3. Microorganisms: bacteria Flashcards
What are the ways in which bacteria can be observed?
- Agar plates - colonies
- Optical microscope - individual bacteria
- Electron microscope - individual bacteria
How is the binomial name of microorganisms constructed?
What are the deadliest pandemics in history?
Black death - the deadliest
Explain how genetic info is stored in bacteria
What is the bacterial adaptation to increase protein synthesis efficiency?
Nucleoid not separated by membrane from ribosomes - transcription + translation coupled - on one DNA strand: polymerase, mRNA, ribosomes, polypeptide - polysome
What are the major targets of antibacterial drugs?
Bacterial metabolism - ex: protein / cell wall synthesis
What bacterial genetic structure is used for phylogentic studies?
16S rRNA - a variable region between bacterial species -> perfect for bacterial identification by sequencing + phylogenetic trees
Why is plasma membrane important in bacteria?
Why is the cell wall important in bacteria?
What is the sequence of Gram staining?
What is the acid-fast cell envelope?
Acid-fast - staining method for non Gram+/Gram- bacteria - have mycolic acids (waxes) on the surface of cell wall - an acid-fast envelope
What is the importance of peptidoglycan? What is the structure of it?
What is the role of peptidoglycan in immune response?
Peptidoglycan triggers immune system for an inflammatory response
What are teichoic acids?
Teichoic acids (TA) - anionic polymers in Gram+ cell wall - provide flexibility by attracting cations (Ca+, K+) - TA are major surface antigens - recognised by imm. system
What are lipopolysaccharides?
Lipopolysaccharides (LPS) - highly acylated saccharolipid - on the surface of outer membrane of Gram- - critical to structural integrity and a permeability barrier to prevent passive diffusion of antibiotics / detergents / toxins / bile salts in gastrointestinal tract - protection
What are the contents of the periplasmic space in Gram- bacteria?
Periplasmic space - contains periplasm - gel-like matrix in the space between the inner and outer bacterial membranes
What is the structure of lipopolysaccharides?
- Lipid A
- Core poplysaccharide
- O-polysaccharide
What are plasmids and why are they important in bacteria?
- circular / linear extrachromosomal DNA
- selective advantage
What is bacterial conjugation? Why is it important?
Bacterial conjugation - DNA transfer process between inter- / intra species bacteria
What is flagella? Why is it important in bacteria?
Flagella - whip-like appendages that extend from the surface - involved in movement
What are pili and fimbriae? Why are they important in bacteria?
- Pili - longer, less #, for conjugation
- Fimbriae - shorter, more #, for adhesion
What is a capsule? Why is it important in bacteria?
Capsule - barrier to toxic compounds, prevents drying out
Why is the capsule important in Streptococcus pneumoniae?
In Streptococcus pneumoniae - capsule - virulence factor
Explain Frederick Griffith’s experiment, why is it important?
Griffith’s experiment - first suggested that bacteria can transfer genetic info through by transformation => when dead virulent mixed with live non virulent - mouse was killed
What are the different nutrient transport types in bacteria?
- Simple / facilitate diffusion (passive)
- Symport (active)
- Antiport (active)
- PTS system (active)
- ABC transport (active)
Explain how simple / facilitated diffusion works
Passive transport - along the conc gradient
Explain how proton symport works
Proton symport - driven by H+ gradient - co-transport
Explain how ABC transport works
ABC transport - driven by ATP hydrolysis
Explain how group translocation works
Group translocation - substrate modified - E input
Explain why bacteria need to have fast metabolism?
For bacteria to survive and spread to other cells - their replication must be faster than immune system response after detecting Ag
There are many examples of specific bacteria, idk if need to know those
Explain how PTS system works
Phosphotransferase transport system (PTS) - uptake and phosphorylation of sugars - composed of multiple proteins - uses E from hydrolysis of phosphoenolpyruvate (PEP)
Process:
1. sugar molecule recognized and bound by a PTS complex
2. bound sugar phosphorylated using a Pi group from PEP
3. sugar-Pi trapped inside bacterial cell - cannot easily pass back through membrane => used as E source / for biosynthesis
Explain how antiport works
Antiport - moves two different molecules / ions in opposite directions across the membrane - ex: sodium-proton exchanger (NHE) - regulates pH
What is the difference in movement mechanism between flagella and pili?
