Bacteria and Viruses

cytoplasmic structures:

• nucleoid

• plasmids

features of nucleoids

• Doble stranded DNA

• Circular chromosomes

• Spatial organization --> super coiled

 

• Bacterial ribosomes are a target for antibacterial drugs

• 16s RNA --> low mutation rate --> used in phylogenetic

features of plasmids

• circular or lineal extrachromosomal DNAs

• not usually essential for bacterial survival

• capable of autonomous replication

• often provide a selective advantage

features of flagella

• circular or lineal extrachromosomal DNAs

• not usually essential for bacterial survival

• capable of autonomous replication

• often provide a selective advantage

• Long helical filament à extend outside the cell

• connecting hook

• Basal body à rotor to turn the flagellum

features of pili and fimbriae

• Protein spikes that extend from surface

• Pili are longer than fimbriae

• Fimbriae are normally more abundant per cell

function of fimbriae and pili

• Functions = adhesion --> T1 fimbriae required for pathogenic strains to adhere

• T4 pili used in extension and retraction of pili, help move along a solid surface

• Sex pilus involved in DNA transfer in conjugation

what are capsules

• Amorphous polysaccharide slime surrounding cells

• Tightly bound to the bacterial cell wall

• Can be present in both Gram-positive & Gram-negative bacteria

Features of Capsules

• Barrier to toxic hydrophobic molecules (e.g. detergents)

• Contain water à prevents desiccation

• presence and composition are strain-specific

• e.g streptococcus pneumoniae --> meningitis, pneumonia, sepsis

non capsulated strains are mainly

antivirulent

active transport - group translocation

• Substrate modified, generally phosphorylated, during transport

E.g. phosphotransferase system (PTS system)

• The energy is provided by the PEP passed along chain of enzymes

• Modification of the sugar à maintains concentration gradient

regulation of metabolism in bacteria

• Adaption to varying supply of carbon sources in different niches

• Gluconeogenesis and TCA cycle --> essential when E.coli infects the urinary tract

•  Glycolysis and Entner-Duodoroff pathway --> growth in the intestinal trac

features of listeria

• Gram positive rods

• Found in coils, farms, dust and intestinal tact

• Use of host sugar phosphates via specific transporter activated in hosts

• Promote rapid intracellular growth

listeria monocytes

• Major human food borne pathogen

• Can cause septicaemia abortion and meningoencephalitis

• Direct cell to cell spread causes avoidance of extracellular defences

what type of ribosomes are in bacteria

70s

why are bacterial ribosomes targets for antibacterial drugs

• very different from eukaryotic ribosomes = more specific

features of bacterial cell membrane

• lipid bilayer structure

• similar to eukaryotic but no steroids such as cholesterol

features of bacterial cell wall

• rigid layers around cytoplasm

• peptidoglycan - mucopeptide or murein

• polysaccharide chains with peptide cross links

• resists osmotic pressure and determines cell shape

• signals to innate cells of bacterial presence

Gram positive basteria cell wall

• chains of glycerol phosphate/ribitol phosphate

• bound covalently to peptidoglycan

• provide rigidity

cell wall - gram negative

• more complex than G+

• thinner peptidoglycan than G+

• absence of teichoic and lipoteichoic acids

periplasmic space of Gram negative contains:

• transport systems for iron, proteins, sugars

• hydrolytic enzymes —> breakdown of large macromolecules

• virulence factors such as collagenases, proteases and beta-lactamase

what makes electron transfer possible in aerobic respiration

presence of components that exist in oxidised or reduced forms, e.g Fe-S clusters

what is the final electron accepter in aerobic respiration

molecular oxygen

what are the key components of aerobic respiration in bacteria

• Dehydrogenases, quinones, cytochromes and one or more terminal oxidases

what is the final electron acceptor in anaerobic respiration

an inorganic compound that is’t O2

what happens in anaerobic respiration in bacteria

• NO3- (nitrate) is reduced to NO2 (nitrite) via nitrate reductase

• Total ATP yield less as only part of Krebs cycle

features of fermentation

• Releases energy from oxidation of organic molecules

• Does not use the Krebs cycle or the electron transport chain

• Derive ATP from substrate-level phosphorylation

• Does not require oxygen (anaerobic process)

• Recycle NADH back to NAD⁺

process of binary fission

• Elongation of cell wall, cell membrane and overall volume, starts chromosome duplication

