Molecular Information Flow

and Protein Processing

DNA and genetic information flow

The nitrogen bases of DNA and

Genetic information flow Part of DNA chain
RNA and the specific pairing
between C, G, T, A via hydrogen
bonds
DNA structure

DNA structure Arrangement of the DNA double helix

DNA structure

Supercoiled DNA
Genetic information flow
Coupled transcription and translation in prokaryotic cells
Genetic elements

Chromosomal gene arrangements Plasmid

and the Operon

Cat: chloramphenicol
resistance;
tet, tetracycline
resistance;
oriT, origin of
conjugative transfer;
tra, transfer functions
DNA replication
DNA replication
Initiation of DNA synthesis

Replication process
DNA replication
The replisome
Replication of circular DNA: the theta structure
Transcription in Bacteria

RNA polymerase

The interaction of RNA polymerase with a bacterial promoter

Units of Transcription and Polycistronic mRNA

A ribosomal rRNA transcription unit from Bacteria and its subsequent processing.

operon and polycistronic mrNA structure.

Termination of transcription

Inverted repeats and transcription termination Rho-dependent termnination

RNA Processing in Eukaryotes and Archaea

Promoter architecture and transcription in Archaea

RNA Processing in Eukaryotes and Archaea

Processing of the primary transcript

into mature mrNA in eukaryotes

Activity of the spliceosome

Protein synthesis (translation)_ Amino acids
Protein synthesis (translation)_ Polypeptides and Proteins

Peptide bond formation Tertiary structure of polypeptides

Secondary structure of polypeptides

Protein synthesis (translation)_ tRNAs
Protein synthesis (translation)_ tRNAs
Protein synthesis (translation)_ Genetic code
Protein synthesis (translation)_ Genetic code

The wobble concept

Translation
initiation

Elongation
Polysome

Freeing trapped ribosomes

Assisted protein folding and Chaperones
Microbial growth and its control
Cell division

Binary fission
 TIMI-1162; No. of Pages 7

Cell division
Review Trends in Microbiology xxx xxxx, Vol. xxx, No. x

Box 1. Terminology (A) Agrobacterium

New poles. Always refers to the poles generated at the most recent
cell division. These poles may, in polar-growing bacteria, become
growth poles that are sometimes referred to as ‘new’ poles in the
literature. Here we refer to new growing poles as ‘growth poles’. In
other bacteria that grow and elongate by dispersed cell growth
(such as Escherichia coli, Bacillus subtilis, and Caulobacter crescen- Transi!on
tus), the new pole does not become the growth pole.
Old poles. These are the result of cell division that occurred before
the most recent division event. In most bacteria, including those
with dispersed or unipolar growth, the old pole is passed on
continuously to daughter cells and remains permanently inert, as
described for E. coli [86]. By contrast, bacteria with bipolar growth
continue to growth from both old and new poles. Whether subpolar
growth in Mycobacterium results in permanently inert polar caps
Key: -Growth pole -Old pole -Septal PG synthesis
over multiple generations remains to be investigated.

-Parent cell PG -New PG

branching morphology of Streptomyces. In a more contro-
versial example, polar growth may help generate cell-to-
(B) Mycobacterium
cell heterogeneity that makes infections by Mycobacterium
notoriously difficult to treat. Variations in growth rates of
old and new poles were reported to lead to inherent differ-
ences in antibiotic susceptibilities between siblings [20];
however, subsequent reports have instead favored a sto-
chastically driven heterogeneity model [21,22]. Aside from
these specific cases, an intriguing and untested hypothesis
posits that polar growth arose so that bacteria can generate
new cells de novo, passing on only new and undamaged
extracellular proteins, cell wall, and membranes. These
progeny would exhibit greater fitness than their parent
cells and improve population success in more stringent
environments. The interplay between cellular aging and
Key: -Rapid subpolar -Slow subpolar
polar or asymmetric growth is reviewed by Kysela et al. [10]. -Inert PG
growth zone growth zone

Mechanisms of polar growth

Cell growth is a complicated process that relies on careful
coordination between its many contributing parts. During
polar growth, cells must identify and maintain growth
poles as specific regions to integrate the biosynthetic com-
plexes that produce nascent peptidoglycan, proteins,
Budding from hyphae
lipids, and other components of the cell envelope. More-
over, these complexes must also be coordinated with DNA
replication during the cell cycle and ultimately cell division.
Below we use Actinomycetales and Rhizobiales as models
-Septal PG synthesis -Parent cell PG -New PG
TRENDS in Microbiology
Figure 1. Unipolar growth (represented by Agrobacterium tumefaciens) is
contrasted with bipolar growth (represented by Mycobacterium smegmatis). (A)
Polar growth
In Agrobacterium, elongation occurs from one pole. During septation the growth
pole becomes an old pole (arrow), septal peptidoglycan (PG) synthesis occurs at
the midcell, and polar elongation stops. After cell division, PG synthesis and polar
growth resume in both sibling cells from the respective new growth poles (green)
created by septation. Therefore, the growth pole is not inert with respect to PG
synthesis. (B) In Mycobacterium, septal PG synthesis creates poles comprising
Biofilms
Quantitave aspect of microbial growth
The Mathematics of bacterial growth