Flagella: spin and move
Pili: attach to some surface - go - retract - advance ->
What are the types of respiration performed by bacteria?
Bacteria perform both aerobic and anaerobic respiration:
- Aerobic: O2 final e acceptor - more efficient - more ATP produced
- Anaerobic: pyruvate / NO3- final e acceptor - less ATP produced
What are the types of bacteria based on how they respire?
- obligate aerobes - need free O2
- obligate anaerobes - don’t need free O2 - can’t udner O2
- facultative anaerobes - don’t need free O2 - can under O2
What are the main common steps of aerobic and anaerobic respiration in bacteria?
Aeorobic:
1. Glycolysis
2. Pyruvate oxidation
3. Kreb’s cycle
4. ETC (O2 final e acceptor)
Anaerobic:
1. Glycolysis
2. Fermentation
How is aerobic respiration performed in bacteria?
Bacteria (a prokaryote) don’t have membrane bound organelles - no mitochondria - aerobic respiration occurs in cell membrane - all ETC proteins - high H+ outside / low H+ inside - ATP synthase driven by proton motive force
ATP used for flagella movement, active transport, enzyme activation ect
What are the types of fermentation in bacteria?
- Lactic fermentation
- Mix acid fermentation
- Butyrate fermentation
- Alcohol fermentation
Explain fermentation
Fermentation:
- coupled reactions which release E from oxidation of organic molecules
- doesn’t use Krebs, ETC, nor O2 as final e acceptor
- derive ATP form substrate level phosphorylation
- recycles NADH to NAD+
What is special about Myobacterium tuberculosis respiration?
Myobacterium tuberculosis has adapted to survive in hostile macrophage vacuoles - can switch from C based metabolism to lipid based metabolism - use glyoxylate shunt enzyme isocitrate lyase (avoid C loss in TCA cycle)
How is fermentation involved in dental disease?
Change in diet - ex higher sugars - lactic acid bacteria ferment more sugars - more lactic acid - change in pH => disolve CaPO4 -> degrades supporting matrix in teeth
How is the bacterial cell division called? Explain the process
Binary fission - always divide in the middle of the cell - exponential growth - different in Gram+/Gram- cells as cell walls are different
How do the bacteria know where the middle of the cell is for bacterial division?
The middle is established by Min proteins (MinC/D- prevent ring formation, MinE- accumulates -> signals where FtsZ ring formation) - create a bipolar gradient - Fts (Filamentous temperature sensitive) proteins - interacts to form divisome - FtsZ ring pinches the wall + membrane
Define what is a divisome
Divisome - a bacterial protein complex which forms the septal ring and defines the division plane in binary fission
What is the general bacterial cell cycle?
- if nutrients unlimited - constant division
- if nutrients limited - stop dividing at some point, may induce sporulation/ VBNC state / persister cell state
What is sporulation in bacteria?
Sporulation - a survival mechanism - not reproductive mechanism! - can survive in unfavourable conditions (heat, desiccation, lack of nutrients) - disperse to new, more hospitable environments
An endospore formation to protect DNA / RNA / proteins - mother cell secretes a protein coat (Ca dipicolinate) - lyses the coat with the materials to release the spore - the dormant state -> spore germinates when the conditions are favourable
Why are spore forming bacteria can be considered a threat to healthcare?
Spore forming / VBNC state bacteria can endure antibiotics / food and water treatment - revive in hosts and cause infections -> severe diseases
Ex.: Bacillus anthracis (anthrax), Clostridium tetani (tetanus)
What is the microbiome?
