated fibrils
from S. citri and suggested that they may be involved in motility. Electron
microscopy and SDS gel electrophoresis have shown that S. melliferum possesses
a cytoskeletal ribbon comprosed of 4- to 5-nm-wide fibrils with an axial
repeat of 9 nm; these fibrils form pairs within the ribbon and are composed
of the 55-kD fibril proteinref1,
Townsend and Plaskittref
further used immunogold staining of thin sections with an antibody to p55
to localize the ribbon built of the fibril protein within S. melliferum
cells. More recently, the structure and localization of this cytoskeleton
was described as a flat, monolayered, membrane-bound ribbon composed of
6 or 7 pairs of fibrils following the inner, shortest helical path of the
The fibril protein, which is completely unrelated to any other eukaryotic
or prokaryotic protein and has been found exclusively in the genome of
was identified as the only component of this ribbonref.
Because this protein would have a diameter of about 5 nm, assuming a spherical
shape, it was proposed that the subunit of the fibrils is a tetramer and
that the filaments form pairs to give the 10-nm axial and lateral spacings
in the cytoskeletal ribbonref.
of intact vitrified S. melliferum cells, however, reveal a more
complex pattern of filamentous structures just underneath the cell membrane.
2 types of filaments (thin and thick) are arranged in parallel, anchored
to each other and to the cell membrane, and jointly form three ribbons
that span the entire cell from the blunt to the tapered end. By calculating
the Hough transformation of the filament regions in several tomograms and
finding the position of the highest contrast, we determined the number
and spacings of the individual filaments. The 2 outer ribbons consist of
five thick filaments with a spacing of 11 nm. These 2 ribbons are joined
together by nine thinner filaments with a spacing of 4 nm. Depending on
the extent of twisting of the cell and the position of the filaments with
regard to the direction of the electron beam during data acquisition, five
or locally fewer than five thick filaments are visible in the tomograms.
Using 3D visualization, the arrangement and path of the 2outer ribbons
underneath the cell membrane through the entire cell body was illustrated.
Although the ribbons cannot be visualized as continuous bands along the
cell membrane of the whole cell because of the "missing wedge" problemref,
it becomes clear that the ribbons follow, in parallel, a helical path from
one end of the cell to the other. By calculating the geodetic lineref
(i.e., the fastest connection between two arbitrary points on the 3D cell
membrane), we could also show that one of the two outer ribbons is locally
shorter; indicating differential length changes of the 2 ribbons. What
is the protein composition of the ribbons? We have been able to show that
isolated and purified filaments composed of the fibril protein exist in
pairs with a total thickness of about 10 nm; hence, we suppose that the
two outer ribbons of the S. melliferum cytoskeleton are made of
the fibril protein. Our structural data showing two different filaments
in the cytoskeleton of S. melliferum raises the question of the
identity of the second protein. Until recently, there has been an ongoing
controversy about the existence of actin or actin-like proteins in prokaryotes,
Bacterial homologs of actin were first identified when the cell-shape determinants
MreB and Mbl (MreB-like) were shown to assemble into helical filamentous
structures that run in spirals around the periphery of the cell under the
cytoplasmic membrane in Bacillus subtilisref.
Depletion of MreB induced the formation of rounded inflated cells that
was ultimately lethal. This phenomenon was also reported for Escherichia
MreB has been found only in bacterial species with rod-shaped, filamentous,
or helical cellsref.
Consistent with this, the helical cells of S. citri have five MreB
homologs. Using Western blot and sequence analysis, we showed that both
the fibril protein and MreB exist in S. melliferum cells and both
are homologous to the sequenced fibril and MreB proteins of S. citri.
Hence, the inner ribbon of the S. melliferum cytoskeleton is composed
of MreB. Because of the instability of MreB filaments, the isolation of
intact triple ribbons proved difficult and therefore, direct and unambiguous
proof for this assignment by immunolabeling was not possible. Nevertheless,
there is evidence supporting our assumption about the protein composition
of the cytoskeleton. Purified MreB from Thermotoga maritima has been shown
to form 4-nm-wide protofilaments in vitroref,
and a linkage between an actin-like protein and the fibrils in Spiroplasma
cells was already proposed by Williamson et al.ref
but has not yet been proven. How does this cytoskeleton enable the movements
of S. melliferum cells? Trachtenberg and Giladref
suggested that the filaments can change their length in a coordinated manner,
driven by conformational changes of their tetrameric subunits from nearly
circular to elliptical. In this regard, the assumptions for our computer
simulations, which are based on light microscopy experiments and the existence
of three ribbons, are (i) the ribbons are connected to each other, (ii)
the inner thin filament ribbon functions elastically during cell movement,
and (iii) length changes of the five filaments of the outer 2 ribbons occur
simultaneously by switching between two conformational states of the filament
subunits. Hence, we can simulate on a molecular level how the different
motility modes are generated. If length changes in the 2 outer ribbons
are coordinated such that one ribbon becomes gradually tense by shortening
while the second one concurrently relaxes, the cell would alternate handedness
between left- and right-handed, with handedness switching at the position
where the state of tension and relaxation of the ribbons reverses. This
point of transition between left- and right-handedness travels throughout
the whole cell, leading to a motion that resembles that of a bacterial
flagellar bundle or of a single eukaryotic flagellum or cilium. A similar
motion can be generated if the distance between the two outer ribbons is
changed locally, thereby creating a deformation or kink, which propagates
throughout the cell body. Thus, the whole Spiroplasma cell functions
as a dynamic helical propeller. Coupling of a biochemical cycle (e.g.,
adenosine 5'-triphosphate hydrolysis) to the dynamics of the filaments
could enable these filaments to propagate deformations that generate propulsive
forces which, in turn, can drive cell motionref.