Cell number:

N = N02n ; n = t/g
N: Final cell number
N0: Initial cell number
n: number of generations
t: duration of exponential growth
g: generation time

n=3.3[log(N)-log(N0)]

If N=107, N0=103 and t=3 (hours)

n = 3.3[log(107)-log(102)]
= 3.3[7-2]
= 16.5
g = t/n=3/16.5=0.18 (hour)
Quantitave aspect of microbial growth
N: Final cell number
N0: Initial cell number
n: number of generations
t: duration of exponential growth
g: generation time

N = N02n
2n = N/N0
log(N/N0) log(N/N0)
n = log2(N/N0) = =
log(2) 0.303
n = 3.3[log(N)-log(N0)] = t/g

t = 3.3*g*log(N) - 3.3*g*log(N0)
(y= ax-b)
The microbial growth cycle
Growth media
Aseptic techniques
Microscopic counts of microbial cell numbers
Viable counting of cell numbers
Turbidimetric Measures of Microbial Cell numbers
Environmental effects on growth

- Temperature

- pH

- Osmolarity

- Oxygen
Controlling Microbial Growth-Heat sterilization

Autoclave:
- Use steam under pressure
and high temperature to
kill cells
- 121˚C, 1 atm, 15-20 mins
à kill all cells

Pasteurization:
- Use heat to significantly
reduce rather than totally
eliminate the
microorganisms found in
liquids
- Milk is pasteurized at 71°C
for 15 seconds
Controlling Microbial Growth: Physical control

- Ultraviolet radiation

- Ionizing radiation

- Filter sterilization
Controlling Microbial Growth: Antimicrobial agents

Antimicrobial agent susceptibility assay using diffusion

methods
Microbial regulatory systems
DNA binding proteins
Negative control

Possitive control
Global control and the lac operon

Diauxic growth of Escherichia coli

on a mixture of glucose and lactose.

cyclic AMP Overall regulation of the lac system

Sensing and Signal Transduction
Quorum sensing
Stringent response
RNA-based regulation: regulatory RNAs
Riboswitches
Attenuation
Feedback inhibition
Post-translational regulation
Molecular Biology of
Microbial Growth
Regulation of Chromosome Replication Initiation

1. SeqA binds to hemimethylated oriC

regionà no replication

2. SeqA binds to hemimethylated

dnaA promoterà no transcription

3. ATPase HdaA hydrolyzes ATP

associated with DnaAà DnaA-ADP
Genome replication in fast growing cells
Chromosome segregation

Mitotic
spindles

Chromosome segregation in eukaryotic cells Chromosome segregation in Caulobacter

Cell division

Divisome Division events

Peptidoglycan biosynthesis
Antibiotic targets and antibiotic resistance
identify resistance to the administered drugs. Though long required for such studies have not yet been developed.
suspected (Tuomanen et al., 1986), accumulating evidence However, recent studies provide strong indications for the
Persistance
now convincingly points to the importance of transiently importance of persister cells in recurrent infectious

Fig. 2. Antibiotic resistance versus persistence. A microbial population (confined by a light-grey ellipse) initially consists of
mainly antibiotic-sensitive cells (dark-grey). (top panel) In addition, the population may also contain resistant cells (black),
resulting from a permanent change at the genetic level. After antibiotic treatment (+Ab), only resistant cells remain. Upon
HipAB toxin-antitoxin module
Viruses and their replication
Viral components
Virion structure

Icosahedral symmetry

The arrangement of rna and protein coat in

a simple virus, tobacco mosaic virus.

Structure of T4, a complex bacteriophage.

Viral envelope

Hepatitis C Virus human immunodeficiency viruses

Viral envelope: lipoprotein

+ Protein: attach to and infect animal cells
+ Lipid: fuse with animal cell membrane
Virus life cycle

The replication cycle of a bacterial virus.

Culturing, Detecting, and Counting viruses
Attachment of Bacteriophage T4
Attachment and Penetration of Bacteriophage T4
Replication of bacteriophage T4
Transcription and Translation

Early proteins: Middle and late proteins

-Enzymes for the synthesis of T4 unusual base - Additional RNA polymerase–modifying
-Proteins to modified RNA-polymerase proteins
-Anti sigma factor - 8 proteins in replisome
-T4 sigma factors - Virion structural and release proteins
Packaging the T4 Genome and Virion Assembly
Temperate Bacteriophages and Lysogens
Bacteriophage Lamda
Animal virus infection
Animal virus infection