Microbiome - collection of all microbes - bacteria / fungi / viruses and their genes that naturally live on/in our bodies - commensals - symbiotic relationship
- mouth
- respiratory tracts
- gut
- urogenital tract
- skin
Previously thought to be sterile but actually not:
- placenta
- lungs
Define what is a commensal
Commensal - organism that uses food supplied in the internal / external environment of the host, without establishing a symbiotic relationship with the host, ex.: feeding on its tissues
Commensals can become pathogenic if introduced into different anatomical site than they belong - in surgeries skin bacteria if infect internal organs - cause infections
What are the positive effects of the microbiome to human hosts?
Positive effects of hosting bacteria in the body:
- can outcompete pathogens in nutrient acquisition
- can produce antimicrobials
- act as a stimulus for immune system development in newborns and adults (if not - allergies / autoimmune)
- gut associated commensals synthesise necessary nutrients / digest substances which can’t be done by human cells
- microbiome may play a role in mental health(?) / neurological conditions (autism, epilepsy, depression) - interact with our nervous system = could be both positive / negative effect if disbalance
What are the negative effects of microbiome to human hosts?
Negative effects of hosting bacteria in the body:
- if commensals displaced from their assigned body part into another - can cause infections (ex Staphylococcus epidermis)
- can induce dysbiosis - disease
- can convert common food into carcinogens
- can make host immunocompromised
- microbiome may play a role in mental health(?) / neurological conditions (autism, epilepsy, depression) - interact with our nervous system = could be both positive / negative effect if disbalance
What is dysbiosis?
Dysbiosis - imbalance between types of microorganism in a personal microbiome - especially of the gut - disbalance thought to contribute to a range of conditions
What are the types of possible pathogenesis?
- Pathogenic
- Non-pathogenic
- Asymptomatic
- Latent
- Opportunistic
How is it determined that a specific pathogen causes disease?
Koch’s postulates - criteria list to identify the pathogen causing disease on larger group / population:
- pathogen must be present in every case
- pathogen must be isolated and grown in pure culture
- specific disease must be reproduced when pathogen inoculated into healthy susceptible host
- pathogen must be recoverable from experimentally infected host
What are the mechanism of pathogen transmission to humans?
- Oral-oral
- Feces-oral
- Blood / sexual
- Vextors (animals / insects)
- Food / water
- Environment
What are the microbial pathogenicity factors?
Pathogenicity factors:
- toxins
- enzymes
- slime
- invasins
- LPS
- adhesins
- Fe uptake
One cell can have several factors used simultaneously / non-simultaneously depending on the host - must possess the genes for the factors
What is the general sequence of events of bacterial infection?
- Exposure
- Adherence
- Invasion
- Colonisation + growth
- Toxicity, tissue damage, further spread
What are the steps of breaking the barrier in bacterial infection?
- Exposion
- Adherence (adhesins + pili + flagella)
- Invasion at entry points - essential life functions sites (ex respiratory tract, UTI, skin breach)
What are the components of Gram- bacterial adherence to host?
Gram- use:
- adhesins
- flagellea: multi subunit structures, can have one / many - polarised / non-polarised location - facilitates breaking the membrane of host cells, recognised as PAMP by TLR5 PRR
- fimbriae = pili (?): multi subunit structure, interacts via receptors on the tips - recognise sugars, sex pili transport virulence factors
pries tai rase paskaitos kad fimbriae=/pili, bet chatgpt sake tas pats?)
What are the components of Gram+ bacterial adherence to host?
Gram+ use:
- Surface proteins
- Flagellae
- Fimbriae = pili
What are the bacterial proteins which allow bacteria to invade and survive in the host? What is the function of each?
- adhesins
- toxins
- invasins
What are the types of bacterial toxins?