MreB filaments give the cell a rodlike shape by forming the inner, elastic
ribbon, whereas the outer filaments composed of the fibril protein enable
the formation of a helix, as well as movement, by interaction with the
Bacteria also produce bacteriocins
(coded by defective phages or by (un)conjugative
antibiotics with a very narrowed spectrum of action :
staphylolysin / LasA protease : cleaves
peptide bonds following Gly-Gly pairs in peptides or proteinsref1,
and as in the case of lysostaphin, its ability to lyse staphylococci results
from cleavages within the pentaglycine cross-links in the peptidoglycan
of S. aureus cellsref.
can cause lysis of a wide range of Staphylococcus
and it has also been shown to inhibit the growth of S. aureus cells
This favors LasA protease as another useful agent in enzyme-based treatment
of S. aureus infections
Colicin-producing strains cannot coexist with sensitive or resistant strains
in a well-mixed culture, yet all three phenotypes are recovered in natural
populations. Recent in vitro results conclude that strain diversity can
be promoted by colicin production in a spatially structured, non-transitive
interaction, as in the classic non-transitive model rock–paper–scissors
(RPS). In the colicin version of the RPS model, strains that produce
colicins (C) kill sensitive (S) strains, which outcompete resistant (R)
strains, which outcompete C strains. Pairwise in vitro competitions between
these three strains are resolved in a predictable order (C beats S, S beats
R, and R beats C), but the complete system of three strains presents the
opportunity for dynamic equilibrium. Here we provide conclusive evidence
of an in vivo antagonistic role for colicins and show that colicins (and
potentially other bacteriocins) may promote, rather than eliminate, microbial
diversity in the environmentref.
In Bacillus subtilis
(the model sporulating Gram-positive bacteria), cells at the beginning
of the sporulation pathway may delay entering the dormant phase by killing
their siblings and feeding on the released nutrients In mutants in which
the genes controlled by Spo0A, a protein that regulates sporulation,
had been altered, 2 operons are strongly induced at the start of sporulation
: their mutations accelerated spore formation
sporulation killing factor (skf) is a group of 8 genes that govern
the synthesis of a peptide antibiotic and the production of an export pump
that confers resistance to the toxin
sporulation delaying protein (sdp) comprises 3 genes and controls
the production of an extracellular-signaling protein that delays spore
formation, probably by increasing energy production by the cell. In addition,
the signaling protein causes enhanced cell sensitivity to the sporulation
Acting synergistically, the B. subtilis killing factor and the signaling
protein thus prevent sporulation in sister cells and cause them to lyse,
releasing nutrients that permit the cannibals to keep growing and to delay
committing to spore formation. Because sporulation becomes irreversible
after its earliest stage, delaying spore formation as long as possible
might be beneficial as a cell that is committed to spore formation could
be at disadvantage relative to other cells should nutrient deprivation
prove to be fleeting
antibiotic-producing bacteria have evolved
a range of mechanisms to escape the lethal effects of their own chemical
warfare; self-protecting mechanisms have contributed to the widespread
resistance of pathogenic bacteria to clinically important antibiotics
antibiotic elimination through specific efflux pumps
antibiotic inactivation by modification of its chemical structure
modification of the antimicrobial target
self-sacrificing : detoxification is accomplished at the expenses
of both the metabolite and the resistance protein. Enediynes, a
set of antibiotics that are among the most potent cytotoxic antitumoral
agents to have been discovered in the past decade. Following prodrug activation,
the enediynes undergo cycloaromatization reactions resulting in
formation of highly reactive diradical intermediates that destroy
bacteria by engaging in atom-transfer chemistry to produce neutral arene
products, in the process abstracting hydrogen atoms from the backbone of
DNA and induce permanent damage to the key macromolecule. Enediynes are
so active that many of the 20 or so naturally occurring substances identified
so far are in clinical trials, and efforts using chemical synthesis to
improve the target specificity of designed enediynes are ongoing. CalC,
a Micromonospora gene, confers resistance to calicheamicinin
vivo by attracting the activated calicheamicin molecule, which in turn
abstracts a single hydrogen from a specific glycine residue in the protein
backbone—in a manner consistent with its action on DNA—and causes irreversible
protein cleavage. CalC acts within the enediyne-producing microorganism
