Cell Structure, Organization, Bacteria and

Archaea
N Nanniga

Glossary:

Cell Envelope - boundary that envelopes a cell. Composed of a cytoplasmic

membrane and a cell wall

Flagellum - proteinaceous filament of several micrometers in length that enables

bacterial motility. Through a basal body, it is integrated into the cell envelope. Proton
motive force drives the rotor located in a stator

Hams - proteinaceous filaments on the surface of the archaeal organism SM1.

Terminates into fishhook-like structures

Penicillin binding proteins - involved in bacterial peptidoglycan assembly outside the

cytoplasmic membrane. Binding specific antibiotics

Peptidoglycan - bacterial wall component built from glycan chains, interconnected by

cross-linked peptide side chains. Glycan chains are made of N-acteylglucosamine and
N-acetylmuramicacids. Cross linking through this peptide side chains provides a
strong network

Pili - proteinaceous filaments on bacterial cell surface adhering to other organisms.

Pseudopeptidoglycan - in archaeal species. It has no D-amino acids. The disaccharide

units of the glycan are made of N-acetylglucosamine and N-acetylalosaminuronic acid

Sacculus - covalently closed structure that has the shape of bacterium. It has glycan
chains interconnected by peptide side chains

S-layer - a protein layer of regularly arranged subunits on the surface of the

prokaryote

Defining Statement

Going from the outside of the cell to the inside, from cellular appendages to the
nucleoid.

Characteristics of Prokaryotes

An overview of Prokaryotic Structure

 Translation and transcription occur in the same compartment

 No membrane bound nucleus

Models:
E.coli, Salmonella typhimurium and Caulobacter crescentus → for gram negative

Bacillus subtilis, enterococcus sp and Pneumococcus sp and S. aureus and Strep spp
→ are gram positives

V. cholerae - has specific DNA segragation mechanisms for its two different
chromosomes

Planctomycetes - lack peptidoglycans in the nucleoid region end enveloped by a

single or double membrane

Gemmata obscuriglobus - double membrane shields a DNA and ribosomes area

from a cytoplasmic area containing ribosomes. This is bounded by an
intracytoplasmic membrane

Its DNA is surrounded by cytoplasmic material

Paryphoplasm - in-between the intracytoplasmic membrane and cytoplasmic

membrane. A ribosome-free compartment

Shape of Prokaryotes

Ranges from rods to spheres. Rods can be straight, curved or helical

Cells operate individuallly, as chains or as two-deminesional sheets or 3d packets

Cell shape is maintained by a rigid cell wall varying in complexity.

Archaea because they do not have peptidoglycan have pseudomureins and chondroitin

Archaea are not susceptible to antibiotics directed against the penicillin binding
proteins in peptidoglycan synthesis.

S-layer - borders the cytoplasmic membrane in other archaea that lacks a

pseudopeptidoglycan or chondroitin. It reinforces

MreB - an actin like protein underneath the cytoplasmic membrane in the helix of rod-
shaped bacteria.

Disruption of this helix results into spherical cells

Shape involves interplay between cytoplasmic MreB and envelope-associated

peptidoglycan synthesizing system

Coccal species lack this MreB

The helical shape of G-negative spirocete is maintained by periplasmic flagella in

addition to peptidoglycan

Prokaryotic species may have appendages like a flagella, pili or a stalk

Cell-envelope - appendages

Prokaryotes carry appendages such as a stalk, flagella or a pili

These serve as attachment to surfaces (stalk), swimming (flagella) or gliding (pili).

Flagella and pili are distinct macromolecular complexes whereby a stalk is a structural
continuation of the cell envelope

Stalk (Prosthecae)

 enables to bind to substrate like in C. crescentus and E. Coli

o Can be a polarly-flagellated free swimming cell, a swarmer or a

sessile stalked cell

When the swarmer shed the flagellum and adjacent pili, the stalk develops at the same
location

Stalks is thinner than the diameter of the cell and is free of cytoplasm

Penicillin binding protein 2 and RodA - required for Elongation and growth of stalk in
C. crescentus. But length extension is not dispersed in E.voli but is carried at its base

Hyphae - prosthecae seen in Hyphomonas and Hyphomicrobium

For Hyphomonas, the stalks is not devoid of cytoplasm. It enables the migration of
DNA and cytoplasm to the distal end of the stalk where a bud is formed.