Types of bacterial toxins:
- exotoxin: actively secreted by bacterium in env or supernatant
- endotoxin: synonym for LPS of Gram- (cell surface bound)
- enterotoxin: exotoxin which is effective in gastrointestinal tract
Pathogens can produce several toxins at once
Explain an example of an exotoxin used in beauty industry
Botulinum toxin - botox - from Clostridium botulinum: in CNS stimulation acetylcholine binds to receptors on muscle - botox prevents acetocholine release -> muscle relaxation -> paralysis -> no wrinkles
Opposite to tetanus toxin
Explain an example of exotoxin in tetanus
Tetanus (stablige) toxin from Clostridium tetani - binds to interneurons and prevents glycine release - lack of inhibitory signals in motor neurons - constant release of acetylcholine - spastic paralysis
Opposite mechanism to botox
How can pathogens damage the host’s membrane?
Two ways:
- enzymatically
- physically
What is iron sequestering?
Iron sequestering - Fe essential for most bacteria metabolism - produce siderophores (small iron-binding molecules) for Fe binding from the env - Fe binds to bacterial surface - taken into the cell - iron released from the siderophore inside the cell - used for essential cellular processes
What are siderophores?
Siderophores - small Fe chelators on microbe surface - most notable function is to sequester Fe from the host (env) - essential metal nutrient to microbial metabolism
Explain the role of bacterial capsules in protection against host’s defense system
Bacterial capsules - thick polysaccharide layers attached to the surface - compositions vary within species - difficult for vaccine development
- Protect against desiccation, phagocytosis
Explain the role of LPS in bacterial protection against host’s defense system
LPS recognised as PAMP by immune system PRRs - activate inflammatory response
What is the background info on Vibrio cholerae?
Vibrio cholerea:
- free dwelling - doesn’t form biofilm unless no host found - biofilm / dormant state (un-culturable) - clinically undetectable
- humans + water - main habitats -> water bodies used a s domestic source of water - transmission
- not transmitted human - human
What is the sequence of events in Vibrio cholerae pathogenesis?
- Attachment - TCP pilin - pili essential in adhesion to the host
- Invasion - enzymatic degradation of outer layer of host
- Growth and replication
- Toxin release - CT AB-subunit (enterotoxin)- doesn’t cause pathological damage to the host - only disbalance in ions -> “rice water stool” / vomiting - huge loss of water => need to restore water to treat
What is the background info on Shigella spp.?
Shigella spp.:
- different serotypes are specific to geographical locations - for some reason don’t mix
- major cause of bacterial dysentery - shigellosis
- many serotypes - different capsules -> difficult to develop a vaccine
- human transmission via faeco-oral contamination
- low infection dose - 10-100 bacteria enough to cause the disease
What is the sequence of events in Shigella spp. pathogenesis?
- Adhesion, proliferation, production of virulence factors - shigatoxins (enterotoxin) => severe inflammation in host
- Shigatoxin injection into epithelial cells via TTSS (type three secretion system = T3SS) => damaged host cell structure + function
- Effector production to promote infection, facilitate reinfection => dampens imm response in host - repress IL8 and antimicrobial peptides
- Can reinfect => imm system eliminates infection
What is the genetic basis of shigatoxin?
Shigatoxin - virulence factor (toxin):
- encoded on chromosome
- acquired from bacteriophage infection and incorporated into the chromosome
- acquired by horizintal gene transfer in a plasmid
- the gene for shigatoxin encodes T3SS, ipa and ipg genes
- there are many genes associated with toxin production: effectors, translocators, chaperones
What are effectors in infection?
Effectors - virulence factors - proteins secreted by bacteria in infection to subvert cellular processes (target signalling pathways, modulating imm response, promote bacterial uptake and replication within host cell) - pathogens manipulate immune system - to promote bacterial survival and growth
Effectors often delivered into host cells through specialized secretion systems
What is T3SS / TTSS??
Type 3 secretion system (T3SS / TTSS) = injectisome (needle structure):
- used to secrete virulence factors: effector proteins / toxins into host cells - promote virulence and colonisation
- Gram- bacteria
- used by Yersenia pestis, Shigella, Salmonella typhi (typhoid fever)
What is the common pathogenesis pattern in Vibrio cholerae, Shigella spp. and Yersinia pestis?