by capturing and detoxifying activated antibiotics that escape the biosynthesis-exportation
system before they attack and damage bacterial DNA
adhesion accessory apparatuses
glycocalyx = it binds cell together
forming multicellular aggregates on rocks, animal tissues, ... Its molecules
are said capsular Ags, in contrast with the molecules of the remaining
part (bacterial body), who are called somatic Ags. It varies
among species and may consist of one of the following forms :
S layer = a paracrystalline (i.e. : non-covalent
bonds, self-assembling in vitro) (glyco)protein layer found outside
the cell walls of some Gram +ve Bacteria or outside the outer membrane
of some Gram -ve Bacteria. It presents pores with Ø ~ 2÷3
(levan in Streptococcus salivarius, dextran in Leuconostoc mesenteriodes,
cellulose in Acetobacter xylinum, mannan in Bacillus circulans
... ), heteropolysaccharides (in pneumonia causing pathogens : Streptococcus
pneumoniae, ..) or (D-Glu)n
(in Bacillus anthracis, Bacillus subtilis, Bacillus
megaterium, ...) tightly bound to the S layer or to the cell wall
(directly if the latter is positive-charged or through cations if the latter
is negatively-charged) : at least in Bacillus
and type 6 Pneumococcus some covalent bonds are present between
cell wall and capsule. Smooth-rough (S-R) variation : a genetic
mutation or an adaptation seen in bacteria, most often evidenced by a change
in the surface of colonies from smooth (S, glossy) to rough (R,
bacterial or microbic dissociation : the change, due to mutation
and selection, in colonial morphology (usually from mucoid (M) or
smooth sapsulated variants to rough) of bacteria in culture on laboratory
The cells in S colonies have polysaccharide capsules and are more antigenically
complete; R cells contain little or no capsule. The term may also refer
to changes in other cell structures such as flagella and somatic antigens,
as well as susceptibility to bacteriophage. Variations are often reversible
and tend to result in mixed types on repeated subculture. The change correlates
with pathogenicity, S strains being generally more virulent and R strains
of the same species less so because :
its polysaccharides inhibit alternative
pathway for complement cascade activation
: group B type III Streptococci have Sia residues that attract factor
H, while type VII and XII Streptococci prevent factor B from binding
C3b on cell wall: in both cases the formation of the C3bBbP complex and
subsequent complement-mediated phagocytosis are prevented.
as it is hydrophilic, it protects against hydrophobicity-mediated non-immune
phagocytosis (but not against opsonin-mediated phagocytosis which occurs
late in infections !), preventing adhesins from binding phagocyte receptors
Anyway surface phagocytosis in pulmonary alveoli (rough surface)
it confers resistance to desiccation
it represents a nutrient storage
As they exclude stains, they can be observed only by negative
When the capsule is monolayered it is called microcapsule (e.g.
in Salmonella) : it becomes observable at TEM only after the Neufeld
The capsule-building ectoenzymes are inherited (in classical 1928 Griffith's
bacterial transformation experiments with Streptococcuspneumoniae
strain 3, the R variants lacked UDP-Glc dehydrogenase, needed to transform
UDP-Glc in UDPGlcA, which is a sugar for the cell wall disaccharide cellobiuronic
acid) but their activity is subordered to nutrient availability (e.g.
: carbohydrates for Aerobacter, sucrose for Leuconostoc,
CO2 for Bacillus anthracis (CO2 + Pyr => OAA
=> aKG => D-Glu)) and growth
phase (elder Streptococci A and C produce hyaluronidase which degrades
hyaluronic acid in cell walls to GlcUA and GlcNAc, causing cell death in
colony center) so that a reversible S => R transition is possible.
The cell wall precursors may be exported from cytoplasm through secretion
systems or (only for some Gram +ve Bacteria with ectomembrane-bound
transglycosylase) come from environment (e.g. : diet sucrose in oral cavity
for Streptococcus mutans => dextran or levan => biofilms (dental
caries) => pH lowering => enamel decalcification). While some biofilms
are useful—sewage treatment plants, for instance, rely on them to remove
contaminants from water—they are estimated to be involved in 65% of human
bacterial infections : when microbes band together in a biofilm they are
1,000 times more resistant to killing by antibiotics, biocides and disinfectants
than free-floating bacteria. ndvB gene is required for the production
of periplasmic glucans, glucose polymers that prevent antibiotics from
reaching sites of action.
adhesins (lectins whose synthesis doesn't
occur if T < 20 °C) protruding outward ...
... fimbriae = inherited trait, much
shorter and more numerous than flagella. They often contain adhesins and
receptors for bacteriophages.