• Septum wall grows inward, chromosomes are pulled towards opposite ends

• Septum is synthesised and cell membrane starts to separate into chamber

fermentation - dental disease

• Diets with high sugar content

• Lactic acid bacteria --> ferments sugar --> lactic acid

• Dissolve calcium phosphate

• Bacterial proteolytic enzymes --> degrades supporting matrix

use of energy and metabolism in TB

• Host cells lipids are essential carbon sources during infection

• Switch from carbohydrate based metabolism of lipid substrates via glyoxylate shunt enzymeisocotrate lyase  --> avoids carbon loss during oxidation in TCA cycle

• Specific substrates are used at different stages of infection

• Can survive under energetically unfavourable and poorly oxygenate conditions

what is an FTS protein

• filamentous temperature sensitive

• act to form the divisome —> a cell division apparatus that forms a septal ring and defines division plane

FtsZ

  tubulin-like GTPasesZ

ZipA

ftsZ anchor

Ftsl

peptidoglycan biosynthesis protein

FtsK

help in chromosome separation

FtsA

similar to actin, ATPase activity

What triggers endospore formation

• survival mechanism —> triggered by adverse conditions

• Bacterial genome is sequested in a safe place until environmental conditions improve

how is the spore protected

Mother cell secretes protein coat (calcium dipicolinate) to protect spore à then lyses to release spore

what is in the core of the spore

• DNA, RNA, protein

what is in inner membrane of spore

lipids/proteins

what is endospore wall made of

peptidoglycan

Diplicolinic acid

form complex with calcium --> bind water --> spore become drier and compact

obligate oxygen requirements

• yes

• aerobic respiration

facultative oxygen requirements

• can use with or without

• aerobic/anaerobic/fermentation

microaerophilic

• work in low oxygen

• aerobic respiration

aerotolerant

• work with or without oxygen

• fermentation/anaerobic

signal

environmental change, signalling molecule

sensor

usually ligand binding, able to change protein confirmation for protein-protein interactions

regulator

usually specific DNA binding protein - binds in control region

regulon

group of genes controlled by a common regulator

 

Two component system

• Consist of a sensor kinase (detects signal) and a response regulator (activates gene expression).

• PhoP/PhoQ in Salmonella, which responds to magnesium levels and triggers expression of virulence factors.

Environmental regulation - 2cs —> gene regulation

• Interaction with transcription protein activator/repressor

• Effects on RNA-polymerase sigma factors

• DNA binding regulator

biofilm

 a structured community of bacterial cells enclosed in a self produced polymeric matrix

quorum sensing

When population density is high enough, they turn on genes together — including toxins, enzymes, and biofilm factors.

role of quorum sensing

• Control of virulence gene expression

• Facilitate dispersion of biofilm

• HHQ and PQS modulate inflammatory and immune response in mammals

• Attenuates LPS induced inflammation and allows for establishment of infection

• Toxin production increases inflammation

How do gene regulatory circuits work together for colonization & pathogenesis?

Bacterial pathogens use cascades and feedback loops to time their actions:

• Early genes: Adhesins, pili/fimbriae → for attachment to host.

• Mid-phase genes: Toxins, invasion systems (like T3SS) → for invasion and immune evasion.

• Late genes: Nutrient acquisition, evasion, stress survival → for long-term survival.

How is gene expression managed at a community level (biofilms)?

• Biofilm matrix genes (like EPS production) are upregulated.

• Virulence genes may be suppressed or timed depending on the stage of biofilm development.

• Stress resistance genes (e.g., oxidative stress, antibiotic resistance) are highly expressed.

• Bacteria deep in the biofilm get less oxygen/nutrients, so gene expression varies by position

role of bacterial cell envelope

modulates bacterial interactions with their environment

effect of secreted proteins from mutualistic and pathogenic associations

•  modify host physiology → necessary for bacterial survival → e.g. promote colonization of host (toxins and effector proteins)

what are secretion systems

• Protein export machinery outside the cells & into other cells.

• Difference in export depending on Gram -positive or –negative bacteria

features of SEC

• general secretion

• Requires signal peptide leader sequence

• moves unfolded proteins

features of TAT

•  twin arginine translocation

• moves folded proteins that have twin arginine motif in signal sequence

how many layers of lipids in gram negative cell wall

2

how does cholera cause diarrhoea

• Cholera toxin (CTX) --> binds to GM1 ganglioside receptor

•  CTX endocytosed and trafficked to EPR

• Activates adenyl cyclase system, increasing cAMP levels

• cAMP triggers inhibition of reabsorption of Na+/K ions and hypersecretion of chloride ions

• Osmotic gradient causes movement of H2O into intestinal lumen --> diarrhoea

 

features of T1SS

• One-step system: Transports proteins directly from cytoplasm to outside the cell.