What is the background info on Yersinia pestis?
- Gram-
- bacteria acquired by flea bites
- have different virulence plasmids
- adhesion mediated by Braun lipoproteins Lpp and other proteins
- effectors defeat imm response: Yop effectors - delivered through T3SS - trigger apoptosis, inhibit phagocytosis and cytokine production
- causes plague
What is the sequence of events in Yersinia pestis pathogenesis?
- Flea bite / respiratory droplets
- Adhesion to host cells
- Immune evasion by T3SS mediated neutralisation system (effector YopJ) + absence of PAMPs
- If flea bite: migration to LN - apoptosis and spread to other LN cells -> multiorgan infection OR if respiratory transmission: infect lungs - lung failure
Can infect and replicate without large imm response - when imm system detects - starts inflamm too many bacteria to tackle => death
What are the secretion systems in bacteria? Why are they important?
Bacterial secretion systems (SS) - protein complexes on bacterial membranes for secretion of substances, intra - inter cellular communication, protection against hots-mediated response - used by pathogenic bacteria to secrete virulence factors to invade hosts
Different SS depending on Gram+ / Gram-
Compare SS of Gram+ and Gram-
Gram+: secrete directly into ECM - simplest mechanism (one membrane)
Gram-: secretion must pass both inner and outer membranes (two membranes)
One step process - one protein
Two step process - two proteins
One step / two step systems are not specifically for Gram+/Gram- - not clearly defined - Gram- and use both one and two step - but these pictures were presented in the lecture soo..
What is the sequence of events in outer membrane protein (OMP) secretion through bacterial SS in Gram-?
Gram- OMP must travel through: cytosol -> inner membrane -> periplasmic space -> outer membrane => bacterial surface
1. Unfolded OMP passes from cytosol into periplasmic space through inner membrane - Sec channel
2. Skp protein binds correct protein, if not correct - degraded by DegP
3. SurA protein aids in transporting OMP through second membrane - Bam complex - protein folds and inserts into the second membrane => functional OMP
(Seems like Sec pathway - didn’t mention which in lecture)
What proteins are used to transport substances from cytosol to periplasmic space?
Sec and TAT proteins in inner bacterial membranes
What is the difference between Sec and TAT proteins?
Sec vs TAT secretion pathway:
Sec:
- transports unfolded proteins
- more widespread
- specific signal sequence for SecA
- E from ATP
TAT:
- transports folded proteins
- less widespread
- signal sequence of 1 arginines
- E form proton motive force
Explain Sec secretion pathway in bacteria
General seretory pathway (Sec) secretion pathway:
- ATP driven - SecA motor protein hydrolysis ATP
- Sequence: translated protein contains a signal sequence - determines where the protein will go - if no signal sequence - protein stays inside the cell
1. If signal for Sec - SecA binds - doesn’t allow protein to fold - pre-secretory / pre-protein - transported through inner (cytoplasmic) membrane into periplasm
2. If signal for other - signal recognition particle binds - doesn’t allow protein to fold - pre-secretory / pre-protein - protein incorporated into inner (cytoplasmic) membrane
3. Once protein is in cytoplasmic membrane / tarnsported into peripolasm - enzyme cleaves off the signalling sequences -> protein correctly folds
Explain TAT secretion pathway in bacteria
Twin arginine translocation (TAT) secretion pathway:
- 2 Arg in signal sequence for TAT
- Sequence: from cytoplasm to periplasm through inner (cytoplasmic) membrane
What are one / two step secretion pathways?