... pili = protein scaffolds of pilin
(convergent evolution : chaperone and usher pilus family, type
IV pilus family, ...) packed tightly into an helical array. They are
longer and fewer (sometimes only one per cell) than fimbrae. They act as
/ microcolony, densely-packed microbial communities develop when
free-swimming (planktonic) cells attach to a surface and form mushroom-like
structures containing stalks, a meshwork of channels, and encased in a
layer of slime comprising proteins, polysaccharides, and DNA. Consequently,
this bacterial fortress is notoriously resistant to antimicrobial agents,
rendering biofilms virtually untreatable : they are responsible for something
like 65% of all infections in the West.
biofilm development occurs in 5 stages during which >n 800 proteins (>
50% of the proteome) showed a sixfold or greater expression level changeref
reversible attachment: cells transiently affix to substratum, and surface
induced gene expression results in a protein profile significantly different
from planktonic bacteria.
irreversible attachment: cells reorient themselves, clusters develop, motility
is lost, and the las quorum sensing regulon becomes activated.
maturation I: cell clusters become thicker than 10 mm and the rhl quorum
sensing system becomes active.
maturation II: cell clusters reach maximum thickness (100 mm) with a protein
profile most different from planktonic cells.
dispersion: cluster structures change, and pores and channels form. Motile
and non-motile bacteria are present as the protein profile begins to resemble
planktonic cells once again.
Upregulated proteins included those involved in anaerobic processes,
denitrification, many efflux pumps, and some quorum sensing proteins. One
major player they found upregulated was a known transcriptional regulator
that turns on antibiotic resistance by inducing transcription of efflux
pumps. Microbiologists have tended to define microbial physiology based
on planktonic bacteria, but in nature bacteria exist almost exclusively
in biofilms : the only time they are planktonic is when making the transition
from one biofilm to another. If bacteria in biofilms are physiologically
different from planktonic bacteria, then all the work done right back to
Louis Pasteur has to be repeated. Within biofilms, cell-cell communication
occurs through quorum sensing, in which signaling
molecules called autoinducers, specific for that species, are produced
and exchanged among bacterial neighbors.
Web resources : Center
for Biofilm Engineering
positive or negative motility or taxis accessory
= membrane-enclosed magnetite (Fe3O4) or greigite
(Fe3S4) crystals that create permanent magnetic dipole
in anaerobic or microaerobic
Bacteria living in marine and freshwater
... magnetotaxis : in the northern emisphere evolution selected
that move "north-seekingly" according to Earth magnetic field, down to
the sediment, where PO2 is low. In the southern emisphere
evolution selected Bacteria with reverse polarization. The orientation
process is passive, while movement along the field is an active process.
The chromosomal 'magnetosome island' contains genes connected with
magnetosome synthesis : gene deletion in Magnetospirillum gryphiswaldense
show that magnetosome alignment is coupled to the presence of the mamJ
gene product. MamJ is an acidic protein associated with a novel filamentous
structure, as revealed by fluorescence microscopy and cryo-electron tomography.
A mechanism in which MamJ interacts with the magnetosome surface as well
as with a cytoskeleton-like structure has been proposed : magnetosome architecture
represents one of the highest structural levels achieved in prokaryotic
: changes in ligand concentrations are sensed by a protein assembly consisting
of transmembrane receptors, a coupling protein (CheW) and a histidine
kinase (CheA). In Escherichia coli, these components are
organized at the cell poles in tight clusters that contain several thousand
copies of each protein. Assemblies of bacterial chemoreceptors work in
a highly cooperative manner, mimicking the behaviour of allosteric proteins.
Conditions that favour steep responses to attractants in mutants with homogeneous
receptor populations also enhance the sensitivity of the response in wild-type
cells. This is consistent with a number of models that assume long-range
cooperative interactions between receptors as a general mechanism for signal
integration and amplification.
flagella(completely different from
the structure of Eukarya flagella !) = 100÷200 mm
length, a motile organelle made up of
flagellar motor embedded in the cell
M protein (in the basal body or motor)
S protein (in stator)
flagellar hook is a short, highly curved
tubular structure that connects the flagellar motor to the long filament
acting as a helical propeller. The hook is made of about 120 copies of
a single protein, FlgE, and its function as a nano-sized universal
joint is essential for dynamic and efficient bacterial motility and taxis.
It transmits the motor torque to the helical propeller over a wide range
of its orientation for swimming and tumbling. FlgE31 is a major proteolytic
fragment of FlgE lacking unfolded terminal regionsref.
flagellar filament : flagellin
(a fibrous helicoidal dextrogire protein which also acts as a type
II T-independent Ag
and binds to TLR5).
Flagellin subunits held together by hydrophobic interactions assemble into
so-called protofilaments in 2 different conformations : L-type and R-type.