Bud develops into a swarmer cell that can be transformed into a stalked cell

Bacterial Flagella

helical tubes with a length of several micrometers and diameter of 24 nm

Arrangement can be polar, peritrichous or both

Polar flagella are longer than peritrichous counterparts

Flagella in Spirillum volutans has about 50 flagella at each pole

Spirochetes carry flagella in the periplasmic space

Integration of flagellum leads to various rings like MS, P and L. specific for a
particular layer

basal body - term for the envelope based structure

Parts:
Basal body with a rotator in the envelope, a bended flexible part called hook and the
rigid filament

Flagellar assembly proteins

Protein export facility (type III) secretion system

for flagellar proteins is apposed against the cytoplasmic side

FliC - for elongation of the flagellar filament. It needs the transport of this from the
cytoplasm through the base to the channel inside the flagellum

Eleven protofilaments constitute the filament

The rotator is like a mechanical rotor

Energy for torque generation is though to result from proton motive forces in
cytoplasmic membrane

For G-negatives like E.Coli - flagella may rotate clockwise or counterclockwise

Clockwise - directionless tumbling

Counterclockwise - swim in straight line

Tumbling → happens when intertwied flagella in counterclockwise rotation change

the helical pitch

Alternating in tumbling and straight swimming is needed

Chemoreceptors - for sensing the food source

Signal transduction - provides connection with basal bodu of flagellum

Flagella of G-positives

Periplasmic flagella arise at a subpolar position from each pole and overlap in the
center

Flagella responsible for helical shape of spirochetes and for Treponema, its motility

Archaeal Flagella

Holobacterium salinarium - smaller dimensions and axial filaments have different

proteins

Diameter of flagella is 10nm whereas in bacteria it is 24 nm

Their proteins are also glycosylated to sustain extreme growth conditions

S-layers are also glycosylated

N-termini of archaeal flagellin and bacterial pilin show homology

Growth of these flagella might take place at their base because of lack of central
channel.

For H.salinarium - the flagella is thought to interact with a cytoplasmic structure

(polar cap) underneath the cytoplasmic membrane

Bio-assembly of archaeal flagellum is thought to occur via a type 2 secretion system

as in type 4 pili

Pili (fimbriae)

comparatively small rod-like proteinaceous appendages

Main body for type IV pilus is composed of pilin protein PilA. These are cleaved by
prepillin peptidase in CM. Secretin allows protrusion of pilus through the OM. Energy
for assembly and retraction of pilus is delivered by NTP-binding proteins

External part of flagellum is made up of flagellar proteins FlaA, FlaB1 and FlaB2.
flagellum is embedded in the envelope with other Fla proteins

preflagellin peptidases cleaves the leader peptide from flagellins to be incorporated in

the flagella

Pili carry adhesive proteins. Nonfimbrial adhesive proteins may also be present

Type 1 pili

resemble P pili emerge from surface of Enterobacteriaceae

Pili is rigid thin filaments which attain a length of 2 micrometers

In UPEC strains, they adhere to surface of epithelial cells with their tips

In the tip, the adhesin FimH is present, a mannose-specific lectin

Main body is composed of FimA subunits arranged into a helix

Bio-assembly of type 1 pili is carried through a chaperone-usher pathway

Type IV pili

reside on plar surface of pathogenic Gram negative bacteria

 Multifunctional, including acting on adhesion, uptake of DNA, twitching motility

and biofilm foramtion
Adhesion and DNA uptake are mediated at pili tips

have length of 1- several micrometers and thickness of 5 nm

 Pili have a helical structure and contain a component of PilA

 Can retract and extend to enable gliding by twitching motility.

Formation of fruiting bodies is termed social gliding involving twitching motility

Swarming is also called a social gliding mechanisms but involves flagella and not pili

Bio-assembly

Hami

novel type of appendages that are peritrichously arranged on surface of

nonmethanogenic archaeal organisms denoted as SM1

 denotes prickle or hook

 several microns and diameter of 7-8 nm

Tips end in a structure resembling a triple fishhook

preceeded by a smooth region then by remaining filament region

suggest that it is for grasping rather than sticking

type 4 pili have also class 3 signal peptides

Cell envelope

functions to protect the integrity of the cell and permits interaction of organism with
the environment

G-negative (outer membrane - peptidoglycan layer and inner membrane)

peptidoglycan layer attached to outer membrane via lipoprotein molecules

Periplasm - compartment between the two membrane and includes the peptidoglycan

G-positive - lacks an outer membrane but has a thick cell wall with peptidoglycan and
wall teichoic acids

WTA are charged anionic polyol phosphates giving a negative charge to G-positive
cell wall

Lipoteichoic acid polymers are inserted into the cytoplasmic membrane spanning the
whole envelope

Mycoplasma, Planctomyces and Chlamydia lack peptidoglycan\

G-positive has an additional layer composed of arranged proteins (S-layer)

In some archaea they are in contact with cytoplasmic membrane and contribute to cell
shape

Capsules

Long polysaccharides associated with outer membrane

E.coli has protrusions in environment that forms a capsule at surface of cell

Polysaccharides are variable in composition and strain specific.