- One step - one protein involved: through SS into ECM / through Sec, TAT into periplasm
- Two step - two poteins involved: through Sec, TAT and through SS into ECM
Explain type 1 protein secretion system
T1SS:
- components: inner membrane protein (IMP)
- fusion protein (MFP)
- outer membrane factor (OMF)
- ATP catalyses substrate transport
Explain type 4 secretion system
T4SS:
- transport through both inner and outer membrane / host membrane
- used in bacterial conjugation for plasmid exchange, in transformation, in effector translocation into host cells
What are the signalling systems used by Gram- bacteria to sense the environment and adjust gene expression?
1 / 2 component systems (1CS / 2CS) - Gram- because 2 membranes involved
1. Signal triggers a receptor
2. Conformational change of the protein
3. Change in gene activity - on / off
What is the signalling system used in Vibrio cholerae?
Vibrio cholerae:
- one component system (1CS) - ToxRS - for toxin production + pili interaction with host
- anti-sigma system - RpoS - facilitates escape response when leaves into water from human gut
What is the signalling system used in Shigella?
Shigella:
- 2 component system (2CS) - EnvZ-OmpR / PhoPQ - drives virulence plasmdi expression
What are the components of a 2 component signalling system?
- Signal
- Sensor
- Regulator
- Regulon
=> pos / neg control
Define what is a regulon in bacterial 2 component signalling system, what does it control
Regulon - a group of genes controlled by a common regulator - overlapping regulons create networks
How does a bacterial 2 component signalling system work?
Bacterial 2CS signalling system - type of signal transduction pathway - allows bacteria to sense + respond to environmental changes
2 main components:
- sensor kinase: membrane-bound protein - detects specific signals: temp, pH, osmolarity, specific molecules
- response regulator: TF that regulates gene expression in response to external signal detected by sensor kinase
Sequence:
1. sensor kinase detects a signal - conformational change - phosphorylates: transfers Pi group from ATP to a conserved histidine residue within its cytoplasmic domain
2. phosphorylated sensor kinase transfers Pi to a conserved aspartate residue in receiver domain of response regulator (DNA-binding protein) - conformational change - can bind to specific DNA sequences and regulate gene expression
3. response regulator can act as activator / repressor of transcription, depending on genes that it regulates and environmental signals
What is a specific example of a 2 component bacterial signalling system?
Regulation of PhoP/PhoQ genes in enterobacteriales - signal = changes in Mg+/Ca+ conc:
- high conc: no induction of genes
- low conc: signals that inside macropages - activation of genes
- activation of PhoP/PhoQ genes - activates arn operon gene cluster - adds sugar on LPS - changed structure - imm syst can’t recognise => adaptation for immune evasion - resistant against antibiotic polymyxin B and antimicrobial peptides
2CS can work on their own or in collaboration with other 2CS
What is a general sequence of events of pathogen life from sensing the env signal that it should become pathogenic to causing a fatal disease?
- Exposure to the host
- Adhesion (T5SS)
- Invasion (T3SS, T4SS)
- Evasion of host defenses
- Proliferation and colonization (T4SS)
- Pathogenicity activation (T2SS secrete toxins, virulence factors)
- Disease manifestation
- Spread and transmission
- Severe disease or fatality
Secretion systems play important roles in the pathogenesis allowing them to deliver virulence factors, evade host defenses, and manipulate host cells to their advantage
How do bacteria self protect by coming together?
Form biofilms - structured communities - pathogenic trait - quorum sensing (QS) - autoinducers - activate / repress genes
What are the quorum sensing molecules used by Gram+ and Gram- bacteria?
- Gram-: acyl-homoserine lactones (AHLs)
- Gram+: autoindusing peptides (AIPs)
How does the quorum sensing mechanism work in P. aeruginosa?
- When in a biofilm - AHL (QS molecule) bound to LasR receptor - activates virulence gene cluster expression
- LasR also activates RhIR gene expression - another set of virulence factors
Genes to disease overview
What are all the functions performed by QS molecules?
What is periplasm?
Periplasm - in between inner and outer bacterial membranes of cell wall - gel-like matrix with proteins, eznymes, other molecules - compartment for protein folding, degradation, modification, synthesis, transport