Supercoiled bundles of 11 protofilaments can form left-handed or right-handed
helices. In the L-type protofilament the central channel of the flagellum
is lined with polar residues : this could be relevant to export of unfolded
proteins through the flagellum - like flagellin, which is exported then
added to the growing filament tip - and for type III virulence protein
secretion through a needle complex that is similar to the flagellum.
“Run and tumble” movement controlled by the direction of the flagellar
spin (counterclockwise spin => left-handed helix => straight run; clockwise
spin => some of the protofilaments switch to form a right-handed helix
=> the cell stops and reorientates in a random manner (tumble)). Escherichia
coli and Salmonella swim fine in water at a neutral pH of 7.0.
And without the weak acids present to lower their internal pH, they also
swim fine in acidic water at pH 5.0. But, with the weak acids and a lower
internal pH - as the outside water becomes more acidic - they slow and
ultimately stop. The flagellar apparatus may secrete virulence factors.
It may be stained with tannic acid. The flagellum may be absent (atrichous),
single (monotrichous), double (if at opposite poles : amphitrichous)
or multiple (if grouped at both poles : lophotrichos, if diffused
on all surface : peritrichos).
axial filaments / endoflagella / axistyles
/ flagellar apparatuses are the spirochetae equivalent of flagellum.
The endoflagella are contained within the periplasmic space between a rigid
peptidoglycan helix and a multi-layer, flexible outer membrane sheath.
When the filaments rotate within this space, the spirochetes move in cork-screw
fashion. This mode of motility in spirochetes is thought to be an adaptation
to viscous environments such as aquatic sediments and the intestinal tracts
of animals. For pathogens, this allows the spirochetes to hide their flagella,
which are normally antigenic, from the host immune defenses.
gas vacuoles =
cellulosome : an extracellular enzyme
complex which consists of a scaffolding protein and many bound cellulases.
Anaerobic microorganisms have evolved a system to break down plant cell
wall materials, including cellulose,
the most abundant carbohydrate polymer in nature. Although anaerobic fungi
as well as anaerobic bacteria are believed to produce cellulosomes, so
far full genetic evidence for their presence has only been obtained in
anaerobic bacteria. To date, cellulosomes have been identified in 12 different
bacterial species, and this list is expected to continue growing. Cellulosomes
comprise a fibrillar protein known as the scaffolding protein or scaffoldin
with cellulosomal enzyme subunits positioned periodically along the fibrils.
Typically, the scaffoldin contains enzyme-binding sites known as cohesins,
and a cellulose-binding domain (CBD) or carbohydrate-binding
module (CBM). The enzyme subunits bind to the cohesins via cohesin-binding
sites known as dockerins. The properties of the scaffoldins vary
between species. Additionally, cellulosomes can contain either one or several
different scaffoldins that can bind different combination of enzymes. This
variation and the presence of many cellulosomal enzymes means that any
single microorganism can secrete a variety of cellulosomes with many different
compositions. The cellulosomal enzymes include cellulases, hemicellulases,
and many ancillary enzymes that can degrade plant cell wall materials.
In biotechnology, there is great interest in exploiting the properties
of cellulosomes. 'Mini-cellulosomes' can be created, which, because
they contain specific cohesins, will only bind to specific enzymes. These
constructs have been used to great effect in cellulosome research in the
study of the synergistic effects of cellulosomal enzymes and the cohesin–dockerin
interaction, for example, but it is also hoped that mini-cellulosome constructs
could be used in the future to develop artificial metabolic pathways that
allow the synthesis of any desired product. There is also great interest
in the heterologous expression of cellulosome genes, such that non-cellulose
degrading organisms can be converted to cellulose degraders. Cellulosomes
have many potential biotechnological applications as the conversion of
cellulosic biomass into sugars by cellulosomes could result in the production
of high-value products such as ethanol or organic acids from inexpensive
cell-cell communication in bacteria
is accomplished through the exchange of chemical signal molecules called
This process, called quorum
sensing, allows bacteria to monitor their environment for the presence
of other bacteria and to respond to fluctuations in the number and/or species
present by altering gene expression to coordinate particular behaviors.
Most quorum-sensing systems are species- or group-specific (eg see Pseudomonas
which presumably prevents confusion in mixed-species environments. However,
some quorum-sensing circuits control behaviors that involve interactions
among bacterial species. These quorum-sensing circuits can involve both
and interspecies communication mechanisms. Finally,
strategies are present in both bacteria and eukaryotes, and these are
apparently designed to combat bacteria that rely on cell-cell communication
for the successful adaptation to particular niches. The AI-2 autoinducer,
unlike all other known autoinducers, which are species-specific, is produced
by > 50 bacterial species and believed to be a universal signaling molecule
: its receptor is LuxP sensor proteinref.