For E.coli, K antigens and O antigens are found

S-layers

For gram negative like G. halobium, the S-layer glycoproteins are inserted into the
outer leaflet of the inner membrane.

For gram-positive bacteria and archaea, this S-layer appears apposed to the cell wall
containing peptidoglycan or pseudopeptidoglycan

For gram-negative - S-layer is in contact with LPS constituent of outer membrane

S-layers arise thorugh self-assembly on cells’ surface

Purified S-layer proteins assemble into sheets in vitro

S-layers have a protective function→ role as molecular sieve.

Outer membrane

integral component in gram-negative bacteria and act as a selective permeability

barrier.

It has lipoproteins, phospholipids and LPSs

Arrangement is assymetric

LPSs are located in outer leaflet in outer membrane whereas the main phospholipids
reside in the inner leaflet

LPSs has three regions:

Lipid A - anchored to outer leaflet

Core oligosaccharide

O-specific polysaccharides (O-antigen)

Outer membrane proteins organized into trimers to allow function as hydrophilic
transmembrane channels

Several porins occur in one and the same cell studied in Gram-negative organisms

Monomeric porin has beta barrel structure, traversing the outer membrane

3 beta barrel structures has a pore for osmoporin (OmpC)

Peptidoglycan Layer

E coli

Constructed from glycan chains interconnected by peptide sude chains

Glycan chains has disaccharide units of N-acetylglucosamine and N-acetylmuramic

acid connected through a beta 1-4 glycosidic bond

Glycan chains carry peptide side chains interconnected through peptide bonds.

For E.coli, these side chains are tetrapeptides interconnected through a peptide bond
between meso-diaminopimelic acid and D-alanine

Differences:

For G-positive staph aureus, the peptide is pentaglycine

peptidoglycan layer represents a single covalent structure which has the shape of the
cell

For gram-negative organism such as E.coli, peptidoglycan layer is monomolecular

and is very thin

Sacculus - little sac. singular sac-like molecules. Not just a static structure

Arranged at less perpendicular to the acis of the cell.

Assembly of peptidoglycan in E. coli takes place in three cellular compartments

enzyme reactions in cytoplasm produces UDP-MurNAc-pentapeptide

In the cytoplasmic membrane where lipid 1 and lipid 2 are formed

Lipid 1 - result of binding UDP-MurNAc pentapeptide to undecaprenyl phosphate

Addition of UDP GlcNAc to lipid 1 prodices lipid 2

Third compartment is periplasm where lipid 2 is inserted into peptidoglycan by

penicillin binding proteins
The prenylated disaccharide pentapeptide has to switch from cytoplasmic to
periplasmic side

Bacillus subtilis

Freeze substitution (rapid freezing) then fixed, dehydrated and stained at low
temperature to study walls of this bacteria

1. electron dense region

2. more translucent zone
3. ruffled electron dense outer layer

Older peptidoglycan becomes dissolved by autolysins as it arrives at the cell surface

For result in frozen-hydrated, cytoplasmic membrane is visible and the cell wall
appears to divide into inner wall zone (lower electron density) and outer wall zone
(higher electron density)

Low electron density zone represents the periplasm of this bacteria

OWZ - decreases density from inside to outside

Its assembly of peptidoglycan is coordinated with synthesis of wall teichoic acids

Coordination is through the use of a undecaprenyl phosphate.

Wall teichoic acids assembled underneath the cytoplasmic membrane and not in the
periplasm as for peptidoglycan

Wall teichoic acid polymer should be transferred to the periplasm to attached to

peptidoglycan.

Peptidoglycan synthesis in cocci are linked to septation

Pseudopeptidoglycan

For gram positive Arcahea, the Methanobacterium cell wall has

pseudopeptidoglycan

For this polymer, the disaccharides have GlcNAc and N-acetylalosaminumuronic acid.
where the NactalNa has replaces MurNAc

They are connected by a BETA 1-3 glycosidic bond

glycn chains carry peptide side chains

BUT THEY LACK D-amino acids

assembly of psuedopeptidoglycan requires undecaprenyl phosphate as in

peptidoglycan and teichoic acid synthesis
Overall Structure

Cytoplasmic membrane envelopes the cytoplasm

Its protein components interact with cytoplasmic and periplasmic proteins

CM is embedded in a proteinaceous framework

Proteins in or at the CM are positioned in a helical arrangement

MreB helix underneath the cytoplasmic membrane

Sec protein translocation machinery is helically arranged in cytoplasmic membrane in