• Doesn’t require a periplasmic intermediate.

• Substrates: Toxins, enzymes (like proteases).

• Common in Gram-negative bacteria.

function of T3SS

• Known as the “injectisome”.

• One-step system: Directly injects proteins (effectors) into host cell cytoplasm.

• Highly associated with virulence.

• Found in bacteria like Salmonella, Shigella, Yersinia, and E. coli.

Regulation of T3SS gene expression

• TTSS contains >20 proteins

• gene expression coupled to secretion

• signals, regulators and networks vary from one system to another

Salmonella typhimurium is …

gram negative

T3SS-1

• Early phase invasion of enterocytes and M cells

• Activation of pro-inflammatory responses

T3SS - 2

• Later phase of infection

• Intracellular survival and replication within macrophages

 

features of T4SS

• Transfers both proteins and DNA.

• Can target other bacteria or host cells.

• Used in conjugation (DNA sharing) and pathogenesis.

features of T6SS

• A contractile nanomachine, like a molecular crossbow.

• Injects toxic proteins into other bacteria or host cells.

• Involved in bacterial competition and virulence.

• cholera

what are dynamic firing cycles in T6SS

• expulsion of a cell-puncturing device loaded with multiple toxins

T7SS

• Used by TB

• ATPase driven export

• specialised to export proteins across thick cell wall

role of Tir

 triggers actin polymerisation and pedestal formation underneath attached bacterium

How to distinguish between commensal and pathogenic E. coli?

• Intestinal cells can sense the T3SS present in pathogenic E. coli

• Trigger NF-KB activation in a non-TLR dependent mechanism

• T3SS recognition by the immune response to differentiate between pathogen & commensal

pathogenic

disease causing bacteria, affects all normal host defences

non-pathogenic

 organisms invade an individual without causing any obvious detectable symptoms

commensal

 an organism that is found normally on those parts of the body that are exposed or communicate to the external environment

changes in normal flora -  hormonal physiology and development

• Female genital tract and lactobacilli

changes in normal flora -  antibiotics select for a resistant flora

• Candida overgrowth in mouth/vagina

• C diff - antibiotic associated colitis

changes in normal flora - new organisms

• Neonate from maternal tract during birth

bacteria need…

• iron

• to adhere to host mucosa

adherence in gram positive bacteria

• adherence to host cells e.g pili, fimbriae

• prevents bacteria from being washed off by significant fluid flow

• formation of a microcolony

• relevance to pathogenicity

exotoxin

secreted by a bacterium into the environment

endotoxin

LPS of gram negative bacteria

enterotoxin

• an exotoxin only active in GI tract

iron sequestering

• Iron is essential

• Limiting in host

• Sequestration is critical for in vivo success

• Produce iron binding compounds called siderophores

• Capture from the host

defensive factors - polysaccharides capsule

• negatively charged

  • Slime

  • Biofilm

defensive factors - immunologic mechanisms

• LPS - cytokine stimulation --> septic shock

• Outer membrane proteins

stages of viral replication

1. adsorption

2. entry

3. uncoating

4. genome replication and transcription

5. synthesis of virus components

6. assembly

7. release and maturation

features of attachemetn

• random collision

• not all cells carrying a receptor for a particular virus can be infected by that virus

• most neutralising antibodies are specific for virion attachment proteins

what is the influenza virus receptor

sialic acid

What are the 2 mechanisms of entry

1. endocytosis

2. fusion of virus envelope with cell membrane

what is uncoating

• release of viral genome

• lysosomes strip off the virus protein coat

• virion can no longer be detected - eclipse period

HIV attachment and entry

• SU protein attached to CD4 on target cell

• CD4 isn’t sufficient —> co-receptor required e.g chemokines

Influenza entry and uncoating

• low pH in the endosome

• causes conformation change in HA

• allows fusion of viral envelope with endosomal membrane

SARS CoV attachment and entry

• S glycoprotein cleaved by TMPRSS2

• facilitates viral activation

• essential host factors for SARS-coV-2 pathogenicity

• TMPRSS2 is a potential target for antiviral drugs

Non-enveloped virus entry and uncoating

• e.g polio

• after receptor attachment, protein taken into endosome

• conformational changes to the viral structural proteins results in:

  • formation of a pore in the endosomal membrane

  • viral RNA released into cytoplasm