It contains boron in the molecule : despite ubiquitous in the biosphere,
especially in oceans, the only well-defined reference to boron in biology
is its role in stabilizing cell wall structures of plants. Millimolar quantities
of borate are found in seawater, meaning that a role for boron in communication
among the marine V. harveyi, makes sense in hindsight.
Bacteria communicate with each other in multiple ways, including the
secretion of signaling molecules that enable a cell population to determine
when it has reached a certain density or that a potential partner is present
Cellular communication can also occur through contact between cells, as
has been shown for Myxococcus xanthus, which undergoes a complex developmental
Certain Escherichia coli, including uropathogenic strains, contained
a bacterial contact-dependent growth-inhibition (CDI) system that
uses direct cell-to-cell contact. Inhibition was conditional, dependent
upon the growth state of the inhibitory cell and the pili expression state
of the target cell. Both a large cell-surface protein designated Contact-dependent
inhibitor A (CdiA) and 2-partner secretion family member CdiB
were required for growth inhibition. The CdiAB system may function to regulate
the growth of specific cells within a differentiated bacterial population.
Many UPEC strains contain fim (type 1 pili), pap (P pili), and sfa (S pili)
The expression of these pili types is normally subject to reversible off/on
switching, generating diversity within bacterial populations by a differentiation
Such a mechanism might play a role in the temporal control of the differentiation
observed for UPEC strains inside bladder cells, during which the bacteria
progress through distinct developmental stages, including a quiescent growth
coli K-12 cells inhibited by CDI appear to be nonviable because of
their lack of growth on agar medium. However, CDI-inhibited cells appeared
to be viable because they excluded propidium iodide, a standard criterion
for distinguishing viable cells from nonviable cellsref.
The identification of this sophisticated mechanism in E. coli, with
possible homologs in a broad range of species, opens the door for exploration
of the potential roles of CDI in controlling bacterial development and
vegetative form : exogrowth and division
by binary fission (formation of septal mesosome). Cell cycle
period is average 20' long, but varies (also according to growth conditions)
from 10' (in Beneckea) up to > 24 hrs in Mycobacterium leprae.
Please note often in vitro doubling times are shorter than in
vivo ones !
the bacterial septum-located DNA translocase FtsK coordinates circular
chromosome segregation with cell division. Rapid translocation of DNA by
FtsK is directed by 8-base-pair DNA motifs (KOPS), so that newly replicated
termini are brought together at the developing septum, thereby facilitating
completion of chromosome segregation. Translocase functions reside in three
domains, a, b and
FtsKab are necessary and sufficient for ATP
hydrolysis-dependent DNA translocation, which is modulated by FtsKg
through its interaction with KOPSref.
quiescent form : no exogrowth => no division.
structures for survival under unfavourable growth conditions (protection
(endo)spores : mainly in Gram +ve genera
(Bacilli(aerobic rods), Clostridii,Thermoactinomyces
and Desulfotomaculum (anaerobic rods), Sporosarcina (aerobic
cocci)) but also Gram -ve (Coxiella burnetii). They arise in 6÷8
hrs after post-logarithmic phase in culture growth ...
depletion of environmental energy sources causes a fall in [GTP]i
accumulation of ppGpp, ppGppp (stringent factors) and ppAppp : such
events cause the chromosome to relax itself into an axial filament and
duplicate itself, duplicating even its origin. At this stage some species
All these modifications are reversible. Bacterial transcription is regulated
by the alarmone ppGpp, which binds near the catalytic site of RNA
polymerase (RNAP) and modulates its activity. DksA protein is a
crucial component of ppGpp-dependent regulation. The 2.0 A resolution structure
of Escherichia coli DksA reveals a globular domain and a coiled
coil with 2 highly conserved Asp residues at its tip that is reminiscent
of the transcript cleavage factor GreA. This structural similarity suggests
that DksA coiled coil protrudes into the RNAP secondary channel (the "backdoor
of gene expression") to coordinate a ppGpp bound Mg2+ ion with
the Asp residues, thereby stabilizing the ppGpp-RNAP complex. Biochemical
analysis demonstrates that DksA affects transcript elongation, albeit differently
from GreA; augments ppGpp effects on initiation; and binds directly to
RNAP, positioning the Asp residues near the active site. Substitution of
these residues eliminates the synergy between DksA and ppGpp. Thus, the
secondary channel emerges as a common regulatory entrance for transcription
before the terminus of the chromosome is duplicated, an asymmetric membranaceous
sept irreversibly divides the cell into a major (sporangium)
and a minor (forespore) compartment.
the sporangium endocytes the prespore (then called anterior chamber
of the spore), that in such a way becomes surrounded by 2 bilayers
whose inner layers are facing up. Such a polarity guarantees the deposition
of peptidoglycan in the intermembrane space. DPA is synthetized in the
sporangium and actively imported into the future spore : acting as a buffer,
it drives the passive influx of Ca2+. 80 genes (grouped into
4 families : spo, ger, ssp and cot) are needed
for sporulation. Spore specific proteins are synthetized thanks to specific
subunits in RNA polymerase : sE and
=> sG in the forespore & sK
in the sporangium.