B. subtilis as in E. coli

Sec helix and MreB helix do not overlap

Membrane proteins with periplasmic domains may be organized into a helix

Membranous invaginations arise from CM like in prototrophic nitrifying and

methanotrophic bacteria

For archaeal membrane, the lipids, hydrophobic side chains are not linked to the
glycerol backbone through an ester linkage but by an ETHER linkage

Hydrophobic side chains are not fatty acids but isoprenoid chains

Cytoplasm

The Cytoplasm

Filled with polyribosomes

After cryoelectron tomography with pattern recognition techniques

they identified 70s ribosomes in a bacterial cell Spiroplasma melliferum

S. melliferum ribosomes comprise a limited fraction of cytoplasmic volume

Polyribosomes may link DNA and cytoplasmic membrane

There is a transient link between nucleoplasm and envelope

Ubiquitous cytoplasmic proteins like ribosomal elongation factor Tu and tubulin-like

cell division protein FtsZ are able to polymerize into linear polymers in vitro

Helical MreB polymers are located underneath the cytoplasmic membrane

Some organisms have phb granules, polyphosphates, sulfur droplets or even
magnetosomes

Gas vesicles -affect buoyant density

Cytoplasmic Proteinaceous Filaments

constitute the cytoskeleton wherein actin filaments and microtubules are present

Protein constituents are actin, and tubulin respectively

Filamentous structures composed of similar proteins occur in bacterial cytoplasm

Prokaryotes also has a tubulin homologue called FtsZ

this FtsZ polymerizes in the cell center into a ring-like structure apposed against the
cytoplasmic membrane

It carries out cytokinetic processes

Cryo electron tomo in C. crescentus and S. melliferum demonstrated the presence of

presumed proteinaceous filaments

In crescentus, they persist in MreB and crescentin deletion mutants

Crescentin resembles intermediate filaments in eukaryotes

This functions in maintaining the curved shape

For S. melliferum, three filament bundles traversing the length of the helical cell

Two of them are composed of MreB

the movement and change of handedness of the helical organism is accomplished by

alteration of MreB filaments

The MreB endoskeleton compensates for the absence of a cell wall

Also the proteinaceous cytoplasmic filamens in the DNA segregation apparaturse of

V. cholerae chromosomes (ChrI). Duplicated ChrI are moved apart by polymerized
ParAI proteins

These are all cytoplasmic

The Nucleoid

Overall structure of the nucleoid

Nucleoplasm the central area that contains the genetic material

Proteins in DNA compaction, DNA replication and transcription are located in the
periphery of the nucleoplasm because they are excluded form the DNA rich region

Nucleoid denotes a visible area in the cell and can be isolated or analyzed genetically

Packing is achieved by

bacterial chromosome is negatively supercoiled

Compaction is thought to occur through macromolecular crowding, DNA

binding proteins and proteins that affect superhelicity. Loosening may occur
through coupled transcription, translation and protein translocation

Supercoiling is produce by DNA gyrase and divides the chromosome in 100 domains

DNA-binding proteins like histone-like protein HU, integration host factor

IHF, factor for inversion stimulation Fis and nucleoid associated protein H-NS
are likely to further reduce the chromosomes spatial dimensions

The HU can bend and compact DNA at nonspecific sites, IHF can bind
specifically as does Fis

H-NS accomplishes compaction by bridging DNA regions

A phisycal process as phase separation due to macromolecular crowding

creates an interface between cytoplasm and nucleoplasm

Note that bacteria do not possess nucleosomes similar to eukaryotes

Substructure of Nucleoid

cellular positioning of DNA replication machinery and specific gene regions like oriC
and terminus

The discoveries are due to the application of fluorescence microscopy

Cytological advances are made that exclude the complication of a multifork

replication.

This multifork replication arises when the doubling time of culture is smaller than the
duration of DNA replication machinery.

DNA replication is effected in a central cellular compartment

In this compartment, the two replication forks of bidirectional replicating

chromosome are in vicinity of each other.

The DNA to be replicated is threaded through a stationary replication factory

Duplicated oriCs move in opposite direction towards the poles

Labelling of OriC and terC revealed that they occupy distinct cellular positions
dependent on progress of DNA replication

Labelling of gene regions in a circular chromosome has showsn that label occurs at
the intermediate positions

The arm is a chromosomal segment between oriC and terC

Left and right arm show a defined arranfement with respect to the length of the axis of
the cell.

GENE POSITION IN A NUCLEOID IS NOT AT ALL RANDOM.

Their position is dynamic that it depends on the DNA REPLICATION STAGE OF

BACTERIAL CHROMOsome