They may be cylindrical, ellipsoidal or spherical in shape with size ...
... smaller than the originary bacterium (from 1 to 5 spores per cell)
type sporulation) (e.g. in Bacillus anthracis)
type sporulation)(e.g. : in Clostridium)
sub-terminal (e.g. : in Bacillus cereus)
... larger than the originary bacterium (distends the cell)
Within 24 hrs the sporangium undergo lysis and mature spore(s) are free.
From inner to outer you find :
core-containing sporoplastorprotoplast :
strome (a gel matrix) is made up of nucleoid, calcium dipicolinic
acid (CDPA or pyridin-2,6-dicarboxylic acid : it replaces H2O
in the manteinance of the quaternary structure of its binding partners
as they're as thermosensitive as the proteins expressed in the vegetative
forms are (except for NADH oxidase in Clostridium botulinum and
aldolase in Bacillus cereus)), polyamines, amino acids and 3-phosphoglycerate.
Refracting index : 1.54.
cortex (peptidoglycans) : its anisotropic expansion confers impermeability
(unstainable !) => low water content structures viewable after Wirtz
=> low metabolic activity and biopolymers more resistant to hydrolysis.
Refracting index : 1.47.
inner cortex or spore wall (20% of the cortex)
outer cortex (80% of the cortex): only 20÷32% peptidoglycan
units are similar to those in cell wall (but containing mesoDmp !). The
remaining 50÷60% units present MurNAc modified to form N-acetylmuramyl-lactame,
while 18÷20% of MurNAc are linked to L-Ala
instead of the usual tetrapetide. Such modifications are driven by a membrane-bound
Glu-mesoDmp hydrolase and a cytosolic Ac-Ala-Glu-mesoDmp lyase.
coats (Cys-rich proteins similar to keratins)
exosporium: present only in some Bacillus species,
made up of proteins, lipids and polysaccharides.
Endospores are heat and dry stable, resisting in amber for more
than 1 million years : anyway endospore-forming cells are not always very
heat-resistant (e.g. : Bacillus anthracis requires only 1-2 minutes
at 100 °C to be killed), but Clostridium botulinum requires
2÷6 hours at 100 °C to be killed compared to the only 30' at
70 °C for non-endospore formers ! Spores can be killed with 10'÷20'
at 120 °C in wet heat or 90'÷180' at 160÷200 °C in
dry heat (Pasteur oven) autoclaving. From soils into wounds or on
vegetables (ingested as aliments, wooden choping boards, ...). Some strains
are used as bioweapons (Bacillus anthracis), some others as biopesticides
(GE vegetables expressing the Bt toxin transgene from Bacillus
thuringiensis var.israelensis against mosquito and blackfly
larvae). Newer spores need activation (coat destabilization by 5÷10'
at 70÷85 °C) before germination in a favourable environment
: high [Ca2+], P > 10 MPa, L-Ala, Ado and
Ino activate (while D-Ala, MgCl2, PMSF
inhibit) a receptor that cleaves and activates a pre-formed p68 => p29spore
lytic enzyme or corticohydrolase that depolymerizes the outer
cortex allowing H2O income during exogrowth. Finally
the spore comes back to the vegetative form, dividing itself 2 hours after
cysts : resting stage formed by some Azotobacter
and Myxobacteria in which the whole cell is surrounded by a protective
layer. They arise from deposition of cell wall layers around the cell and
are resistant to dehydratation but not to heat : they are mainly
involved in nitrogen fixation and protection.
coccus (from the Greek kokkox = berry;
plural : cocci): cells that are spherical in shape.
streptococcus (from the Greek streptox
= necklace) : arranged in chains, like beads on a string.
Diplococcus: arranged in pairs. (e.g. : Streptococcus
staphylococcus: arranged like clusters of grapes. Random
planes of division.
tetrad: arranged in a group of 4, looking almost like a
square under the microscope. 2 planes of division.
sarcina (plural : sarcinae) : arranged in a group of 8. Sarcinae
look like small cubes and may be difficult to distinguish from tetrads.
3 planes of division.
bacillus (plural : bacilli) : rod-shaped cells. A single plane of
Diplobacillus: arranged in pairs.
Streptobacillus: arranged in end-to-end chains (e.g. : Mycobacteria,
Coryneform bacillus: arranged at angles to form V- and L-shaped
arrangements (e.g. Corynebacterium)
coccobacillus (e.g.: Gardnella vaginalis) : intermediate
to coccus and bacillus
spiral-shaped & no arrangement.
Spirillum (plural: spirilla) : rigid
vibrio: a bacterium with curved or comma-shaped cells. No
pleiomorphic : do not display a constant shape even during growth
in an otherwise unchanging, homogeneous environment
fruiting body : macroscopic reproductive structure produced by some
bacteria, including Myxobacteria. Fruiting bodies are distinctive
in size, shape, and coloration for each species.
Escherichia coli concentrates Zn and Fe by several orders of magnitude
relative to the concentration in a typical growth medium until they achieve
a quota of about 2 . 105 atoms per cel, which is
equivalent to a total concentration of about 0.1 mM.
Metals such as Cu and Mn are maintained in the 10 to 100 mM range. Other
metals are also concentrated by the E.coli cell to a narrow, fixed, total
concentration as follows : K and Mg, 108 atoms per cell, > 10
Ca, Zn, and Fe, 105 atoms per cell, 0.1 mM;
Cu, Mn, Mo, and Se, 104 atoms per cell, 10 mM;
V, Co, and Ni, low abundance.
Understanding the life strategy of highly motile Bdellovibrio
bacteriovorus, which preys on other gram-negative bacteria, including
plant, animal, and human pathogensref,
could lead to the identification of novel antimicrobials. This extremely
small bacterium—it averages 0.2–0.5 by 0.5–2.5 mm—has
a relatively large genome of over 3.7 Mb, encoding 3584 predicted genes.
There is no indication of horizontal gene transfer from its prey, even
though B. bacteriovorus has easy access to its prey's genomic information.
Additionally, the genome lacks the genes to synthesize 11 and to degrade
10 amino acids, suggesting it relies on its prey for some essential amino
acids. The bacterium also harbors a huge contingent of lytic enzymes, numbering
over 200 genes, that are potential new antimicrobial substances. Bdellovibrio
has been considered for use as a living biocontrol agent reduce or modify
populations of pathogenic microbes (e.g. plant pathogenic Erwinia
: most of the field uses stain 109 J, and not HD100)ref
Twort-d'Herelle phenomenon : the phenomenon of transmissible bacterial
lysis; bacteriophagia. When to a broth culture of typhoid or dysentery
bacilli there is added a drop of filtered broth emulsion of the stool from
a convalescent typhoid or dysentery patient, complete lysis of the bacterial
culture will occur in a few hours. If a drop of this lysed culture is added
to another culture of the bacilli, lysis will take place exactly as in
the first. A drop of this culture will then dissolve a third culture, and
so on through hundreds of transfers. d'Herelle attributed this phenomenon
to the action of an ultramicroscopic parasite of bacteria, which he named
researchers studying ageing in cells focus on 2 key characteristics:
asymmetric cell division and the stage of the life cycle leading up to
reproduction. The bacterium Escherichia coli, however, lacks both.
The single-celled organism splits into 2 apparently identical daughter
cells, which in turn divide, and so on. As a result, many scientists believed
that it, and similar bacteria, were immortal. The bacteria's apparently
symmetrical division makes it difficult to track cells. Stewart and his
teammates tackled the problem by taking pictures of a group of rectangular
coli cells every 2 minutes. Their complete record included over 35,000
cells. In the lab, E. coli reproduces in half an hour. A custom-made
computer program analysed the snapshots. The computer identified and tracked
the tips of each bacterial cell. E. coli divides down the middle,
giving each daughter cell one newly regenerated tip. But the cell's other
tip is passed down from its mother, or grandmother, or some older ancestor.
The bacteria inheriting the older end reproduced 1% more slowly than their
counterparts with each cell divisionref.
Stewart's group was unable to follow bacteria until death, as after 10
generations the dish became too crowded to spot individuals. Single-celled
organisms that divide asymmetrically, such as yeast and the bacterium Caulobacter
vibrioides (a.k.a. Caulobacter crescentus), were recently
also revealed to reproduce more slowly as they grow old.
bacterial microcompartments are primitive organelles composed entirely
of protein subunits. Genomic sequence databases reveal the widespread occurrence
of microcompartments across diverse microbes. The prototypical bacterial
microcompartment is the carboxysome, a protein shell for sequestering
carbon fixation reactions. 3D crystal structures of multiple carboxysome
shell proteins have been revealed, revealing a hexameric unit as the basic
microcompartment building block and showing how these hexamers assemble
to form flat facets of the polyhedral shell. The structures suggest how
molecular transport across the shell may be controlled and how structural
variations might govern the assembly and architecture of these subcellular
The Prokaryotes: A Handbook on the Biology of Bacteria, Second Edition,
Vol. 1-4, 1991. Springer-Verlag, New York NY. A. Balows, H. Truper, M.
Dworkin, W. Harder & K.-H. Schleifer
Bergey's Manual of Systematic Bacteriology, 1st Edition,
Vol. 1-4, 1989. Williams & Williams, Baltimore MD. John Holt (editor-in-chief).
Bergey's classification : a system of classification of bacteria
in which the organisms are grouped according to Gram reaction, metabolism,
and morphology, with each group being further subdivided into orders, families,
genera, and species.